Plastimatch error

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Plastimatch error

Zhang, Yi
Hi,

I have encountered following error while trying to peform B-spline deformable registration on Plastmatch:

ERROR: In ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line 1575
vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
process was null when state was queried, result (1) = Error.

Please help.
Thanks!
Vickie
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Re: Plastimatch error

Sharp, Gregory C.
 
Hi Vickie,

Can you please tell me your OS, Slicer Version, and
extension version (extension URL)?

Thank you,
Greg

-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Zhang, Yi
Sent: Thursday, February 17, 2011 12:26 AM
To: [hidden email]
Subject: [slicer-users] Plastimatch error

Hi,

I have encountered following error while trying to peform B-spline deformable
registration on Plastmatch:

ERROR: In
..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line
1575
vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
process was null when state was queried, result (1) = Error.

Please help.
Thanks!
Vickie
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[hidden email]
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To unsubscribe: send email to [hidden email] with
unsubscribe as the subject
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Re: Plastimatch error

Zhang, Yi
Sorry,
OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm using the Parallels Desktop since I don't own a PC. (do you think that could be the problem?)
Slicer version: Slicer3-3.6-2010-06-10-win32
extension version: http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010-06-10-win32

Actually, not only B-spline, but other two functionalities give me the same error - DICOM/DICOM RT import and landmark deformable registration.

Thanks,
Vickie
On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:

>
> Hi Vickie,
>
> Can you please tell me your OS, Slicer Version, and
> extension version (extension URL)?
>
> Thank you,
> Greg
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Zhang, Yi
> Sent: Thursday, February 17, 2011 12:26 AM
> To: [hidden email]
> Subject: [slicer-users] Plastimatch error
>
> Hi,
>
> I have encountered following error while trying to peform B-spline deformable
> registration on Plastmatch:
>
> ERROR: In
> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line
> 1575
> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
> process was null when state was queried, result (1) = Error.
>
> Please help.
> Thanks!
> Vickie
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with
> unsubscribe as the subject
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>

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Re: Plastimatch error

Sharp, Gregory C.

Hi Vickie,

Unfortunately I couldn't reproduce the problem.  You are using a good
configuration of versions which is supposed to work.

We should test if the problem is with Parallels.  Can you please try
downloading and running another extension, such as ExampleCommandLine?  
(By the way, why do you run Slicer on Parallels instead of the OSX native
version?)

Also, can you tell me if there is any output in the "standard output"
part of the error log?

An alternative route is to run plastimatch independent of Slicer, then
loading the results into Slicer for further analysis.  Let me know if you
like to pursue that route and I can walk you through.

Greg


On Thu, 17 Feb 2011 10:22:33 -0800
"Zhang, Yi" <[hidden email]> wrote:

> Sorry,
> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
> using the Parallels Desktop since I don't own a PC. (do you think that
> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
> extension version:
> http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010-06-10-win32
>
> Actually, not only B-spline, but other two functionalities give me the same
> error - DICOM/DICOM RT import and landmark deformable registration.
>
> Thanks,
> Vickie
> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>
> >
> > Hi Vickie,
> >
> > Can you please tell me your OS, Slicer Version, and
> > extension version (extension URL)?
> >
> > Thank you,
> > Greg
> >
> > -----Original Message-----
> > From: [hidden email]
> > [mailto:[hidden email]] On Behalf Of Zhang, Yi
> > Sent: Thursday, February 17, 2011 12:26 AM
> > To: [hidden email]
> > Subject: [slicer-users] Plastimatch error
> >
> > Hi,
> >
> > I have encountered following error while trying to peform B-spline
> > deformable registration on Plastmatch:
> >
> > ERROR: In
> > ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
> > line 1575
> > vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
> > process was null when state was queried, result (1) = Error.
> >
> > Please help.
> > Thanks!
> > Vickie
> > _______________________________________________
> > slicer-users mailing list
> > [hidden email]
> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> > To unsubscribe: send email to
> > [hidden email] with unsubscribe as the
> > subject
> >
> >
> > The information in this e-mail is intended only for the person to whom it
> > is addressed. If you believe this e-mail was sent to you in error and the
> > e-mail contains patient information, please contact the Partners
> > Compliance HelpLine at http://www.partners.org/complianceline . If the
> > e-mail was sent to you in error but does not contain patient information,
> > please contact the sender and properly dispose of the e-mail.
> >
>


--
Greg Sharp, PhD
Department of Radiation Oncology
Massachusetts General Hospital
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Re: Plastimatch error

Zhang, Yi
Hi Greg,

I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And installed Plastimatch from http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
Tested with 2 3D images.
It ran for 75.42 secs and completed with errors.

ERROR: In /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1522
vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration completed with errors

I have two 3D mask images in nrrd format, same resolution, same matrix size and FOV.
Using Plastimatch B-spline Registration, I left stage 0 and stage 2 unchecked. For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max iterations = 50
Afer 75.42 seconds, it completed with following error:

Looks like the linux is working better, but still gives errors. Any suggestions?

Thanks,
Vickie

FYI: output from "Information"

B-spline deformable registration standard output:

fixed image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
Loading fixed image...
done!
moving image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
Loading moving image...
done!
[1] xf_in->m_type = 0, xf_out->m_type = 0
Converting fixed
Converting moving
Done.
SUBSAMPLE: (1 1 1), (1 1 1)
moving_ss size = 256 256 22
fixed_ss size = 256 256 22
bspline_xform_initialize
rdims = (1,1,1)
vox_per_rgn = (640,640,80)
cdims = (4 4 4)
xform_any_to_gpuit_bsp complete
BSPLINE PARMS
max_its = 50
BSPLINE XFORM HEADER
vox_per_rgn = 640 640 80
roi_offset = 0 0 0
roi_dim = 256 256 22
Setting NMAX, MMAX = 192 33
>>> START    
RUNNING THE L-BFGS-B CODE

           * * *

Machine precision = 2.220E-16
 N =  192    M =  33
 This problem is unconstrained.
MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
                    CMIN   0.00 CAVG   0.00 CMAX   0.00
MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
                    CMIN  -0.47 CAVG  -0.00 CMAX   0.55
MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
                    CMIN  -2.33 CAVG  -0.01 CMAX   2.75
MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
                    CMIN  -3.54 CAVG  -0.02 CMAX   4.65
MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
                    CMIN  -8.39 CAVG  -0.02 CMAX  12.27
MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
                    CMIN  -4.44 CAVG  -0.02 CMAX   6.07
MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
                    CMIN  -5.12 CAVG  -0.02 CMAX   7.14
MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
                    CMIN -27.43 CAVG  -0.06 CMAX  45.42
MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
                    CMIN  -5.81 CAVG  -0.02 CMAX   8.33
MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
                    CMIN  -5.21 CAVG  -0.02 CMAX   7.29
MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
                    CMIN  -5.14 CAVG  -0.02 CMAX   7.16
MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
                    CMIN  -5.18 CAVG  -0.02 CMAX   7.25
MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
                    CMIN  -5.14 CAVG  -0.02 CMAX   7.18
MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
                    CMIN  -5.17 CAVG  -0.02 CMAX   7.22
MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.18
MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
                    CMIN  -5.16 CAVG  -0.02 CMAX   7.20
MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
                    CMIN  -5.87 CAVG  -0.04 CMAX   8.12
MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
                    CMIN  -5.29 CAVG  -0.02 CMAX   7.37
MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
                    CMIN  -5.17 CAVG  -0.02 CMAX   7.22
MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
                    CMIN  -8.56 CAVG  -0.09 CMAX  11.31
MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
                    CMIN  -5.63 CAVG  -0.03 CMAX   7.77
MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
                    CMIN  -5.23 CAVG  -0.02 CMAX   7.28
MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
                    CMIN  -5.16 CAVG  -0.02 CMAX   7.20
MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
                    CMIN  -5.63 CAVG  -0.04 CMAX   7.56
MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
                    CMIN  -5.26 CAVG  -0.02 CMAX   7.27
MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
                    CMIN  -5.11 CAVG  -0.04 CMAX   7.84
MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
                    CMIN  -5.03 CAVG  -0.05 CMAX   8.18
MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
                    CMIN  -7.75 CAVG  -0.06 CMAX   9.52
MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
                    CMIN -19.57 CAVG  -0.14 CMAX  15.94
MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
                    CMIN -14.77 CAVG  -0.12 CMAX  13.34
MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
                    CMIN -10.03 CAVG   0.00 CMAX  11.79
MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
                    CMIN -12.47 CAVG  -0.11 CMAX  12.07
MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
                    CMIN -13.62 CAVG  -0.12 CMAX  12.84
[2] xf_out->m_type = 8, xf_in->m_type = 0
Warping...
Running: plm_warp_native
Converting input image...
Converting xform...
bspline_xform_initialize
Error allocating memory for q_lut

On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:

>
> Hi Vickie,
>
> Unfortunately I couldn't reproduce the problem.  You are using a good
> configuration of versions which is supposed to work.
>
> We should test if the problem is with Parallels.  Can you please try
> downloading and running another extension, such as ExampleCommandLine?  
> (By the way, why do you run Slicer on Parallels instead of the OSX native
> version?)
>
> Also, can you tell me if there is any output in the "standard output"
> part of the error log?
>
> An alternative route is to run plastimatch independent of Slicer, then
> loading the results into Slicer for further analysis.  Let me know if you
> like to pursue that route and I can walk you through.
>
> Greg
>
>
> On Thu, 17 Feb 2011 10:22:33 -0800
> "Zhang, Yi" <[hidden email]> wrote:
>
>> Sorry,
>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>> using the Parallels Desktop since I don't own a PC. (do you think that
>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>> extension version:
>> http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010-06-10-win32
>>
>> Actually, not only B-spline, but other two functionalities give me the same
>> error - DICOM/DICOM RT import and landmark deformable registration.
>>
>> Thanks,
>> Vickie
>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>
>>>
>>> Hi Vickie,
>>>
>>> Can you please tell me your OS, Slicer Version, and
>>> extension version (extension URL)?
>>>
>>> Thank you,
>>> Greg
>>>
>>> -----Original Message-----
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Zhang, Yi
>>> Sent: Thursday, February 17, 2011 12:26 AM
>>> To: [hidden email]
>>> Subject: [slicer-users] Plastimatch error
>>>
>>> Hi,
>>>
>>> I have encountered following error while trying to peform B-spline
>>> deformable registration on Plastmatch:
>>>
>>> ERROR: In
>>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>>> line 1575
>>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>>> process was null when state was queried, result (1) = Error.
>>>
>>> Please help.
>>> Thanks!
>>> Vickie
>>> _______________________________________________
>>> slicer-users mailing list
>>> [hidden email]
>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>> To unsubscribe: send email to
>>> [hidden email] with unsubscribe as the
>>> subject
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it
>>> is addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail contains patient information, please contact the Partners
>>> Compliance HelpLine at http://www.partners.org/complianceline . If the
>>> e-mail was sent to you in error but does not contain patient information,
>>> please contact the sender and properly dispose of the e-mail.
>>>
>>
>
>
> --
> Greg Sharp, PhD
> Department of Radiation Oncology
> Massachusetts General Hospital

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Re: Plastimatch error

Sharp, Gregory C.
 
Hi Vickie,

This is very helpful.  It looks like the registration code
is running out of memory building the lookup table.

I think this can be solved by changing the grid spacing.
Can you tell me your image resolution and voxel spacing?
Then I will suggest some modified settings.

Greg

-----Original Message-----
From: Zhang, Yi [mailto:[hidden email]]
Sent: Fri 2/18/2011 4:54 PM
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Plastimatch error
 
Hi Greg,

I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
installed Plastimatch from
http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
Tested with 2 3D images.
It ran for 75.42 secs and completed with errors.

ERROR: In
/home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
ic.cxx, line 1522
vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
completed with errors

I have two 3D mask images in nrrd format, same resolution, same matrix size and
FOV.
Using Plastimatch B-spline Registration, I left stage 0 and stage 2 unchecked.
For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max iterations =
50
Afer 75.42 seconds, it completed with following error:

Looks like the linux is working better, but still gives errors. Any suggestions?

Thanks,
Vickie

FYI: output from "Information"

B-spline deformable registration standard output:

fixed
image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
Loading fixed image...
done!
moving
image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
Loading moving image...
done!
[1] xf_in->m_type = 0, xf_out->m_type = 0
Converting fixed
Converting moving
Done.
SUBSAMPLE: (1 1 1), (1 1 1)
moving_ss size = 256 256 22
fixed_ss size = 256 256 22
bspline_xform_initialize
rdims = (1,1,1)
vox_per_rgn = (640,640,80)
cdims = (4 4 4)
xform_any_to_gpuit_bsp complete
BSPLINE PARMS
max_its = 50
BSPLINE XFORM HEADER
vox_per_rgn = 640 640 80
roi_offset = 0 0 0
roi_dim = 256 256 22
Setting NMAX, MMAX = 192 33
>>> START    
RUNNING THE L-BFGS-B CODE

           * * *

Machine precision = 2.220E-16
 N =  192    M =  33
 This problem is unconstrained.
MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
                    CMIN   0.00 CAVG   0.00 CMAX   0.00
MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
                    CMIN  -0.47 CAVG  -0.00 CMAX   0.55
MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
                    CMIN  -2.33 CAVG  -0.01 CMAX   2.75
MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
                    CMIN  -3.54 CAVG  -0.02 CMAX   4.65
MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
                    CMIN  -8.39 CAVG  -0.02 CMAX  12.27
MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
                    CMIN  -4.44 CAVG  -0.02 CMAX   6.07
MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
                    CMIN  -5.12 CAVG  -0.02 CMAX   7.14
MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
                    CMIN -27.43 CAVG  -0.06 CMAX  45.42
MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
                    CMIN  -5.81 CAVG  -0.02 CMAX   8.33
MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
                    CMIN  -5.21 CAVG  -0.02 CMAX   7.29
MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
                    CMIN  -5.14 CAVG  -0.02 CMAX   7.16
MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
                    CMIN  -5.18 CAVG  -0.02 CMAX   7.25
MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
                    CMIN  -5.14 CAVG  -0.02 CMAX   7.18
MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
                    CMIN  -5.17 CAVG  -0.02 CMAX   7.22
MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.18
MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
                    CMIN  -5.16 CAVG  -0.02 CMAX   7.20
MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
                    CMIN  -5.87 CAVG  -0.04 CMAX   8.12
MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
                    CMIN  -5.29 CAVG  -0.02 CMAX   7.37
MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
                    CMIN  -5.17 CAVG  -0.02 CMAX   7.22
MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
                    CMIN  -8.56 CAVG  -0.09 CMAX  11.31
MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
                    CMIN  -5.63 CAVG  -0.03 CMAX   7.77
MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
                    CMIN  -5.23 CAVG  -0.02 CMAX   7.28
MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
                    CMIN  -5.16 CAVG  -0.02 CMAX   7.20
MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
                    CMIN  -5.63 CAVG  -0.04 CMAX   7.56
MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
                    CMIN  -5.26 CAVG  -0.02 CMAX   7.27
MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
                    CMIN  -5.11 CAVG  -0.04 CMAX   7.84
MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
                    CMIN  -5.03 CAVG  -0.05 CMAX   8.18
MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
                    CMIN  -7.75 CAVG  -0.06 CMAX   9.52
MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
                    CMIN -19.57 CAVG  -0.14 CMAX  15.94
MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
                    CMIN -14.77 CAVG  -0.12 CMAX  13.34
MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
                    CMIN -10.03 CAVG   0.00 CMAX  11.79
MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
                    CMIN -12.47 CAVG  -0.11 CMAX  12.07
MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
                    CMIN -13.62 CAVG  -0.12 CMAX  12.84
[2] xf_out->m_type = 8, xf_in->m_type = 0
Warping...
Running: plm_warp_native
Converting input image...
Converting xform...
bspline_xform_initialize
Error allocating memory for q_lut

On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:

>
> Hi Vickie,
>
> Unfortunately I couldn't reproduce the problem.  You are using a good
> configuration of versions which is supposed to work.
>
> We should test if the problem is with Parallels.  Can you please try
> downloading and running another extension, such as ExampleCommandLine?  
> (By the way, why do you run Slicer on Parallels instead of the OSX native
> version?)
>
> Also, can you tell me if there is any output in the "standard output"
> part of the error log?
>
> An alternative route is to run plastimatch independent of Slicer, then
> loading the results into Slicer for further analysis.  Let me know if you
> like to pursue that route and I can walk you through.
>
> Greg
>
>
> On Thu, 17 Feb 2011 10:22:33 -0800
> "Zhang, Yi" <[hidden email]> wrote:
>
>> Sorry,
>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>> using the Parallels Desktop since I don't own a PC. (do you think that
>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>> extension version:
>>
http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010
-06-10-win32

>>
>> Actually, not only B-spline, but other two functionalities give me the same
>> error - DICOM/DICOM RT import and landmark deformable registration.
>>
>> Thanks,
>> Vickie
>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>
>>>
>>> Hi Vickie,
>>>
>>> Can you please tell me your OS, Slicer Version, and
>>> extension version (extension URL)?
>>>
>>> Thank you,
>>> Greg
>>>
>>> -----Original Message-----
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Zhang, Yi
>>> Sent: Thursday, February 17, 2011 12:26 AM
>>> To: [hidden email]
>>> Subject: [slicer-users] Plastimatch error
>>>
>>> Hi,
>>>
>>> I have encountered following error while trying to peform B-spline
>>> deformable registration on Plastmatch:
>>>
>>> ERROR: In
>>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>>> line 1575
>>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>>> process was null when state was queried, result (1) = Error.
>>>
>>> Please help.
>>> Thanks!
>>> Vickie
>
> --
> Greg Sharp, PhD
> Department of Radiation Oncology
> Massachusetts General Hospital


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Re: Plastimatch error

Zhang, Yi
Image matrix: 256 by 256 by 22
image resolution: 0.15625 by 0.15625 by 1.25mm
FOV: 40 by 40 by 27.5 mm
Thanks,
Vickie
On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:

>
> Hi Vickie,
>
> This is very helpful.  It looks like the registration code
> is running out of memory building the lookup table.
>
> I think this can be solved by changing the grid spacing.
> Can you tell me your image resolution and voxel spacing?
> Then I will suggest some modified settings.
>
> Greg
>
> -----Original Message-----
> From: Zhang, Yi [mailto:[hidden email]]
> Sent: Fri 2/18/2011 4:54 PM
> To: Sharp, Gregory C.
> Cc: [hidden email]
> Subject: Re: [slicer-users] Plastimatch error
>
> Hi Greg,
>
> I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
> installed Plastimatch from
> http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
> Tested with 2 3D images.
> It ran for 75.42 secs and completed with errors.
>
> ERROR: In
> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
> ic.cxx, line 1522
> vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
> completed with errors
>
> I have two 3D mask images in nrrd format, same resolution, same matrix size and
> FOV.
> Using Plastimatch B-spline Registration, I left stage 0 and stage 2 unchecked.
> For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max iterations =
> 50
> Afer 75.42 seconds, it completed with following error:
>
> Looks like the linux is working better, but still gives errors. Any suggestions?
>
> Thanks,
> Vickie
>
> FYI: output from "Information"
>
> B-spline deformable registration standard output:
>
> fixed
> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
> Loading fixed image...
> done!
> moving
> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
> Loading moving image...
> done!
> [1] xf_in->m_type = 0, xf_out->m_type = 0
> Converting fixed
> Converting moving
> Done.
> SUBSAMPLE: (1 1 1), (1 1 1)
> moving_ss size = 256 256 22
> fixed_ss size = 256 256 22
> bspline_xform_initialize
> rdims = (1,1,1)
> vox_per_rgn = (640,640,80)
> cdims = (4 4 4)
> xform_any_to_gpuit_bsp complete
> BSPLINE PARMS
> max_its = 50
> BSPLINE XFORM HEADER
> vox_per_rgn = 640 640 80
> roi_offset = 0 0 0
> roi_dim = 256 256 22
> Setting NMAX, MMAX = 192 33
>>>> START
> RUNNING THE L-BFGS-B CODE
>
>           * * *
>
> Machine precision = 2.220E-16
> N =  192    M =  33
> This problem is unconstrained.
> MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
>                    CMIN   0.00 CAVG   0.00 CMAX   0.00
> MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
>                    CMIN  -0.47 CAVG  -0.00 CMAX   0.55
> MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
>                    CMIN  -2.33 CAVG  -0.01 CMAX   2.75
> MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
>                    CMIN  -3.54 CAVG  -0.02 CMAX   4.65
> MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
>                    CMIN  -8.39 CAVG  -0.02 CMAX  12.27
> MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
>                    CMIN  -4.44 CAVG  -0.02 CMAX   6.07
> MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
>                    CMIN  -5.12 CAVG  -0.02 CMAX   7.14
> MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
>                    CMIN -27.43 CAVG  -0.06 CMAX  45.42
> MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
>                    CMIN  -5.81 CAVG  -0.02 CMAX   8.33
> MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
>                    CMIN  -5.21 CAVG  -0.02 CMAX   7.29
> MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
>                    CMIN  -5.14 CAVG  -0.02 CMAX   7.16
> MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
>                    CMIN  -5.18 CAVG  -0.02 CMAX   7.25
> MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
>                    CMIN  -5.14 CAVG  -0.02 CMAX   7.18
> MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
>                    CMIN  -5.17 CAVG  -0.02 CMAX   7.22
> MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.18
> MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
>                    CMIN  -5.16 CAVG  -0.02 CMAX   7.20
> MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
>                    CMIN  -5.87 CAVG  -0.04 CMAX   8.12
> MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
>                    CMIN  -5.29 CAVG  -0.02 CMAX   7.37
> MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
>                    CMIN  -5.17 CAVG  -0.02 CMAX   7.22
> MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
>                    CMIN  -8.56 CAVG  -0.09 CMAX  11.31
> MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
>                    CMIN  -5.63 CAVG  -0.03 CMAX   7.77
> MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
>                    CMIN  -5.23 CAVG  -0.02 CMAX   7.28
> MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
>                    CMIN  -5.16 CAVG  -0.02 CMAX   7.20
> MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
>                    CMIN  -5.63 CAVG  -0.04 CMAX   7.56
> MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
>                    CMIN  -5.26 CAVG  -0.02 CMAX   7.27
> MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
>                    CMIN  -5.11 CAVG  -0.04 CMAX   7.84
> MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
>                    CMIN  -5.03 CAVG  -0.05 CMAX   8.18
> MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
>                    CMIN  -7.75 CAVG  -0.06 CMAX   9.52
> MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
>                    CMIN -19.57 CAVG  -0.14 CMAX  15.94
> MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
>                    CMIN -14.77 CAVG  -0.12 CMAX  13.34
> MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
>                    CMIN -10.03 CAVG   0.00 CMAX  11.79
> MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
>                    CMIN -12.47 CAVG  -0.11 CMAX  12.07
> MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
>                    CMIN -13.62 CAVG  -0.12 CMAX  12.84
> [2] xf_out->m_type = 8, xf_in->m_type = 0
> Warping...
> Running: plm_warp_native
> Converting input image...
> Converting xform...
> bspline_xform_initialize
> Error allocating memory for q_lut
>
> On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:
>
>>
>> Hi Vickie,
>>
>> Unfortunately I couldn't reproduce the problem.  You are using a good
>> configuration of versions which is supposed to work.
>>
>> We should test if the problem is with Parallels.  Can you please try
>> downloading and running another extension, such as ExampleCommandLine?
>> (By the way, why do you run Slicer on Parallels instead of the OSX native
>> version?)
>>
>> Also, can you tell me if there is any output in the "standard output"
>> part of the error log?
>>
>> An alternative route is to run plastimatch independent of Slicer, then
>> loading the results into Slicer for further analysis.  Let me know if you
>> like to pursue that route and I can walk you through.
>>
>> Greg
>>
>>
>> On Thu, 17 Feb 2011 10:22:33 -0800
>> "Zhang, Yi" <[hidden email]> wrote:
>>
>>> Sorry,
>>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>>> using the Parallels Desktop since I don't own a PC. (do you think that
>>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>>> extension version:
>>>
> http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010
> -06-10-win32
>>>
>>> Actually, not only B-spline, but other two functionalities give me the same
>>> error - DICOM/DICOM RT import and landmark deformable registration.
>>>
>>> Thanks,
>>> Vickie
>>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Can you please tell me your OS, Slicer Version, and
>>>> extension version (extension URL)?
>>>>
>>>> Thank you,
>>>> Greg
>>>>
>>>> -----Original Message-----
>>>> From: [hidden email]
>>>> [mailto:[hidden email]] On Behalf Of Zhang, Yi
>>>> Sent: Thursday, February 17, 2011 12:26 AM
>>>> To: [hidden email]
>>>> Subject: [slicer-users] Plastimatch error
>>>>
>>>> Hi,
>>>>
>>>> I have encountered following error while trying to peform B-spline
>>>> deformable registration on Plastmatch:
>>>>
>>>> ERROR: In
>>>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>>>> line 1575
>>>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>>>> process was null when state was queried, result (1) = Error.
>>>>
>>>> Please help.
>>>> Thanks!
>>>> Vickie
>>
>> --
>> Greg Sharp, PhD
>> Department of Radiation Oncology
>> Massachusetts General Hospital
>
>
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
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Re: Plastimatch error

Sharp, Gregory C.

Hi Vickie,

Please try setting the "Grid Size" parameter to something
smaller than the image size.  For a smoother deformation,
you may try 10 mm or 20 mm.  For a wigglier deformation, you
may try something like 1 mm or 5 mm.

Greg


-----Original Message-----
From: Zhang, Yi [mailto:[hidden email]]
Sent: Sun 2/20/2011 10:28 PM
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Plastimatch error
 
Image matrix: 256 by 256 by 22
image resolution: 0.15625 by 0.15625 by 1.25mm
FOV: 40 by 40 by 27.5 mm
Thanks,
Vickie
On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:

>
> Hi Vickie,
>
> This is very helpful.  It looks like the registration code
> is running out of memory building the lookup table.
>
> I think this can be solved by changing the grid spacing.
> Can you tell me your image resolution and voxel spacing?
> Then I will suggest some modified settings.
>
> Greg
>
> -----Original Message-----
> From: Zhang, Yi [mailto:[hidden email]]
> Sent: Fri 2/18/2011 4:54 PM
> To: Sharp, Gregory C.
> Cc: [hidden email]
> Subject: Re: [slicer-users] Plastimatch error
>
> Hi Greg,
>
> I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
> installed Plastimatch from
> http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
> Tested with 2 3D images.
> It ran for 75.42 secs and completed with errors.
>
> ERROR: In
>
/home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
> ic.cxx, line 1522
> vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
> completed with errors
>
> I have two 3D mask images in nrrd format, same resolution, same matrix size
and
> FOV.
> Using Plastimatch B-spline Registration, I left stage 0 and stage 2 unchecked.
> For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max iterations
=
> 50
> Afer 75.42 seconds, it completed with following error:
>
> Looks like the linux is working better, but still gives errors. Any
suggestions?

>
> Thanks,
> Vickie
>
> FYI: output from "Information"
>
> B-spline deformable registration standard output:
>
> fixed
> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
> Loading fixed image...
> done!
> moving
> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
> Loading moving image...
> done!
> [1] xf_in->m_type = 0, xf_out->m_type = 0
> Converting fixed
> Converting moving
> Done.
> SUBSAMPLE: (1 1 1), (1 1 1)
> moving_ss size = 256 256 22
> fixed_ss size = 256 256 22
> bspline_xform_initialize
> rdims = (1,1,1)
> vox_per_rgn = (640,640,80)
> cdims = (4 4 4)
> xform_any_to_gpuit_bsp complete
> BSPLINE PARMS
> max_its = 50
> BSPLINE XFORM HEADER
> vox_per_rgn = 640 640 80
> roi_offset = 0 0 0
> roi_dim = 256 256 22
> Setting NMAX, MMAX = 192 33
>>>> START
> RUNNING THE L-BFGS-B CODE
>
>           * * *
>
> Machine precision = 2.220E-16
> N =  192    M =  33
> This problem is unconstrained.
> MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
>                    CMIN   0.00 CAVG   0.00 CMAX   0.00
> MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
>                    CMIN  -0.47 CAVG  -0.00 CMAX   0.55
> MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
>                    CMIN  -2.33 CAVG  -0.01 CMAX   2.75
> MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
>                    CMIN  -3.54 CAVG  -0.02 CMAX   4.65
> MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
>                    CMIN  -8.39 CAVG  -0.02 CMAX  12.27
> MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
>                    CMIN  -4.44 CAVG  -0.02 CMAX   6.07
> MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
>                    CMIN  -5.12 CAVG  -0.02 CMAX   7.14
> MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
>                    CMIN -27.43 CAVG  -0.06 CMAX  45.42
> MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
>                    CMIN  -5.81 CAVG  -0.02 CMAX   8.33
> MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
>                    CMIN  -5.21 CAVG  -0.02 CMAX   7.29
> MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
>                    CMIN  -5.14 CAVG  -0.02 CMAX   7.16
> MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
>                    CMIN  -5.18 CAVG  -0.02 CMAX   7.25
> MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
>                    CMIN  -5.14 CAVG  -0.02 CMAX   7.18
> MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
>                    CMIN  -5.17 CAVG  -0.02 CMAX   7.22
> MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.18
> MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
>                    CMIN  -5.16 CAVG  -0.02 CMAX   7.20
> MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
>                    CMIN  -5.87 CAVG  -0.04 CMAX   8.12
> MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
>                    CMIN  -5.29 CAVG  -0.02 CMAX   7.37
> MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
>                    CMIN  -5.17 CAVG  -0.02 CMAX   7.22
> MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
>                    CMIN  -8.56 CAVG  -0.09 CMAX  11.31
> MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
>                    CMIN  -5.63 CAVG  -0.03 CMAX   7.77
> MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
>                    CMIN  -5.23 CAVG  -0.02 CMAX   7.28
> MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
>                    CMIN  -5.16 CAVG  -0.02 CMAX   7.20
> MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
>                    CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
>                    CMIN  -5.63 CAVG  -0.04 CMAX   7.56
> MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
>                    CMIN  -5.26 CAVG  -0.02 CMAX   7.27
> MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
>                    CMIN  -5.11 CAVG  -0.04 CMAX   7.84
> MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
>                    CMIN  -5.03 CAVG  -0.05 CMAX   8.18
> MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
>                    CMIN  -7.75 CAVG  -0.06 CMAX   9.52
> MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
>                    CMIN -19.57 CAVG  -0.14 CMAX  15.94
> MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
>                    CMIN -14.77 CAVG  -0.12 CMAX  13.34
> MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
>                    CMIN -10.03 CAVG   0.00 CMAX  11.79
> MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
>                    CMIN -12.47 CAVG  -0.11 CMAX  12.07
> MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
>                    CMIN -13.62 CAVG  -0.12 CMAX  12.84
> [2] xf_out->m_type = 8, xf_in->m_type = 0
> Warping...
> Running: plm_warp_native
> Converting input image...
> Converting xform...
> bspline_xform_initialize
> Error allocating memory for q_lut
>
> On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:
>
>>
>> Hi Vickie,
>>
>> Unfortunately I couldn't reproduce the problem.  You are using a good
>> configuration of versions which is supposed to work.
>>
>> We should test if the problem is with Parallels.  Can you please try
>> downloading and running another extension, such as ExampleCommandLine?
>> (By the way, why do you run Slicer on Parallels instead of the OSX native
>> version?)
>>
>> Also, can you tell me if there is any output in the "standard output"
>> part of the error log?
>>
>> An alternative route is to run plastimatch independent of Slicer, then
>> loading the results into Slicer for further analysis.  Let me know if you
>> like to pursue that route and I can walk you through.
>>
>> Greg
>>
>>
>> On Thu, 17 Feb 2011 10:22:33 -0800
>> "Zhang, Yi" <[hidden email]> wrote:
>>
>>> Sorry,
>>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>>> using the Parallels Desktop since I don't own a PC. (do you think that
>>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>>> extension version:
>>>
>
http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010

> -06-10-win32
>>>
>>> Actually, not only B-spline, but other two functionalities give me the same
>>> error - DICOM/DICOM RT import and landmark deformable registration.
>>>
>>> Thanks,
>>> Vickie
>>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Can you please tell me your OS, Slicer Version, and
>>>> extension version (extension URL)?
>>>>
>>>> Thank you,
>>>> Greg
>>>>
>>>> -----Original Message-----
>>>> From: [hidden email]
>>>> [mailto:[hidden email]] On Behalf Of Zhang, Yi
>>>> Sent: Thursday, February 17, 2011 12:26 AM
>>>> To: [hidden email]
>>>> Subject: [slicer-users] Plastimatch error
>>>>
>>>> Hi,
>>>>
>>>> I have encountered following error while trying to peform B-spline
>>>> deformable registration on Plastmatch:
>>>>
>>>> ERROR: In
>>>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>>>> line 1575
>>>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>>>> process was null when state was queried, result (1) = Error.
>>>>
>>>> Please help.
>>>> Thanks!
>>>> Vickie
>>
>> --
>> Greg Sharp, PhD
>> Department of Radiation Oncology
>> Massachusetts General Hospital
>
>
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
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Re: Plastimatch error

Zhang, Yi
Hi Greg,

Sorry I was out of the office last few days.
I tried 5 or 10 mm grid size, but still I'm getting errors.
again, both volumes are:
Image matrix: 256 by 256 by 22
Image resolution: 0.15625 by 0.15625 by 1.25mm

Stage 1:
subsampling rate: 1,1,1
Grid size (mm): 10
Max iterations: 30

result: completed with errors: (B-spline deformable registration), 20.91s
Error log:
ERROR: In /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1522
vtkCommandLineModuleLogic (0x1270af00): B-spline deformable registration completed with errors
"Information":
B-spline deformable registration standard output:

fixed image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeC.nrrd
Loading fixed image...
done!
moving image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeB.nrrd
Loading moving image...
done!
[1] xf_in->m_type = 0, xf_out->m_type = 0
Converting fixed
Converting moving
Done.
SUBSAMPLE: (1 1 1), (1 1 1)
moving_ss size = 256 256 22
fixed_ss size = 256 256 22
bspline_xform_initialize
rdims = (4,4,3)
vox_per_rgn = (64,64,8)
cdims = (7 7 6)
xform_any_to_gpuit_bsp complete
BSPLINE PARMS
max_its = 30
BSPLINE XFORM HEADER
vox_per_rgn = 64 64 8
roi_offset = 0 0 0
roi_dim = 256 256 22
Setting NMAX, MMAX = 882 49
>>> START
RUNNING THE L-BFGS-B CODE

           * * *

Machine precision = 2.220E-16
 N =  882    M =  49
 This problem is unconstrained.
MSE[   0] 172793.406 NV 1430550 GM  3440.164 GN 40055.410 [    0.699 secs]
                    CMIN   0.00 CAVG   0.00 CMAX   0.00
MSE[   1] 168788.625 NV 1436510 GM -14022.742 GN 44458.961 [    0.701 secs]
                    CMIN  -0.26 CAVG  -0.00 CMAX   0.27
MSE[   2] 156002.094 NV 1427438 GM -9776.679 GN 38473.344 [    0.721 secs]
                    CMIN  -1.29 CAVG  -0.01 CMAX   1.36
MSE[   3] 113203.945 NV 1376563 GM -1506.240 GN 36962.977 [    0.701 secs]
                    CMIN  -5.42 CAVG  -0.02 CMAX   5.73
MSE[   4] 182364.469 NV 1221763 GM  8802.257 GN 44880.477 [    0.665 secs]
                    CMIN -16.33 CAVG  -0.06 CMAX  23.58
MSE[   5] 88962.250 NV 1334618 GM  2365.741 GN 29213.508 [    0.686 secs]
                    CMIN  -8.32 CAVG  -0.03 CMAX  10.47
MSE[   6] 74965.664 NV 1301347 GM -3784.107 GN 22351.080 [    0.680 secs]
                    CMIN  -8.87 CAVG  -0.05 CMAX  11.16
MSE[   7] 68752.648 NV 1261210 GM -9005.963 GN 20776.543 [    0.672 secs]
                    CMIN  -9.90 CAVG  -0.05 CMAX  10.98
MSE[   8] 62334.117 NV 1253569 GM   -84.478 GN 13559.529 [    0.670 secs]
                    CMIN -10.70 CAVG  -0.03 CMAX  11.15
MSE[   9] 59037.574 NV 1242716 GM  9142.486 GN 15676.164 [    0.669 secs]
                    CMIN -11.83 CAVG  -0.02 CMAX  11.41
MSE[  10] 56116.086 NV 1223911 GM  5785.482 GN 11916.921 [    0.665 secs]
                    CMIN -13.08 CAVG  -0.03 CMAX  12.40
MSE[  11] 51500.602 NV 1178880 GM  1053.619 GN 11454.988 [    0.656 secs]
                    CMIN -16.59 CAVG  -0.05 CMAX  14.58
MSE[  12] 48438.137 NV 1149236 GM -3097.842 GN  9308.528 [    0.649 secs]
                    CMIN -19.33 CAVG  -0.08 CMAX  16.23
MSE[  13] 45976.199 NV 1122297 GM -1455.273 GN  7629.981 [    0.644 secs]
                    CMIN -22.45 CAVG  -0.09 CMAX  17.95
MSE[  14] 44144.320 NV 1106619 GM -1121.861 GN  6836.752 [    0.641 secs]
                    CMIN -24.13 CAVG  -0.09 CMAX  19.08
MSE[  15] 42542.715 NV 1052552 GM -2756.149 GN  8741.547 [    0.630 secs]
                    CMIN -30.40 CAVG  -0.08 CMAX  25.25
MSE[  16] 40959.645 NV 1040040 GM  2106.021 GN 11453.347 [    0.627 secs]
                    CMIN -31.82 CAVG  -0.05 CMAX  27.37
MSE[  17] 38835.320 NV 1047948 GM   171.968 GN  5861.133 [    0.629 secs]
                    CMIN -30.59 CAVG  -0.05 CMAX  26.64
MSE[  18] 38289.160 NV 1033359 GM  2835.816 GN  6007.721 [    0.634 secs]
                    CMIN -31.34 CAVG  -0.05 CMAX  28.26
MSE[  19] 37757.949 NV 1022548 GM   764.146 GN  5460.470 [    0.624 secs]
                    CMIN -32.10 CAVG  -0.05 CMAX  29.80
MSE[  20] 36572.082 NV 990523 GM  -990.091 GN  5187.105 [    0.618 secs]
                    CMIN -34.10 CAVG  -0.06 CMAX  34.08
MSE[  21] 35282.254 NV 952616 GM -3800.624 GN  7294.177 [    0.618 secs]
                    CMIN -35.25 CAVG  -0.07 CMAX  38.78
MSE[  22] 33919.004 NV 938209 GM  -242.454 GN  5740.723 [    0.608 secs]
                    CMIN -33.92 CAVG  -0.08 CMAX  40.26
MSE[  23] 33370.039 NV 916397 GM  1086.198 GN  5384.354 [    0.603 secs]
                    CMIN -34.06 CAVG  -0.07 CMAX  42.59
MSE[  24] 32082.525 NV 927453 GM   492.501 GN  5629.464 [    0.605 secs]
                    CMIN -31.95 CAVG  -0.07 CMAX  41.66
MSE[  25] 31317.986 NV 923391 GM   430.064 GN  3504.146 [    0.604 secs]
                    CMIN -31.63 CAVG  -0.07 CMAX  42.50
MSE[  26] 30691.617 NV 920224 GM    70.180 GN  3819.907 [    0.610 secs]
                    CMIN -31.26 CAVG  -0.07 CMAX  43.41
MSE[  27] 30035.088 NV 914436 GM  -474.841 GN  4630.180 [    0.603 secs]
                    CMIN -30.58 CAVG  -0.06 CMAX  44.40
MSE[  28] 29283.193 NV 902584 GM  -565.189 GN  6579.526 [    0.600 secs]
                    CMIN -29.99 CAVG  -0.06 CMAX  46.43
MSE[  29] 28504.350 NV 899740 GM   403.089 GN  5322.814 [    0.599 secs]
                    CMIN -30.24 CAVG  -0.06 CMAX  47.21
MSE[  30] 27685.469 NV 880915 GM  -360.044 GN  6465.846 [    0.595 secs]
                    CMIN -32.59 CAVG  -0.06 CMAX  49.30
[2] xf_out->m_type = 8, xf_in->m_type = 0
Warping...
Running: plm_warp_native
Converting input image...
Converting xform...
bspline_xform_initialize
rdims = (4,4,3)
vox_per_rgn = (64,64,8)
cdims = (7 7 6)
Input pih
Origin
[-20, -20, -13]
Spacing
[0.15625, 0.15625, 1.25]
Region
ImageRegion (0x7fffd0b054d0)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [256, 256, 22]
Running: gpuit_bsp_to_itk_bsp_raw
Setting bsp_spacing
[10, 10, 10]
Setting bsp_origin
[-30, -30, -23]
Setting bsp_region
ImageRegion (0x7fffd0b04ee0)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [7, 7, 6]
Setting bsp_direction = 1 0 0 0 1 0 0 0 1
Running: xform_itk_bsp_to_itk_bsp
Setting bsp_spacing
[10, 10, 10]
Setting bsp_origin
[-30, -30, -23]
Setting bsp_region
ImageRegion (0x7fffd0b04c30)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [7, 7, 6]
Setting bsp_direction = 1 0 0 0 1 0 0 0 1
Completed: xform_itk_bsp_to_itk_bsp
Creating output volume...
Unhandled image type in Plm_image::convert (14 -> 4)


Thanks,
Vickie
On Feb 21, 2011, at 9:04 AM, Sharp, Gregory C. wrote:

>
> Hi Vickie,
>
> Please try setting the "Grid Size" parameter to something
> smaller than the image size.  For a smoother deformation,
> you may try 10 mm or 20 mm.  For a wigglier deformation, you
> may try something like 1 mm or 5 mm.
>
> Greg
>
>
> -----Original Message-----
> From: Zhang, Yi [mailto:[hidden email]]
> Sent: Sun 2/20/2011 10:28 PM
> To: Sharp, Gregory C.
> Cc: [hidden email]
> Subject: Re: [slicer-users] Plastimatch error
>
> Image matrix: 256 by 256 by 22
> image resolution: 0.15625 by 0.15625 by 1.25mm
> FOV: 40 by 40 by 27.5 mm
> Thanks,
> Vickie
> On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:
>
>>
>> Hi Vickie,
>>
>> This is very helpful.  It looks like the registration code
>> is running out of memory building the lookup table.
>>
>> I think this can be solved by changing the grid spacing.
>> Can you tell me your image resolution and voxel spacing?
>> Then I will suggest some modified settings.
>>
>> Greg
>>
>> -----Original Message-----
>> From: Zhang, Yi [mailto:[hidden email]]
>> Sent: Fri 2/18/2011 4:54 PM
>> To: Sharp, Gregory C.
>> Cc: [hidden email]
>> Subject: Re: [slicer-users] Plastimatch error
>>
>> Hi Greg,
>>
>> I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
>> installed Plastimatch from
>> http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
>> Tested with 2 3D images.
>> It ran for 75.42 secs and completed with errors.
>>
>> ERROR: In
>>
> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>> ic.cxx, line 1522
>> vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
>> completed with errors
>>
>> I have two 3D mask images in nrrd format, same resolution, same matrix size
> and
>> FOV.
>> Using Plastimatch B-spline Registration, I left stage 0 and stage 2 unchecked.
>> For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max iterations
> =
>> 50
>> Afer 75.42 seconds, it completed with following error:
>>
>> Looks like the linux is working better, but still gives errors. Any
> suggestions?
>>
>> Thanks,
>> Vickie
>>
>> FYI: output from "Information"
>>
>> B-spline deformable registration standard output:
>>
>> fixed
>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
>> Loading fixed image...
>> done!
>> moving
>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
>> Loading moving image...
>> done!
>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>> Converting fixed
>> Converting moving
>> Done.
>> SUBSAMPLE: (1 1 1), (1 1 1)
>> moving_ss size = 256 256 22
>> fixed_ss size = 256 256 22
>> bspline_xform_initialize
>> rdims = (1,1,1)
>> vox_per_rgn = (640,640,80)
>> cdims = (4 4 4)
>> xform_any_to_gpuit_bsp complete
>> BSPLINE PARMS
>> max_its = 50
>> BSPLINE XFORM HEADER
>> vox_per_rgn = 640 640 80
>> roi_offset = 0 0 0
>> roi_dim = 256 256 22
>> Setting NMAX, MMAX = 192 33
>>>>> START
>> RUNNING THE L-BFGS-B CODE
>>
>>          * * *
>>
>> Machine precision = 2.220E-16
>> N =  192    M =  33
>> This problem is unconstrained.
>> MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
>>                   CMIN   0.00 CAVG   0.00 CMAX   0.00
>> MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
>>                   CMIN  -0.47 CAVG  -0.00 CMAX   0.55
>> MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
>>                   CMIN  -2.33 CAVG  -0.01 CMAX   2.75
>> MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
>>                   CMIN  -3.54 CAVG  -0.02 CMAX   4.65
>> MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
>>                   CMIN  -8.39 CAVG  -0.02 CMAX  12.27
>> MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
>>                   CMIN  -4.44 CAVG  -0.02 CMAX   6.07
>> MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
>>                   CMIN  -5.12 CAVG  -0.02 CMAX   7.14
>> MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
>>                   CMIN -27.43 CAVG  -0.06 CMAX  45.42
>> MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
>>                   CMIN  -5.81 CAVG  -0.02 CMAX   8.33
>> MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
>>                   CMIN  -5.21 CAVG  -0.02 CMAX   7.29
>> MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
>>                   CMIN  -5.14 CAVG  -0.02 CMAX   7.16
>> MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
>>                   CMIN  -5.18 CAVG  -0.02 CMAX   7.25
>> MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
>>                   CMIN  -5.14 CAVG  -0.02 CMAX   7.18
>> MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
>>                   CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>> MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.18
>> MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
>>                   CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>> MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
>>                   CMIN  -5.87 CAVG  -0.04 CMAX   8.12
>> MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
>>                   CMIN  -5.29 CAVG  -0.02 CMAX   7.37
>> MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
>>                   CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>> MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
>>                   CMIN  -8.56 CAVG  -0.09 CMAX  11.31
>> MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
>>                   CMIN  -5.63 CAVG  -0.03 CMAX   7.77
>> MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
>>                   CMIN  -5.23 CAVG  -0.02 CMAX   7.28
>> MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
>>                   CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>> MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
>>                   CMIN  -5.63 CAVG  -0.04 CMAX   7.56
>> MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
>>                   CMIN  -5.26 CAVG  -0.02 CMAX   7.27
>> MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
>>                   CMIN  -5.11 CAVG  -0.04 CMAX   7.84
>> MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
>>                   CMIN  -5.03 CAVG  -0.05 CMAX   8.18
>> MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
>>                   CMIN  -7.75 CAVG  -0.06 CMAX   9.52
>> MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
>>                   CMIN -19.57 CAVG  -0.14 CMAX  15.94
>> MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
>>                   CMIN -14.77 CAVG  -0.12 CMAX  13.34
>> MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
>>                   CMIN -10.03 CAVG   0.00 CMAX  11.79
>> MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
>>                   CMIN -12.47 CAVG  -0.11 CMAX  12.07
>> MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
>>                   CMIN -13.62 CAVG  -0.12 CMAX  12.84
>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>> Warping...
>> Running: plm_warp_native
>> Converting input image...
>> Converting xform...
>> bspline_xform_initialize
>> Error allocating memory for q_lut
>>
>> On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:
>>
>>>
>>> Hi Vickie,
>>>
>>> Unfortunately I couldn't reproduce the problem.  You are using a good
>>> configuration of versions which is supposed to work.
>>>
>>> We should test if the problem is with Parallels.  Can you please try
>>> downloading and running another extension, such as ExampleCommandLine?
>>> (By the way, why do you run Slicer on Parallels instead of the OSX native
>>> version?)
>>>
>>> Also, can you tell me if there is any output in the "standard output"
>>> part of the error log?
>>>
>>> An alternative route is to run plastimatch independent of Slicer, then
>>> loading the results into Slicer for further analysis.  Let me know if you
>>> like to pursue that route and I can walk you through.
>>>
>>> Greg
>>>
>>>
>>> On Thu, 17 Feb 2011 10:22:33 -0800
>>> "Zhang, Yi" <[hidden email]> wrote:
>>>
>>>> Sorry,
>>>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>>>> using the Parallels Desktop since I don't own a PC. (do you think that
>>>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>>>> extension version:
>>>>
>>
> http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010
>> -06-10-win32
>>>>
>>>> Actually, not only B-spline, but other two functionalities give me the same
>>>> error - DICOM/DICOM RT import and landmark deformable registration.
>>>>
>>>> Thanks,
>>>> Vickie
>>>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>>>
>>>>>
>>>>> Hi Vickie,
>>>>>
>>>>> Can you please tell me your OS, Slicer Version, and
>>>>> extension version (extension URL)?
>>>>>
>>>>> Thank you,
>>>>> Greg
>>>>>
>>>>> -----Original Message-----
>>>>> From: [hidden email]
>>>>> [mailto:[hidden email]] On Behalf Of Zhang, Yi
>>>>> Sent: Thursday, February 17, 2011 12:26 AM
>>>>> To: [hidden email]
>>>>> Subject: [slicer-users] Plastimatch error
>>>>>
>>>>> Hi,
>>>>>
>>>>> I have encountered following error while trying to peform B-spline
>>>>> deformable registration on Plastmatch:
>>>>>
>>>>> ERROR: In
>>>>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>>>>> line 1575
>>>>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>>>>> process was null when state was queried, result (1) = Error.
>>>>>
>>>>> Please help.
>>>>> Thanks!
>>>>> Vickie
>>>
>>> --
>>> Greg Sharp, PhD
>>> Department of Radiation Oncology
>>> Massachusetts General Hospital
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance HelpLine
> at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
>> but does not contain patient information, please contact the sender and
> properly
>> dispose of the e-mail.
>>
>
>

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Re: Plastimatch error

Sharp, Gregory C.

Hi Vickie,

Thanks for your patience and persistence!  

You have hit a bug in plastimatch which thankfully is already fixed.  
Can you try to update your plastimatch?  You will need to point the
extensions "Where to search" URL to a different location:

For 32-bit linux it is here:

http://ext.slicer.org/ext/Slicer-3-6/16108%2dlinux%2dx86/

For 64-bit linux it is here:

http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/

Greg

-----Original Message-----
From: Zhang, Yi [mailto:[hidden email]]
Sent: Thu 2/24/2011 6:24 PM
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Plastimatch error
 
Hi Greg,

Sorry I was out of the office last few days.
I tried 5 or 10 mm grid size, but still I'm getting errors.
again, both volumes are:
Image matrix: 256 by 256 by 22
Image resolution: 0.15625 by 0.15625 by 1.25mm

Stage 1:
subsampling rate: 1,1,1
Grid size (mm): 10
Max iterations: 30

result: completed with errors: (B-spline deformable registration), 20.91s
Error log:
ERROR: In
/home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
ic.cxx, line 1522
vtkCommandLineModuleLogic (0x1270af00): B-spline deformable registration
completed with errors
"Information":
B-spline deformable registration standard output:

fixed
image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeC.nrrd
Loading fixed image...
done!
moving
image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeB.nrrd
Loading moving image...
done!
[1] xf_in->m_type = 0, xf_out->m_type = 0
Converting fixed
Converting moving
Done.
SUBSAMPLE: (1 1 1), (1 1 1)
moving_ss size = 256 256 22
fixed_ss size = 256 256 22
bspline_xform_initialize
rdims = (4,4,3)
vox_per_rgn = (64,64,8)
cdims = (7 7 6)
xform_any_to_gpuit_bsp complete
BSPLINE PARMS
max_its = 30
BSPLINE XFORM HEADER
vox_per_rgn = 64 64 8
roi_offset = 0 0 0
roi_dim = 256 256 22
Setting NMAX, MMAX = 882 49
>>> START
RUNNING THE L-BFGS-B CODE

           * * *

Machine precision = 2.220E-16
 N =  882    M =  49
 This problem is unconstrained.
MSE[   0] 172793.406 NV 1430550 GM  3440.164 GN 40055.410 [    0.699 secs]
                    CMIN   0.00 CAVG   0.00 CMAX   0.00
MSE[   1] 168788.625 NV 1436510 GM -14022.742 GN 44458.961 [    0.701 secs]
                    CMIN  -0.26 CAVG  -0.00 CMAX   0.27
MSE[   2] 156002.094 NV 1427438 GM -9776.679 GN 38473.344 [    0.721 secs]
                    CMIN  -1.29 CAVG  -0.01 CMAX   1.36
MSE[   3] 113203.945 NV 1376563 GM -1506.240 GN 36962.977 [    0.701 secs]
                    CMIN  -5.42 CAVG  -0.02 CMAX   5.73
MSE[   4] 182364.469 NV 1221763 GM  8802.257 GN 44880.477 [    0.665 secs]
                    CMIN -16.33 CAVG  -0.06 CMAX  23.58
MSE[   5] 88962.250 NV 1334618 GM  2365.741 GN 29213.508 [    0.686 secs]
                    CMIN  -8.32 CAVG  -0.03 CMAX  10.47
MSE[   6] 74965.664 NV 1301347 GM -3784.107 GN 22351.080 [    0.680 secs]
                    CMIN  -8.87 CAVG  -0.05 CMAX  11.16
MSE[   7] 68752.648 NV 1261210 GM -9005.963 GN 20776.543 [    0.672 secs]
                    CMIN  -9.90 CAVG  -0.05 CMAX  10.98
MSE[   8] 62334.117 NV 1253569 GM   -84.478 GN 13559.529 [    0.670 secs]
                    CMIN -10.70 CAVG  -0.03 CMAX  11.15
MSE[   9] 59037.574 NV 1242716 GM  9142.486 GN 15676.164 [    0.669 secs]
                    CMIN -11.83 CAVG  -0.02 CMAX  11.41
MSE[  10] 56116.086 NV 1223911 GM  5785.482 GN 11916.921 [    0.665 secs]
                    CMIN -13.08 CAVG  -0.03 CMAX  12.40
MSE[  11] 51500.602 NV 1178880 GM  1053.619 GN 11454.988 [    0.656 secs]
                    CMIN -16.59 CAVG  -0.05 CMAX  14.58
MSE[  12] 48438.137 NV 1149236 GM -3097.842 GN  9308.528 [    0.649 secs]
                    CMIN -19.33 CAVG  -0.08 CMAX  16.23
MSE[  13] 45976.199 NV 1122297 GM -1455.273 GN  7629.981 [    0.644 secs]
                    CMIN -22.45 CAVG  -0.09 CMAX  17.95
MSE[  14] 44144.320 NV 1106619 GM -1121.861 GN  6836.752 [    0.641 secs]
                    CMIN -24.13 CAVG  -0.09 CMAX  19.08
MSE[  15] 42542.715 NV 1052552 GM -2756.149 GN  8741.547 [    0.630 secs]
                    CMIN -30.40 CAVG  -0.08 CMAX  25.25
MSE[  16] 40959.645 NV 1040040 GM  2106.021 GN 11453.347 [    0.627 secs]
                    CMIN -31.82 CAVG  -0.05 CMAX  27.37
MSE[  17] 38835.320 NV 1047948 GM   171.968 GN  5861.133 [    0.629 secs]
                    CMIN -30.59 CAVG  -0.05 CMAX  26.64
MSE[  18] 38289.160 NV 1033359 GM  2835.816 GN  6007.721 [    0.634 secs]
                    CMIN -31.34 CAVG  -0.05 CMAX  28.26
MSE[  19] 37757.949 NV 1022548 GM   764.146 GN  5460.470 [    0.624 secs]
                    CMIN -32.10 CAVG  -0.05 CMAX  29.80
MSE[  20] 36572.082 NV 990523 GM  -990.091 GN  5187.105 [    0.618 secs]
                    CMIN -34.10 CAVG  -0.06 CMAX  34.08
MSE[  21] 35282.254 NV 952616 GM -3800.624 GN  7294.177 [    0.618 secs]
                    CMIN -35.25 CAVG  -0.07 CMAX  38.78
MSE[  22] 33919.004 NV 938209 GM  -242.454 GN  5740.723 [    0.608 secs]
                    CMIN -33.92 CAVG  -0.08 CMAX  40.26
MSE[  23] 33370.039 NV 916397 GM  1086.198 GN  5384.354 [    0.603 secs]
                    CMIN -34.06 CAVG  -0.07 CMAX  42.59
MSE[  24] 32082.525 NV 927453 GM   492.501 GN  5629.464 [    0.605 secs]
                    CMIN -31.95 CAVG  -0.07 CMAX  41.66
MSE[  25] 31317.986 NV 923391 GM   430.064 GN  3504.146 [    0.604 secs]
                    CMIN -31.63 CAVG  -0.07 CMAX  42.50
MSE[  26] 30691.617 NV 920224 GM    70.180 GN  3819.907 [    0.610 secs]
                    CMIN -31.26 CAVG  -0.07 CMAX  43.41
MSE[  27] 30035.088 NV 914436 GM  -474.841 GN  4630.180 [    0.603 secs]
                    CMIN -30.58 CAVG  -0.06 CMAX  44.40
MSE[  28] 29283.193 NV 902584 GM  -565.189 GN  6579.526 [    0.600 secs]
                    CMIN -29.99 CAVG  -0.06 CMAX  46.43
MSE[  29] 28504.350 NV 899740 GM   403.089 GN  5322.814 [    0.599 secs]
                    CMIN -30.24 CAVG  -0.06 CMAX  47.21
MSE[  30] 27685.469 NV 880915 GM  -360.044 GN  6465.846 [    0.595 secs]
                    CMIN -32.59 CAVG  -0.06 CMAX  49.30
[2] xf_out->m_type = 8, xf_in->m_type = 0
Warping...
Running: plm_warp_native
Converting input image...
Converting xform...
bspline_xform_initialize
rdims = (4,4,3)
vox_per_rgn = (64,64,8)
cdims = (7 7 6)
Input pih
Origin
[-20, -20, -13]
Spacing
[0.15625, 0.15625, 1.25]
Region
ImageRegion (0x7fffd0b054d0)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [256, 256, 22]
Running: gpuit_bsp_to_itk_bsp_raw
Setting bsp_spacing
[10, 10, 10]
Setting bsp_origin
[-30, -30, -23]
Setting bsp_region
ImageRegion (0x7fffd0b04ee0)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [7, 7, 6]
Setting bsp_direction = 1 0 0 0 1 0 0 0 1
Running: xform_itk_bsp_to_itk_bsp
Setting bsp_spacing
[10, 10, 10]
Setting bsp_origin
[-30, -30, -23]
Setting bsp_region
ImageRegion (0x7fffd0b04c30)
  Dimension: 3
  Index: [0, 0, 0]
  Size: [7, 7, 6]
Setting bsp_direction = 1 0 0 0 1 0 0 0 1
Completed: xform_itk_bsp_to_itk_bsp
Creating output volume...
Unhandled image type in Plm_image::convert (14 -> 4)


Thanks,
Vickie
On Feb 21, 2011, at 9:04 AM, Sharp, Gregory C. wrote:

>
> Hi Vickie,
>
> Please try setting the "Grid Size" parameter to something
> smaller than the image size.  For a smoother deformation,
> you may try 10 mm or 20 mm.  For a wigglier deformation, you
> may try something like 1 mm or 5 mm.
>
> Greg
>
>
> -----Original Message-----
> From: Zhang, Yi [mailto:[hidden email]]
> Sent: Sun 2/20/2011 10:28 PM
> To: Sharp, Gregory C.
> Cc: [hidden email]
> Subject: Re: [slicer-users] Plastimatch error
>
> Image matrix: 256 by 256 by 22
> image resolution: 0.15625 by 0.15625 by 1.25mm
> FOV: 40 by 40 by 27.5 mm
> Thanks,
> Vickie
> On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:
>
>>
>> Hi Vickie,
>>
>> This is very helpful.  It looks like the registration code
>> is running out of memory building the lookup table.
>>
>> I think this can be solved by changing the grid spacing.
>> Can you tell me your image resolution and voxel spacing?
>> Then I will suggest some modified settings.
>>
>> Greg
>>
>> -----Original Message-----
>> From: Zhang, Yi [mailto:[hidden email]]
>> Sent: Fri 2/18/2011 4:54 PM
>> To: Sharp, Gregory C.
>> Cc: [hidden email]
>> Subject: Re: [slicer-users] Plastimatch error
>>
>> Hi Greg,
>>
>> I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
>> installed Plastimatch from
>> http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
>> Tested with 2 3D images.
>> It ran for 75.42 secs and completed with errors.
>>
>> ERROR: In
>>
>
/home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>> ic.cxx, line 1522
>> vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
>> completed with errors
>>
>> I have two 3D mask images in nrrd format, same resolution, same matrix size
> and
>> FOV.
>> Using Plastimatch B-spline Registration, I left stage 0 and stage 2
unchecked.
>> For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max
iterations

> =
>> 50
>> Afer 75.42 seconds, it completed with following error:
>>
>> Looks like the linux is working better, but still gives errors. Any
> suggestions?
>>
>> Thanks,
>> Vickie
>>
>> FYI: output from "Information"
>>
>> B-spline deformable registration standard output:
>>
>> fixed
>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
>> Loading fixed image...
>> done!
>> moving
>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
>> Loading moving image...
>> done!
>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>> Converting fixed
>> Converting moving
>> Done.
>> SUBSAMPLE: (1 1 1), (1 1 1)
>> moving_ss size = 256 256 22
>> fixed_ss size = 256 256 22
>> bspline_xform_initialize
>> rdims = (1,1,1)
>> vox_per_rgn = (640,640,80)
>> cdims = (4 4 4)
>> xform_any_to_gpuit_bsp complete
>> BSPLINE PARMS
>> max_its = 50
>> BSPLINE XFORM HEADER
>> vox_per_rgn = 640 640 80
>> roi_offset = 0 0 0
>> roi_dim = 256 256 22
>> Setting NMAX, MMAX = 192 33
>>>>> START
>> RUNNING THE L-BFGS-B CODE
>>
>>          * * *
>>
>> Machine precision = 2.220E-16
>> N =  192    M =  33
>> This problem is unconstrained.
>> MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
>>                   CMIN   0.00 CAVG   0.00 CMAX   0.00
>> MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
>>                   CMIN  -0.47 CAVG  -0.00 CMAX   0.55
>> MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
>>                   CMIN  -2.33 CAVG  -0.01 CMAX   2.75
>> MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
>>                   CMIN  -3.54 CAVG  -0.02 CMAX   4.65
>> MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
>>                   CMIN  -8.39 CAVG  -0.02 CMAX  12.27
>> MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
>>                   CMIN  -4.44 CAVG  -0.02 CMAX   6.07
>> MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
>>                   CMIN  -5.12 CAVG  -0.02 CMAX   7.14
>> MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
>>                   CMIN -27.43 CAVG  -0.06 CMAX  45.42
>> MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
>>                   CMIN  -5.81 CAVG  -0.02 CMAX   8.33
>> MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
>>                   CMIN  -5.21 CAVG  -0.02 CMAX   7.29
>> MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
>>                   CMIN  -5.14 CAVG  -0.02 CMAX   7.16
>> MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
>>                   CMIN  -5.18 CAVG  -0.02 CMAX   7.25
>> MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
>>                   CMIN  -5.14 CAVG  -0.02 CMAX   7.18
>> MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
>>                   CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>> MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.18
>> MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
>>                   CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>> MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
>>                   CMIN  -5.87 CAVG  -0.04 CMAX   8.12
>> MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
>>                   CMIN  -5.29 CAVG  -0.02 CMAX   7.37
>> MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
>>                   CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>> MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
>>                   CMIN  -8.56 CAVG  -0.09 CMAX  11.31
>> MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
>>                   CMIN  -5.63 CAVG  -0.03 CMAX   7.77
>> MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
>>                   CMIN  -5.23 CAVG  -0.02 CMAX   7.28
>> MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
>>                   CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>> MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
>>                   CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
>>                   CMIN  -5.63 CAVG  -0.04 CMAX   7.56
>> MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
>>                   CMIN  -5.26 CAVG  -0.02 CMAX   7.27
>> MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
>>                   CMIN  -5.11 CAVG  -0.04 CMAX   7.84
>> MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
>>                   CMIN  -5.03 CAVG  -0.05 CMAX   8.18
>> MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
>>                   CMIN  -7.75 CAVG  -0.06 CMAX   9.52
>> MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
>>                   CMIN -19.57 CAVG  -0.14 CMAX  15.94
>> MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
>>                   CMIN -14.77 CAVG  -0.12 CMAX  13.34
>> MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
>>                   CMIN -10.03 CAVG   0.00 CMAX  11.79
>> MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
>>                   CMIN -12.47 CAVG  -0.11 CMAX  12.07
>> MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
>>                   CMIN -13.62 CAVG  -0.12 CMAX  12.84
>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>> Warping...
>> Running: plm_warp_native
>> Converting input image...
>> Converting xform...
>> bspline_xform_initialize
>> Error allocating memory for q_lut
>>
>> On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:
>>
>>>
>>> Hi Vickie,
>>>
>>> Unfortunately I couldn't reproduce the problem.  You are using a good
>>> configuration of versions which is supposed to work.
>>>
>>> We should test if the problem is with Parallels.  Can you please try
>>> downloading and running another extension, such as ExampleCommandLine?
>>> (By the way, why do you run Slicer on Parallels instead of the OSX native
>>> version?)
>>>
>>> Also, can you tell me if there is any output in the "standard output"
>>> part of the error log?
>>>
>>> An alternative route is to run plastimatch independent of Slicer, then
>>> loading the results into Slicer for further analysis.  Let me know if you
>>> like to pursue that route and I can walk you through.
>>>
>>> Greg
>>>
>>>
>>> On Thu, 17 Feb 2011 10:22:33 -0800
>>> "Zhang, Yi" <[hidden email]> wrote:
>>>
>>>> Sorry,
>>>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>>>> using the Parallels Desktop since I don't own a PC. (do you think that
>>>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>>>> extension version:
>>>>
>>
>
http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010

>> -06-10-win32
>>>>
>>>> Actually, not only B-spline, but other two functionalities give me the same
>>>> error - DICOM/DICOM RT import and landmark deformable registration.
>>>>
>>>> Thanks,
>>>> Vickie
>>>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>>>
>>>>>
>>>>> Hi Vickie,
>>>>>
>>>>> Can you please tell me your OS, Slicer Version, and
>>>>> extension version (extension URL)?
>>>>>
>>>>> Thank you,
>>>>> Greg
>>>>>
>>>>> -----Original Message-----
>>>>> From: [hidden email]
>>>>> [mailto:[hidden email]] On Behalf Of Zhang, Yi
>>>>> Sent: Thursday, February 17, 2011 12:26 AM
>>>>> To: [hidden email]
>>>>> Subject: [slicer-users] Plastimatch error
>>>>>
>>>>> Hi,
>>>>>
>>>>> I have encountered following error while trying to peform B-spline
>>>>> deformable registration on Plastmatch:
>>>>>
>>>>> ERROR: In
>>>>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>>>>> line 1575
>>>>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>>>>> process was null when state was queried, result (1) = Error.
>>>>>
>>>>> Please help.
>>>>> Thanks!
>>>>> Vickie
>>>
>>> --
>>> Greg Sharp, PhD
>>> Department of Radiation Oncology
>>> Massachusetts General Hospital
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance HelpLine
> at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
>> but does not contain patient information, please contact the sender and
> properly
>> dispose of the e-mail.
>>
>
>


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Re: Plastimatch error

Zhang, Yi
Hi Greg,

After downloading plastimatch from http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/<http://ext.slicer.org/ext/Slicer-3-6/16102-linux-x86_64/>
<http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/>I don't see plastimatch under Modules anymore. It seems to have disappeared from Slicer3. Any ideas?

Vickie
On Feb 24, 2011, at 6:30 PM, Sharp, Gregory C. wrote:


Hi Vickie,

Thanks for your patience and persistence!

You have hit a bug in plastimatch which thankfully is already fixed.
Can you try to update your plastimatch?  You will need to point the
extensions "Where to search" URL to a different location:

For 32-bit linux it is here:

http://ext.slicer.org/ext/Slicer-3-6/16108%2dlinux%2dx86/

For 64-bit linux it is here:

http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/

Greg

-----Original Message-----
From: Zhang, Yi [mailto:[hidden email]]
Sent: Thu 2/24/2011 6:24 PM
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Plastimatch error

Hi Greg,

Sorry I was out of the office last few days.
I tried 5 or 10 mm grid size, but still I'm getting errors.
again, both volumes are:
Image matrix: 256 by 256 by 22
Image resolution: 0.15625 by 0.15625 by 1.25mm

Stage 1:
subsampling rate: 1,1,1
Grid size (mm): 10
Max iterations: 30

result: completed with errors: (B-spline deformable registration), 20.91s
Error log:
ERROR: In
/home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
ic.cxx, line 1522
vtkCommandLineModuleLogic (0x1270af00): B-spline deformable registration
completed with errors
"Information":
B-spline deformable registration standard output:

fixed
image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeC.nrrd
Loading fixed image...
done!
moving
image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeB.nrrd
Loading moving image...
done!
[1] xf_in->m_type = 0, xf_out->m_type = 0
Converting fixed
Converting moving
Done.
SUBSAMPLE: (1 1 1), (1 1 1)
moving_ss size = 256 256 22
fixed_ss size = 256 256 22
bspline_xform_initialize
rdims = (4,4,3)
vox_per_rgn = (64,64,8)
cdims = (7 7 6)
xform_any_to_gpuit_bsp complete
BSPLINE PARMS
max_its = 30
BSPLINE XFORM HEADER
vox_per_rgn = 64 64 8
roi_offset = 0 0 0
roi_dim = 256 256 22
Setting NMAX, MMAX = 882 49
START
RUNNING THE L-BFGS-B CODE

          * * *

Machine precision = 2.220E-16
N =  882    M =  49
This problem is unconstrained.
MSE[   0] 172793.406 NV 1430550 GM  3440.164 GN 40055.410 [    0.699 secs]
                   CMIN   0.00 CAVG   0.00 CMAX   0.00
MSE[   1] 168788.625 NV 1436510 GM -14022.742 GN 44458.961 [    0.701 secs]
                   CMIN  -0.26 CAVG  -0.00 CMAX   0.27
MSE[   2] 156002.094 NV 1427438 GM -9776.679 GN 38473.344 [    0.721 secs]
                   CMIN  -1.29 CAVG  -0.01 CMAX   1.36
MSE[   3] 113203.945 NV 1376563 GM -1506.240 GN 36962.977 [    0.701 secs]
                   CMIN  -5.42 CAVG  -0.02 CMAX   5.73
MSE[   4] 182364.469 NV 1221763 GM  8802.257 GN 44880.477 [    0.665 secs]
                   CMIN -16.33 CAVG  -0.06 CMAX  23.58
MSE[   5] 88962.250 NV 1334618 GM  2365.741 GN 29213.508 [    0.686 secs]
                   CMIN  -8.32 CAVG  -0.03 CMAX  10.47
MSE[   6] 74965.664 NV 1301347 GM -3784.107 GN 22351.080 [    0.680 secs]
                   CMIN  -8.87 CAVG  -0.05 CMAX  11.16
MSE[   7] 68752.648 NV 1261210 GM -9005.963 GN 20776.543 [    0.672 secs]
                   CMIN  -9.90 CAVG  -0.05 CMAX  10.98
MSE[   8] 62334.117 NV 1253569 GM   -84.478 GN 13559.529 [    0.670 secs]
                   CMIN -10.70 CAVG  -0.03 CMAX  11.15
MSE[   9] 59037.574 NV 1242716 GM  9142.486 GN 15676.164 [    0.669 secs]
                   CMIN -11.83 CAVG  -0.02 CMAX  11.41
MSE[  10] 56116.086 NV 1223911 GM  5785.482 GN 11916.921 [    0.665 secs]
                   CMIN -13.08 CAVG  -0.03 CMAX  12.40
MSE[  11] 51500.602 NV 1178880 GM  1053.619 GN 11454.988 [    0.656 secs]
                   CMIN -16.59 CAVG  -0.05 CMAX  14.58
MSE[  12] 48438.137 NV 1149236 GM -3097.842 GN  9308.528 [    0.649 secs]
                   CMIN -19.33 CAVG  -0.08 CMAX  16.23
MSE[  13] 45976.199 NV 1122297 GM -1455.273 GN  7629.981 [    0.644 secs]
                   CMIN -22.45 CAVG  -0.09 CMAX  17.95
MSE[  14] 44144.320 NV 1106619 GM -1121.861 GN  6836.752 [    0.641 secs]
                   CMIN -24.13 CAVG  -0.09 CMAX  19.08
MSE[  15] 42542.715 NV 1052552 GM -2756.149 GN  8741.547 [    0.630 secs]
                   CMIN -30.40 CAVG  -0.08 CMAX  25.25
MSE[  16] 40959.645 NV 1040040 GM  2106.021 GN 11453.347 [    0.627 secs]
                   CMIN -31.82 CAVG  -0.05 CMAX  27.37
MSE[  17] 38835.320 NV 1047948 GM   171.968 GN  5861.133 [    0.629 secs]
                   CMIN -30.59 CAVG  -0.05 CMAX  26.64
MSE[  18] 38289.160 NV 1033359 GM  2835.816 GN  6007.721 [    0.634 secs]
                   CMIN -31.34 CAVG  -0.05 CMAX  28.26
MSE[  19] 37757.949 NV 1022548 GM   764.146 GN  5460.470 [    0.624 secs]
                   CMIN -32.10 CAVG  -0.05 CMAX  29.80
MSE[  20] 36572.082 NV 990523 GM  -990.091 GN  5187.105 [    0.618 secs]
                   CMIN -34.10 CAVG  -0.06 CMAX  34.08
MSE[  21] 35282.254 NV 952616 GM -3800.624 GN  7294.177 [    0.618 secs]
                   CMIN -35.25 CAVG  -0.07 CMAX  38.78
MSE[  22] 33919.004 NV 938209 GM  -242.454 GN  5740.723 [    0.608 secs]
                   CMIN -33.92 CAVG  -0.08 CMAX  40.26
MSE[  23] 33370.039 NV 916397 GM  1086.198 GN  5384.354 [    0.603 secs]
                   CMIN -34.06 CAVG  -0.07 CMAX  42.59
MSE[  24] 32082.525 NV 927453 GM   492.501 GN  5629.464 [    0.605 secs]
                   CMIN -31.95 CAVG  -0.07 CMAX  41.66
MSE[  25] 31317.986 NV 923391 GM   430.064 GN  3504.146 [    0.604 secs]
                   CMIN -31.63 CAVG  -0.07 CMAX  42.50
MSE[  26] 30691.617 NV 920224 GM    70.180 GN  3819.907 [    0.610 secs]
                   CMIN -31.26 CAVG  -0.07 CMAX  43.41
MSE[  27] 30035.088 NV 914436 GM  -474.841 GN  4630.180 [    0.603 secs]
                   CMIN -30.58 CAVG  -0.06 CMAX  44.40
MSE[  28] 29283.193 NV 902584 GM  -565.189 GN  6579.526 [    0.600 secs]
                   CMIN -29.99 CAVG  -0.06 CMAX  46.43
MSE[  29] 28504.350 NV 899740 GM   403.089 GN  5322.814 [    0.599 secs]
                   CMIN -30.24 CAVG  -0.06 CMAX  47.21
MSE[  30] 27685.469 NV 880915 GM  -360.044 GN  6465.846 [    0.595 secs]
                   CMIN -32.59 CAVG  -0.06 CMAX  49.30
[2] xf_out->m_type = 8, xf_in->m_type = 0
Warping...
Running: plm_warp_native
Converting input image...
Converting xform...
bspline_xform_initialize
rdims = (4,4,3)
vox_per_rgn = (64,64,8)
cdims = (7 7 6)
Input pih
Origin
[-20, -20, -13]
Spacing
[0.15625, 0.15625, 1.25]
Region
ImageRegion (0x7fffd0b054d0)
 Dimension: 3
 Index: [0, 0, 0]
 Size: [256, 256, 22]
Running: gpuit_bsp_to_itk_bsp_raw
Setting bsp_spacing
[10, 10, 10]
Setting bsp_origin
[-30, -30, -23]
Setting bsp_region
ImageRegion (0x7fffd0b04ee0)
 Dimension: 3
 Index: [0, 0, 0]
 Size: [7, 7, 6]
Setting bsp_direction = 1 0 0 0 1 0 0 0 1
Running: xform_itk_bsp_to_itk_bsp
Setting bsp_spacing
[10, 10, 10]
Setting bsp_origin
[-30, -30, -23]
Setting bsp_region
ImageRegion (0x7fffd0b04c30)
 Dimension: 3
 Index: [0, 0, 0]
 Size: [7, 7, 6]
Setting bsp_direction = 1 0 0 0 1 0 0 0 1
Completed: xform_itk_bsp_to_itk_bsp
Creating output volume...
Unhandled image type in Plm_image::convert (14 -> 4)


Thanks,
Vickie
On Feb 21, 2011, at 9:04 AM, Sharp, Gregory C. wrote:


Hi Vickie,

Please try setting the "Grid Size" parameter to something
smaller than the image size.  For a smoother deformation,
you may try 10 mm or 20 mm.  For a wigglier deformation, you
may try something like 1 mm or 5 mm.

Greg


-----Original Message-----
From: Zhang, Yi [mailto:[hidden email]]
Sent: Sun 2/20/2011 10:28 PM
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Plastimatch error

Image matrix: 256 by 256 by 22
image resolution: 0.15625 by 0.15625 by 1.25mm
FOV: 40 by 40 by 27.5 mm
Thanks,
Vickie
On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:


Hi Vickie,

This is very helpful.  It looks like the registration code
is running out of memory building the lookup table.

I think this can be solved by changing the grid spacing.
Can you tell me your image resolution and voxel spacing?
Then I will suggest some modified settings.

Greg

-----Original Message-----
From: Zhang, Yi [mailto:[hidden email]]
Sent: Fri 2/18/2011 4:54 PM
To: Sharp, Gregory C.
Cc: [hidden email]
Subject: Re: [slicer-users] Plastimatch error

Hi Greg,

I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
installed Plastimatch from
http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
Tested with 2 3D images.
It ran for 75.42 secs and completed with errors.

ERROR: In


/home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
ic.cxx, line 1522
vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
completed with errors

I have two 3D mask images in nrrd format, same resolution, same matrix size
and
FOV.
Using Plastimatch B-spline Registration, I left stage 0 and stage 2
unchecked.
For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max
iterations
=
50
Afer 75.42 seconds, it completed with following error:

Looks like the linux is working better, but still gives errors. Any
suggestions?

Thanks,
Vickie

FYI: output from "Information"

B-spline deformable registration standard output:

fixed
image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
Loading fixed image...
done!
moving
image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
Loading moving image...
done!
[1] xf_in->m_type = 0, xf_out->m_type = 0
Converting fixed
Converting moving
Done.
SUBSAMPLE: (1 1 1), (1 1 1)
moving_ss size = 256 256 22
fixed_ss size = 256 256 22
bspline_xform_initialize
rdims = (1,1,1)
vox_per_rgn = (640,640,80)
cdims = (4 4 4)
xform_any_to_gpuit_bsp complete
BSPLINE PARMS
max_its = 50
BSPLINE XFORM HEADER
vox_per_rgn = 640 640 80
roi_offset = 0 0 0
roi_dim = 256 256 22
Setting NMAX, MMAX = 192 33
START
RUNNING THE L-BFGS-B CODE

        * * *

Machine precision = 2.220E-16
N =  192    M =  33
This problem is unconstrained.
MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
                 CMIN   0.00 CAVG   0.00 CMAX   0.00
MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
                 CMIN  -0.47 CAVG  -0.00 CMAX   0.55
MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
                 CMIN  -2.33 CAVG  -0.01 CMAX   2.75
MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
                 CMIN  -3.54 CAVG  -0.02 CMAX   4.65
MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
                 CMIN  -8.39 CAVG  -0.02 CMAX  12.27
MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
                 CMIN  -4.44 CAVG  -0.02 CMAX   6.07
MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
                 CMIN  -5.12 CAVG  -0.02 CMAX   7.14
MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
                 CMIN -27.43 CAVG  -0.06 CMAX  45.42
MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
                 CMIN  -5.81 CAVG  -0.02 CMAX   8.33
MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
                 CMIN  -5.21 CAVG  -0.02 CMAX   7.29
MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
                 CMIN  -5.14 CAVG  -0.02 CMAX   7.16
MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
                 CMIN  -5.18 CAVG  -0.02 CMAX   7.25
MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
                 CMIN  -5.14 CAVG  -0.02 CMAX   7.18
MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
                 CMIN  -5.17 CAVG  -0.02 CMAX   7.22
MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.18
MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
                 CMIN  -5.16 CAVG  -0.02 CMAX   7.20
MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
                 CMIN  -5.87 CAVG  -0.04 CMAX   8.12
MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
                 CMIN  -5.29 CAVG  -0.02 CMAX   7.37
MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
                 CMIN  -5.17 CAVG  -0.02 CMAX   7.22
MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
                 CMIN  -8.56 CAVG  -0.09 CMAX  11.31
MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
                 CMIN  -5.63 CAVG  -0.03 CMAX   7.77
MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
                 CMIN  -5.23 CAVG  -0.02 CMAX   7.28
MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
                 CMIN  -5.16 CAVG  -0.02 CMAX   7.20
MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
                 CMIN  -5.63 CAVG  -0.04 CMAX   7.56
MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
                 CMIN  -5.26 CAVG  -0.02 CMAX   7.27
MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
                 CMIN  -5.11 CAVG  -0.04 CMAX   7.84
MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
                 CMIN  -5.03 CAVG  -0.05 CMAX   8.18
MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
                 CMIN  -7.75 CAVG  -0.06 CMAX   9.52
MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
                 CMIN -19.57 CAVG  -0.14 CMAX  15.94
MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
                 CMIN -14.77 CAVG  -0.12 CMAX  13.34
MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
                 CMIN -10.03 CAVG   0.00 CMAX  11.79
MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
                 CMIN -12.47 CAVG  -0.11 CMAX  12.07
MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
                 CMIN -13.62 CAVG  -0.12 CMAX  12.84
[2] xf_out->m_type = 8, xf_in->m_type = 0
Warping...
Running: plm_warp_native
Converting input image...
Converting xform...
bspline_xform_initialize
Error allocating memory for q_lut

On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:


Hi Vickie,

Unfortunately I couldn't reproduce the problem.  You are using a good
configuration of versions which is supposed to work.

We should test if the problem is with Parallels.  Can you please try
downloading and running another extension, such as ExampleCommandLine?
(By the way, why do you run Slicer on Parallels instead of the OSX native
version?)

Also, can you tell me if there is any output in the "standard output"
part of the error log?

An alternative route is to run plastimatch independent of Slicer, then
loading the results into Slicer for further analysis.  Let me know if you
like to pursue that route and I can walk you through.

Greg


On Thu, 17 Feb 2011 10:22:33 -0800
"Zhang, Yi" <[hidden email]> wrote:

Sorry,
OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
using the Parallels Desktop since I don't own a PC. (do you think that
could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
extension version:



http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010
-06-10-win32

Actually, not only B-spline, but other two functionalities give me the same
error - DICOM/DICOM RT import and landmark deformable registration.

Thanks,
Vickie
On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:


Hi Vickie,

Can you please tell me your OS, Slicer Version, and
extension version (extension URL)?

Thank you,
Greg

-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Zhang, Yi
Sent: Thursday, February 17, 2011 12:26 AM
To: [hidden email]
Subject: [slicer-users] Plastimatch error

Hi,

I have encountered following error while trying to peform B-spline
deformable registration on Plastmatch:

ERROR: In
..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
line 1575
vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
process was null when state was queried, result (1) = Error.

Please help.
Thanks!
Vickie

--
Greg Sharp, PhD
Department of Radiation Oncology
Massachusetts General Hospital




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Re: Plastimatch error

Sharp, Gregory C.

Hi Vickie,

Oops, my bad.  You are right.  That version is not compatible.

Would you consider upgrading your Slicer version to 2010-11-03?

Greg


On Thu, 24 Feb 2011 20:11:31 -0800
"Zhang, Yi" <[hidden email]> wrote:

> Hi Greg,
>
> After downloading plastimatch from
> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/<http://ext.slicer.org/ext/Slicer-3-6/16102-linux-x86_64/>
> <http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/>I don't see
> plastimatch under Modules anymore. It seems to have disappeared from
> Slicer3. Any ideas?
>
> Vickie
> On Feb 24, 2011, at 6:30 PM, Sharp, Gregory C. wrote:
>
>
> Hi Vickie,
>
> Thanks for your patience and persistence!
>
> You have hit a bug in plastimatch which thankfully is already fixed.
> Can you try to update your plastimatch?  You will need to point the
> extensions "Where to search" URL to a different location:
>
> For 32-bit linux it is here:
>
> http://ext.slicer.org/ext/Slicer-3-6/16108%2dlinux%2dx86/
>
> For 64-bit linux it is here:
>
> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/
>
> Greg
>
> -----Original Message-----
> From: Zhang, Yi [mailto:[hidden email]]
> Sent: Thu 2/24/2011 6:24 PM
> To: Sharp, Gregory C.
> Cc: [hidden email]
> Subject: Re: [slicer-users] Plastimatch error
>
> Hi Greg,
>
> Sorry I was out of the office last few days.
> I tried 5 or 10 mm grid size, but still I'm getting errors.
> again, both volumes are:
> Image matrix: 256 by 256 by 22
> Image resolution: 0.15625 by 0.15625 by 1.25mm
>
> Stage 1:
> subsampling rate: 1,1,1
> Grid size (mm): 10
> Max iterations: 30
>
> result: completed with errors: (B-spline deformable registration), 20.91s
> Error log:
> ERROR: In
> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
> ic.cxx, line 1522
> vtkCommandLineModuleLogic (0x1270af00): B-spline deformable registration
> completed with errors
> "Information":
> B-spline deformable registration standard output:
>
> fixed
> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeC.nrrd
> Loading fixed image...
> done!
> moving
> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeB.nrrd
> Loading moving image...
> done!
> [1] xf_in->m_type = 0, xf_out->m_type = 0
> Converting fixed
> Converting moving
> Done.
> SUBSAMPLE: (1 1 1), (1 1 1)
> moving_ss size = 256 256 22
> fixed_ss size = 256 256 22
> bspline_xform_initialize
> rdims = (4,4,3)
> vox_per_rgn = (64,64,8)
> cdims = (7 7 6)
> xform_any_to_gpuit_bsp complete
> BSPLINE PARMS
> max_its = 30
> BSPLINE XFORM HEADER
> vox_per_rgn = 64 64 8
> roi_offset = 0 0 0
> roi_dim = 256 256 22
> Setting NMAX, MMAX = 882 49
> START
> RUNNING THE L-BFGS-B CODE
>
>           * * *
>
> Machine precision = 2.220E-16
> N =  882    M =  49
> This problem is unconstrained.
> MSE[   0] 172793.406 NV 1430550 GM  3440.164 GN 40055.410 [    0.699 secs]
>                    CMIN   0.00 CAVG   0.00 CMAX   0.00
> MSE[   1] 168788.625 NV 1436510 GM -14022.742 GN 44458.961 [    0.701 secs]
>                    CMIN  -0.26 CAVG  -0.00 CMAX   0.27
> MSE[   2] 156002.094 NV 1427438 GM -9776.679 GN 38473.344 [    0.721 secs]
>                    CMIN  -1.29 CAVG  -0.01 CMAX   1.36
> MSE[   3] 113203.945 NV 1376563 GM -1506.240 GN 36962.977 [    0.701 secs]
>                    CMIN  -5.42 CAVG  -0.02 CMAX   5.73
> MSE[   4] 182364.469 NV 1221763 GM  8802.257 GN 44880.477 [    0.665 secs]
>                    CMIN -16.33 CAVG  -0.06 CMAX  23.58
> MSE[   5] 88962.250 NV 1334618 GM  2365.741 GN 29213.508 [    0.686 secs]
>                    CMIN  -8.32 CAVG  -0.03 CMAX  10.47
> MSE[   6] 74965.664 NV 1301347 GM -3784.107 GN 22351.080 [    0.680 secs]
>                    CMIN  -8.87 CAVG  -0.05 CMAX  11.16
> MSE[   7] 68752.648 NV 1261210 GM -9005.963 GN 20776.543 [    0.672 secs]
>                    CMIN  -9.90 CAVG  -0.05 CMAX  10.98
> MSE[   8] 62334.117 NV 1253569 GM   -84.478 GN 13559.529 [    0.670 secs]
>                    CMIN -10.70 CAVG  -0.03 CMAX  11.15
> MSE[   9] 59037.574 NV 1242716 GM  9142.486 GN 15676.164 [    0.669 secs]
>                    CMIN -11.83 CAVG  -0.02 CMAX  11.41
> MSE[  10] 56116.086 NV 1223911 GM  5785.482 GN 11916.921 [    0.665 secs]
>                    CMIN -13.08 CAVG  -0.03 CMAX  12.40
> MSE[  11] 51500.602 NV 1178880 GM  1053.619 GN 11454.988 [    0.656 secs]
>                    CMIN -16.59 CAVG  -0.05 CMAX  14.58
> MSE[  12] 48438.137 NV 1149236 GM -3097.842 GN  9308.528 [    0.649 secs]
>                    CMIN -19.33 CAVG  -0.08 CMAX  16.23
> MSE[  13] 45976.199 NV 1122297 GM -1455.273 GN  7629.981 [    0.644 secs]
>                    CMIN -22.45 CAVG  -0.09 CMAX  17.95
> MSE[  14] 44144.320 NV 1106619 GM -1121.861 GN  6836.752 [    0.641 secs]
>                    CMIN -24.13 CAVG  -0.09 CMAX  19.08
> MSE[  15] 42542.715 NV 1052552 GM -2756.149 GN  8741.547 [    0.630 secs]
>                    CMIN -30.40 CAVG  -0.08 CMAX  25.25
> MSE[  16] 40959.645 NV 1040040 GM  2106.021 GN 11453.347 [    0.627 secs]
>                    CMIN -31.82 CAVG  -0.05 CMAX  27.37
> MSE[  17] 38835.320 NV 1047948 GM   171.968 GN  5861.133 [    0.629 secs]
>                    CMIN -30.59 CAVG  -0.05 CMAX  26.64
> MSE[  18] 38289.160 NV 1033359 GM  2835.816 GN  6007.721 [    0.634 secs]
>                    CMIN -31.34 CAVG  -0.05 CMAX  28.26
> MSE[  19] 37757.949 NV 1022548 GM   764.146 GN  5460.470 [    0.624 secs]
>                    CMIN -32.10 CAVG  -0.05 CMAX  29.80
> MSE[  20] 36572.082 NV 990523 GM  -990.091 GN  5187.105 [    0.618 secs]
>                    CMIN -34.10 CAVG  -0.06 CMAX  34.08
> MSE[  21] 35282.254 NV 952616 GM -3800.624 GN  7294.177 [    0.618 secs]
>                    CMIN -35.25 CAVG  -0.07 CMAX  38.78
> MSE[  22] 33919.004 NV 938209 GM  -242.454 GN  5740.723 [    0.608 secs]
>                    CMIN -33.92 CAVG  -0.08 CMAX  40.26
> MSE[  23] 33370.039 NV 916397 GM  1086.198 GN  5384.354 [    0.603 secs]
>                    CMIN -34.06 CAVG  -0.07 CMAX  42.59
> MSE[  24] 32082.525 NV 927453 GM   492.501 GN  5629.464 [    0.605 secs]
>                    CMIN -31.95 CAVG  -0.07 CMAX  41.66
> MSE[  25] 31317.986 NV 923391 GM   430.064 GN  3504.146 [    0.604 secs]
>                    CMIN -31.63 CAVG  -0.07 CMAX  42.50
> MSE[  26] 30691.617 NV 920224 GM    70.180 GN  3819.907 [    0.610 secs]
>                    CMIN -31.26 CAVG  -0.07 CMAX  43.41
> MSE[  27] 30035.088 NV 914436 GM  -474.841 GN  4630.180 [    0.603 secs]
>                    CMIN -30.58 CAVG  -0.06 CMAX  44.40
> MSE[  28] 29283.193 NV 902584 GM  -565.189 GN  6579.526 [    0.600 secs]
>                    CMIN -29.99 CAVG  -0.06 CMAX  46.43
> MSE[  29] 28504.350 NV 899740 GM   403.089 GN  5322.814 [    0.599 secs]
>                    CMIN -30.24 CAVG  -0.06 CMAX  47.21
> MSE[  30] 27685.469 NV 880915 GM  -360.044 GN  6465.846 [    0.595 secs]
>                    CMIN -32.59 CAVG  -0.06 CMAX  49.30
> [2] xf_out->m_type = 8, xf_in->m_type = 0
> Warping...
> Running: plm_warp_native
> Converting input image...
> Converting xform...
> bspline_xform_initialize
> rdims = (4,4,3)
> vox_per_rgn = (64,64,8)
> cdims = (7 7 6)
> Input pih
> Origin
> [-20, -20, -13]
> Spacing
> [0.15625, 0.15625, 1.25]
> Region
> ImageRegion (0x7fffd0b054d0)
>  Dimension: 3
>  Index: [0, 0, 0]
>  Size: [256, 256, 22]
> Running: gpuit_bsp_to_itk_bsp_raw
> Setting bsp_spacing
> [10, 10, 10]
> Setting bsp_origin
> [-30, -30, -23]
> Setting bsp_region
> ImageRegion (0x7fffd0b04ee0)
>  Dimension: 3
>  Index: [0, 0, 0]
>  Size: [7, 7, 6]
> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
> Running: xform_itk_bsp_to_itk_bsp
> Setting bsp_spacing
> [10, 10, 10]
> Setting bsp_origin
> [-30, -30, -23]
> Setting bsp_region
> ImageRegion (0x7fffd0b04c30)
>  Dimension: 3
>  Index: [0, 0, 0]
>  Size: [7, 7, 6]
> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
> Completed: xform_itk_bsp_to_itk_bsp
> Creating output volume...
> Unhandled image type in Plm_image::convert (14 -> 4)
>
>
> Thanks,
> Vickie
> On Feb 21, 2011, at 9:04 AM, Sharp, Gregory C. wrote:
>
>
> Hi Vickie,
>
> Please try setting the "Grid Size" parameter to something
> smaller than the image size.  For a smoother deformation,
> you may try 10 mm or 20 mm.  For a wigglier deformation, you
> may try something like 1 mm or 5 mm.
>
> Greg
>
>
> -----Original Message-----
> From: Zhang, Yi [mailto:[hidden email]]
> Sent: Sun 2/20/2011 10:28 PM
> To: Sharp, Gregory C.
> Cc: [hidden email]
> Subject: Re: [slicer-users] Plastimatch error
>
> Image matrix: 256 by 256 by 22
> image resolution: 0.15625 by 0.15625 by 1.25mm
> FOV: 40 by 40 by 27.5 mm
> Thanks,
> Vickie
> On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:
>
>
> Hi Vickie,
>
> This is very helpful.  It looks like the registration code
> is running out of memory building the lookup table.
>
> I think this can be solved by changing the grid spacing.
> Can you tell me your image resolution and voxel spacing?
> Then I will suggest some modified settings.
>
> Greg
>
> -----Original Message-----
> From: Zhang, Yi [mailto:[hidden email]]
> Sent: Fri 2/18/2011 4:54 PM
> To: Sharp, Gregory C.
> Cc: [hidden email]
> Subject: Re: [slicer-users] Plastimatch error
>
> Hi Greg,
>
> I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
> installed Plastimatch from
> http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
> Tested with 2 3D images.
> It ran for 75.42 secs and completed with errors.
>
> ERROR: In
>
>
> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
> ic.cxx, line 1522
> vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
> completed with errors
>
> I have two 3D mask images in nrrd format, same resolution, same matrix size
> and
> FOV.
> Using Plastimatch B-spline Registration, I left stage 0 and stage 2
> unchecked.
> For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max
> iterations
> =
> 50
> Afer 75.42 seconds, it completed with following error:
>
> Looks like the linux is working better, but still gives errors. Any
> suggestions?
>
> Thanks,
> Vickie
>
> FYI: output from "Information"
>
> B-spline deformable registration standard output:
>
> fixed
> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
> Loading fixed image...
> done!
> moving
> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
> Loading moving image...
> done!
> [1] xf_in->m_type = 0, xf_out->m_type = 0
> Converting fixed
> Converting moving
> Done.
> SUBSAMPLE: (1 1 1), (1 1 1)
> moving_ss size = 256 256 22
> fixed_ss size = 256 256 22
> bspline_xform_initialize
> rdims = (1,1,1)
> vox_per_rgn = (640,640,80)
> cdims = (4 4 4)
> xform_any_to_gpuit_bsp complete
> BSPLINE PARMS
> max_its = 50
> BSPLINE XFORM HEADER
> vox_per_rgn = 640 640 80
> roi_offset = 0 0 0
> roi_dim = 256 256 22
> Setting NMAX, MMAX = 192 33
> START
> RUNNING THE L-BFGS-B CODE
>
>         * * *
>
> Machine precision = 2.220E-16
> N =  192    M =  33
> This problem is unconstrained.
> MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
>                  CMIN   0.00 CAVG   0.00 CMAX   0.00
> MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
>                  CMIN  -0.47 CAVG  -0.00 CMAX   0.55
> MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
>                  CMIN  -2.33 CAVG  -0.01 CMAX   2.75
> MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
>                  CMIN  -3.54 CAVG  -0.02 CMAX   4.65
> MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
>                  CMIN  -8.39 CAVG  -0.02 CMAX  12.27
> MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
>                  CMIN  -4.44 CAVG  -0.02 CMAX   6.07
> MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
>                  CMIN  -5.12 CAVG  -0.02 CMAX   7.14
> MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
>                  CMIN -27.43 CAVG  -0.06 CMAX  45.42
> MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
>                  CMIN  -5.81 CAVG  -0.02 CMAX   8.33
> MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
>                  CMIN  -5.21 CAVG  -0.02 CMAX   7.29
> MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
>                  CMIN  -5.14 CAVG  -0.02 CMAX   7.16
> MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
>                  CMIN  -5.18 CAVG  -0.02 CMAX   7.25
> MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
>                  CMIN  -5.14 CAVG  -0.02 CMAX   7.18
> MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
>                  CMIN  -5.17 CAVG  -0.02 CMAX   7.22
> MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.18
> MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
>                  CMIN  -5.16 CAVG  -0.02 CMAX   7.20
> MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
>                  CMIN  -5.87 CAVG  -0.04 CMAX   8.12
> MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
>                  CMIN  -5.29 CAVG  -0.02 CMAX   7.37
> MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
>                  CMIN  -5.17 CAVG  -0.02 CMAX   7.22
> MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
>                  CMIN  -8.56 CAVG  -0.09 CMAX  11.31
> MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
>                  CMIN  -5.63 CAVG  -0.03 CMAX   7.77
> MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
>                  CMIN  -5.23 CAVG  -0.02 CMAX   7.28
> MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
>                  CMIN  -5.16 CAVG  -0.02 CMAX   7.20
> MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
> MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
>                  CMIN  -5.63 CAVG  -0.04 CMAX   7.56
> MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
>                  CMIN  -5.26 CAVG  -0.02 CMAX   7.27
> MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
>                  CMIN  -5.11 CAVG  -0.04 CMAX   7.84
> MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
>                  CMIN  -5.03 CAVG  -0.05 CMAX   8.18
> MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
>                  CMIN  -7.75 CAVG  -0.06 CMAX   9.52
> MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
>                  CMIN -19.57 CAVG  -0.14 CMAX  15.94
> MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
>                  CMIN -14.77 CAVG  -0.12 CMAX  13.34
> MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
>                  CMIN -10.03 CAVG   0.00 CMAX  11.79
> MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
>                  CMIN -12.47 CAVG  -0.11 CMAX  12.07
> MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
>                  CMIN -13.62 CAVG  -0.12 CMAX  12.84
> [2] xf_out->m_type = 8, xf_in->m_type = 0
> Warping...
> Running: plm_warp_native
> Converting input image...
> Converting xform...
> bspline_xform_initialize
> Error allocating memory for q_lut
>
> On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:
>
>
> Hi Vickie,
>
> Unfortunately I couldn't reproduce the problem.  You are using a good
> configuration of versions which is supposed to work.
>
> We should test if the problem is with Parallels.  Can you please try
> downloading and running another extension, such as ExampleCommandLine?
> (By the way, why do you run Slicer on Parallels instead of the OSX native
> version?)
>
> Also, can you tell me if there is any output in the "standard output"
> part of the error log?
>
> An alternative route is to run plastimatch independent of Slicer, then
> loading the results into Slicer for further analysis.  Let me know if you
> like to pursue that route and I can walk you through.
>
> Greg
>
>
> On Thu, 17 Feb 2011 10:22:33 -0800
> "Zhang, Yi" <[hidden email]> wrote:
>
> Sorry,
> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
> using the Parallels Desktop since I don't own a PC. (do you think that
> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
> extension version:
>
>
>
> http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010
> -06-10-win32
>
> Actually, not only B-spline, but other two functionalities give me the same
> error - DICOM/DICOM RT import and landmark deformable registration.
>
> Thanks,
> Vickie
> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>
>
> Hi Vickie,
>
> Can you please tell me your OS, Slicer Version, and
> extension version (extension URL)?
>
> Thank you,
> Greg
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Zhang, Yi
> Sent: Thursday, February 17, 2011 12:26 AM
> To: [hidden email]
> Subject: [slicer-users] Plastimatch error
>
> Hi,
>
> I have encountered following error while trying to peform B-spline
> deformable registration on Plastmatch:
>
> ERROR: In
> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
> line 1575
> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
> process was null when state was queried, result (1) = Error.
>
> Please help.
> Thanks!
> Vickie
>
> --
> Greg Sharp, PhD
> Department of Radiation Oncology
> Massachusetts General Hospital
>
>
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
>
>
>


--
Greg Sharp, PhD
Department of Radiation Oncology
Massachusetts General Hospital
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Re: Plastimatch error

Zhang, Yi
Hi Greg,

I tried to upgrade Slicer to 2010-11-3 on our linux network. However, I got an error running Slicer3 - "/usr/lib64/libstdc++.so.6: version 'GLIBCXX_3.4.9' not found"
So I think our network does not have the updated GLIBC to run most updated Slicer3.
I downloaded the mac version of Slicer3 to my mac computer - Slicer3-3.6.2-2010-11-03-darwin-x86 and Slicer3 is running. I cannot locate plastimatch from the extension manager (path: http://ext.slicer.org/ext/Slicer-3-6/15432-darwin-x86).

Do you have a working plastimatch on a mac version of Slicer3? If you do, what is the path to find that plastimatch?

Thanks,
Vickie

On Feb 25, 2011, at 6:25 AM, Gregory Sharp wrote:

>
> Hi Vickie,
>
> Oops, my bad.  You are right.  That version is not compatible.
>
> Would you consider upgrading your Slicer version to 2010-11-03?
>
> Greg
>
>
> On Thu, 24 Feb 2011 20:11:31 -0800
> "Zhang, Yi" <[hidden email]> wrote:
>
>> Hi Greg,
>>
>> After downloading plastimatch from
>> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/<http://ext.slicer.org/ext/Slicer-3-6/16102-linux-x86_64/>
>> <http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/>I don't see
>> plastimatch under Modules anymore. It seems to have disappeared from
>> Slicer3. Any ideas?
>>
>> Vickie
>> On Feb 24, 2011, at 6:30 PM, Sharp, Gregory C. wrote:
>>
>>
>> Hi Vickie,
>>
>> Thanks for your patience and persistence!
>>
>> You have hit a bug in plastimatch which thankfully is already fixed.
>> Can you try to update your plastimatch?  You will need to point the
>> extensions "Where to search" URL to a different location:
>>
>> For 32-bit linux it is here:
>>
>> http://ext.slicer.org/ext/Slicer-3-6/16108%2dlinux%2dx86/
>>
>> For 64-bit linux it is here:
>>
>> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/
>>
>> Greg
>>
>> -----Original Message-----
>> From: Zhang, Yi [mailto:[hidden email]]
>> Sent: Thu 2/24/2011 6:24 PM
>> To: Sharp, Gregory C.
>> Cc: [hidden email]
>> Subject: Re: [slicer-users] Plastimatch error
>>
>> Hi Greg,
>>
>> Sorry I was out of the office last few days.
>> I tried 5 or 10 mm grid size, but still I'm getting errors.
>> again, both volumes are:
>> Image matrix: 256 by 256 by 22
>> Image resolution: 0.15625 by 0.15625 by 1.25mm
>>
>> Stage 1:
>> subsampling rate: 1,1,1
>> Grid size (mm): 10
>> Max iterations: 30
>>
>> result: completed with errors: (B-spline deformable registration), 20.91s
>> Error log:
>> ERROR: In
>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>> ic.cxx, line 1522
>> vtkCommandLineModuleLogic (0x1270af00): B-spline deformable registration
>> completed with errors
>> "Information":
>> B-spline deformable registration standard output:
>>
>> fixed
>> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeC.nrrd
>> Loading fixed image...
>> done!
>> moving
>> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeB.nrrd
>> Loading moving image...
>> done!
>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>> Converting fixed
>> Converting moving
>> Done.
>> SUBSAMPLE: (1 1 1), (1 1 1)
>> moving_ss size = 256 256 22
>> fixed_ss size = 256 256 22
>> bspline_xform_initialize
>> rdims = (4,4,3)
>> vox_per_rgn = (64,64,8)
>> cdims = (7 7 6)
>> xform_any_to_gpuit_bsp complete
>> BSPLINE PARMS
>> max_its = 30
>> BSPLINE XFORM HEADER
>> vox_per_rgn = 64 64 8
>> roi_offset = 0 0 0
>> roi_dim = 256 256 22
>> Setting NMAX, MMAX = 882 49
>> START
>> RUNNING THE L-BFGS-B CODE
>>
>>          * * *
>>
>> Machine precision = 2.220E-16
>> N =  882    M =  49
>> This problem is unconstrained.
>> MSE[   0] 172793.406 NV 1430550 GM  3440.164 GN 40055.410 [    0.699 secs]
>>                   CMIN   0.00 CAVG   0.00 CMAX   0.00
>> MSE[   1] 168788.625 NV 1436510 GM -14022.742 GN 44458.961 [    0.701 secs]
>>                   CMIN  -0.26 CAVG  -0.00 CMAX   0.27
>> MSE[   2] 156002.094 NV 1427438 GM -9776.679 GN 38473.344 [    0.721 secs]
>>                   CMIN  -1.29 CAVG  -0.01 CMAX   1.36
>> MSE[   3] 113203.945 NV 1376563 GM -1506.240 GN 36962.977 [    0.701 secs]
>>                   CMIN  -5.42 CAVG  -0.02 CMAX   5.73
>> MSE[   4] 182364.469 NV 1221763 GM  8802.257 GN 44880.477 [    0.665 secs]
>>                   CMIN -16.33 CAVG  -0.06 CMAX  23.58
>> MSE[   5] 88962.250 NV 1334618 GM  2365.741 GN 29213.508 [    0.686 secs]
>>                   CMIN  -8.32 CAVG  -0.03 CMAX  10.47
>> MSE[   6] 74965.664 NV 1301347 GM -3784.107 GN 22351.080 [    0.680 secs]
>>                   CMIN  -8.87 CAVG  -0.05 CMAX  11.16
>> MSE[   7] 68752.648 NV 1261210 GM -9005.963 GN 20776.543 [    0.672 secs]
>>                   CMIN  -9.90 CAVG  -0.05 CMAX  10.98
>> MSE[   8] 62334.117 NV 1253569 GM   -84.478 GN 13559.529 [    0.670 secs]
>>                   CMIN -10.70 CAVG  -0.03 CMAX  11.15
>> MSE[   9] 59037.574 NV 1242716 GM  9142.486 GN 15676.164 [    0.669 secs]
>>                   CMIN -11.83 CAVG  -0.02 CMAX  11.41
>> MSE[  10] 56116.086 NV 1223911 GM  5785.482 GN 11916.921 [    0.665 secs]
>>                   CMIN -13.08 CAVG  -0.03 CMAX  12.40
>> MSE[  11] 51500.602 NV 1178880 GM  1053.619 GN 11454.988 [    0.656 secs]
>>                   CMIN -16.59 CAVG  -0.05 CMAX  14.58
>> MSE[  12] 48438.137 NV 1149236 GM -3097.842 GN  9308.528 [    0.649 secs]
>>                   CMIN -19.33 CAVG  -0.08 CMAX  16.23
>> MSE[  13] 45976.199 NV 1122297 GM -1455.273 GN  7629.981 [    0.644 secs]
>>                   CMIN -22.45 CAVG  -0.09 CMAX  17.95
>> MSE[  14] 44144.320 NV 1106619 GM -1121.861 GN  6836.752 [    0.641 secs]
>>                   CMIN -24.13 CAVG  -0.09 CMAX  19.08
>> MSE[  15] 42542.715 NV 1052552 GM -2756.149 GN  8741.547 [    0.630 secs]
>>                   CMIN -30.40 CAVG  -0.08 CMAX  25.25
>> MSE[  16] 40959.645 NV 1040040 GM  2106.021 GN 11453.347 [    0.627 secs]
>>                   CMIN -31.82 CAVG  -0.05 CMAX  27.37
>> MSE[  17] 38835.320 NV 1047948 GM   171.968 GN  5861.133 [    0.629 secs]
>>                   CMIN -30.59 CAVG  -0.05 CMAX  26.64
>> MSE[  18] 38289.160 NV 1033359 GM  2835.816 GN  6007.721 [    0.634 secs]
>>                   CMIN -31.34 CAVG  -0.05 CMAX  28.26
>> MSE[  19] 37757.949 NV 1022548 GM   764.146 GN  5460.470 [    0.624 secs]
>>                   CMIN -32.10 CAVG  -0.05 CMAX  29.80
>> MSE[  20] 36572.082 NV 990523 GM  -990.091 GN  5187.105 [    0.618 secs]
>>                   CMIN -34.10 CAVG  -0.06 CMAX  34.08
>> MSE[  21] 35282.254 NV 952616 GM -3800.624 GN  7294.177 [    0.618 secs]
>>                   CMIN -35.25 CAVG  -0.07 CMAX  38.78
>> MSE[  22] 33919.004 NV 938209 GM  -242.454 GN  5740.723 [    0.608 secs]
>>                   CMIN -33.92 CAVG  -0.08 CMAX  40.26
>> MSE[  23] 33370.039 NV 916397 GM  1086.198 GN  5384.354 [    0.603 secs]
>>                   CMIN -34.06 CAVG  -0.07 CMAX  42.59
>> MSE[  24] 32082.525 NV 927453 GM   492.501 GN  5629.464 [    0.605 secs]
>>                   CMIN -31.95 CAVG  -0.07 CMAX  41.66
>> MSE[  25] 31317.986 NV 923391 GM   430.064 GN  3504.146 [    0.604 secs]
>>                   CMIN -31.63 CAVG  -0.07 CMAX  42.50
>> MSE[  26] 30691.617 NV 920224 GM    70.180 GN  3819.907 [    0.610 secs]
>>                   CMIN -31.26 CAVG  -0.07 CMAX  43.41
>> MSE[  27] 30035.088 NV 914436 GM  -474.841 GN  4630.180 [    0.603 secs]
>>                   CMIN -30.58 CAVG  -0.06 CMAX  44.40
>> MSE[  28] 29283.193 NV 902584 GM  -565.189 GN  6579.526 [    0.600 secs]
>>                   CMIN -29.99 CAVG  -0.06 CMAX  46.43
>> MSE[  29] 28504.350 NV 899740 GM   403.089 GN  5322.814 [    0.599 secs]
>>                   CMIN -30.24 CAVG  -0.06 CMAX  47.21
>> MSE[  30] 27685.469 NV 880915 GM  -360.044 GN  6465.846 [    0.595 secs]
>>                   CMIN -32.59 CAVG  -0.06 CMAX  49.30
>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>> Warping...
>> Running: plm_warp_native
>> Converting input image...
>> Converting xform...
>> bspline_xform_initialize
>> rdims = (4,4,3)
>> vox_per_rgn = (64,64,8)
>> cdims = (7 7 6)
>> Input pih
>> Origin
>> [-20, -20, -13]
>> Spacing
>> [0.15625, 0.15625, 1.25]
>> Region
>> ImageRegion (0x7fffd0b054d0)
>> Dimension: 3
>> Index: [0, 0, 0]
>> Size: [256, 256, 22]
>> Running: gpuit_bsp_to_itk_bsp_raw
>> Setting bsp_spacing
>> [10, 10, 10]
>> Setting bsp_origin
>> [-30, -30, -23]
>> Setting bsp_region
>> ImageRegion (0x7fffd0b04ee0)
>> Dimension: 3
>> Index: [0, 0, 0]
>> Size: [7, 7, 6]
>> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
>> Running: xform_itk_bsp_to_itk_bsp
>> Setting bsp_spacing
>> [10, 10, 10]
>> Setting bsp_origin
>> [-30, -30, -23]
>> Setting bsp_region
>> ImageRegion (0x7fffd0b04c30)
>> Dimension: 3
>> Index: [0, 0, 0]
>> Size: [7, 7, 6]
>> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
>> Completed: xform_itk_bsp_to_itk_bsp
>> Creating output volume...
>> Unhandled image type in Plm_image::convert (14 -> 4)
>>
>>
>> Thanks,
>> Vickie
>> On Feb 21, 2011, at 9:04 AM, Sharp, Gregory C. wrote:
>>
>>
>> Hi Vickie,
>>
>> Please try setting the "Grid Size" parameter to something
>> smaller than the image size.  For a smoother deformation,
>> you may try 10 mm or 20 mm.  For a wigglier deformation, you
>> may try something like 1 mm or 5 mm.
>>
>> Greg
>>
>>
>> -----Original Message-----
>> From: Zhang, Yi [mailto:[hidden email]]
>> Sent: Sun 2/20/2011 10:28 PM
>> To: Sharp, Gregory C.
>> Cc: [hidden email]
>> Subject: Re: [slicer-users] Plastimatch error
>>
>> Image matrix: 256 by 256 by 22
>> image resolution: 0.15625 by 0.15625 by 1.25mm
>> FOV: 40 by 40 by 27.5 mm
>> Thanks,
>> Vickie
>> On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:
>>
>>
>> Hi Vickie,
>>
>> This is very helpful.  It looks like the registration code
>> is running out of memory building the lookup table.
>>
>> I think this can be solved by changing the grid spacing.
>> Can you tell me your image resolution and voxel spacing?
>> Then I will suggest some modified settings.
>>
>> Greg
>>
>> -----Original Message-----
>> From: Zhang, Yi [mailto:[hidden email]]
>> Sent: Fri 2/18/2011 4:54 PM
>> To: Sharp, Gregory C.
>> Cc: [hidden email]
>> Subject: Re: [slicer-users] Plastimatch error
>>
>> Hi Greg,
>>
>> I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
>> installed Plastimatch from
>> http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
>> Tested with 2 3D images.
>> It ran for 75.42 secs and completed with errors.
>>
>> ERROR: In
>>
>>
>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>> ic.cxx, line 1522
>> vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
>> completed with errors
>>
>> I have two 3D mask images in nrrd format, same resolution, same matrix size
>> and
>> FOV.
>> Using Plastimatch B-spline Registration, I left stage 0 and stage 2
>> unchecked.
>> For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max
>> iterations
>> =
>> 50
>> Afer 75.42 seconds, it completed with following error:
>>
>> Looks like the linux is working better, but still gives errors. Any
>> suggestions?
>>
>> Thanks,
>> Vickie
>>
>> FYI: output from "Information"
>>
>> B-spline deformable registration standard output:
>>
>> fixed
>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
>> Loading fixed image...
>> done!
>> moving
>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
>> Loading moving image...
>> done!
>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>> Converting fixed
>> Converting moving
>> Done.
>> SUBSAMPLE: (1 1 1), (1 1 1)
>> moving_ss size = 256 256 22
>> fixed_ss size = 256 256 22
>> bspline_xform_initialize
>> rdims = (1,1,1)
>> vox_per_rgn = (640,640,80)
>> cdims = (4 4 4)
>> xform_any_to_gpuit_bsp complete
>> BSPLINE PARMS
>> max_its = 50
>> BSPLINE XFORM HEADER
>> vox_per_rgn = 640 640 80
>> roi_offset = 0 0 0
>> roi_dim = 256 256 22
>> Setting NMAX, MMAX = 192 33
>> START
>> RUNNING THE L-BFGS-B CODE
>>
>>        * * *
>>
>> Machine precision = 2.220E-16
>> N =  192    M =  33
>> This problem is unconstrained.
>> MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
>>                 CMIN   0.00 CAVG   0.00 CMAX   0.00
>> MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
>>                 CMIN  -0.47 CAVG  -0.00 CMAX   0.55
>> MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
>>                 CMIN  -2.33 CAVG  -0.01 CMAX   2.75
>> MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
>>                 CMIN  -3.54 CAVG  -0.02 CMAX   4.65
>> MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
>>                 CMIN  -8.39 CAVG  -0.02 CMAX  12.27
>> MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
>>                 CMIN  -4.44 CAVG  -0.02 CMAX   6.07
>> MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
>>                 CMIN  -5.12 CAVG  -0.02 CMAX   7.14
>> MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
>>                 CMIN -27.43 CAVG  -0.06 CMAX  45.42
>> MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
>>                 CMIN  -5.81 CAVG  -0.02 CMAX   8.33
>> MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
>>                 CMIN  -5.21 CAVG  -0.02 CMAX   7.29
>> MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
>>                 CMIN  -5.14 CAVG  -0.02 CMAX   7.16
>> MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
>>                 CMIN  -5.18 CAVG  -0.02 CMAX   7.25
>> MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
>>                 CMIN  -5.14 CAVG  -0.02 CMAX   7.18
>> MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
>>                 CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>> MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.18
>> MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
>>                 CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>> MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
>>                 CMIN  -5.87 CAVG  -0.04 CMAX   8.12
>> MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
>>                 CMIN  -5.29 CAVG  -0.02 CMAX   7.37
>> MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
>>                 CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>> MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
>>                 CMIN  -8.56 CAVG  -0.09 CMAX  11.31
>> MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
>>                 CMIN  -5.63 CAVG  -0.03 CMAX   7.77
>> MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
>>                 CMIN  -5.23 CAVG  -0.02 CMAX   7.28
>> MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
>>                 CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>> MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>> MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
>>                 CMIN  -5.63 CAVG  -0.04 CMAX   7.56
>> MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
>>                 CMIN  -5.26 CAVG  -0.02 CMAX   7.27
>> MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
>>                 CMIN  -5.11 CAVG  -0.04 CMAX   7.84
>> MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
>>                 CMIN  -5.03 CAVG  -0.05 CMAX   8.18
>> MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
>>                 CMIN  -7.75 CAVG  -0.06 CMAX   9.52
>> MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
>>                 CMIN -19.57 CAVG  -0.14 CMAX  15.94
>> MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
>>                 CMIN -14.77 CAVG  -0.12 CMAX  13.34
>> MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
>>                 CMIN -10.03 CAVG   0.00 CMAX  11.79
>> MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
>>                 CMIN -12.47 CAVG  -0.11 CMAX  12.07
>> MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
>>                 CMIN -13.62 CAVG  -0.12 CMAX  12.84
>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>> Warping...
>> Running: plm_warp_native
>> Converting input image...
>> Converting xform...
>> bspline_xform_initialize
>> Error allocating memory for q_lut
>>
>> On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:
>>
>>
>> Hi Vickie,
>>
>> Unfortunately I couldn't reproduce the problem.  You are using a good
>> configuration of versions which is supposed to work.
>>
>> We should test if the problem is with Parallels.  Can you please try
>> downloading and running another extension, such as ExampleCommandLine?
>> (By the way, why do you run Slicer on Parallels instead of the OSX native
>> version?)
>>
>> Also, can you tell me if there is any output in the "standard output"
>> part of the error log?
>>
>> An alternative route is to run plastimatch independent of Slicer, then
>> loading the results into Slicer for further analysis.  Let me know if you
>> like to pursue that route and I can walk you through.
>>
>> Greg
>>
>>
>> On Thu, 17 Feb 2011 10:22:33 -0800
>> "Zhang, Yi" <[hidden email]> wrote:
>>
>> Sorry,
>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>> using the Parallels Desktop since I don't own a PC. (do you think that
>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>> extension version:
>>
>>
>>
>> http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010
>> -06-10-win32
>>
>> Actually, not only B-spline, but other two functionalities give me the same
>> error - DICOM/DICOM RT import and landmark deformable registration.
>>
>> Thanks,
>> Vickie
>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>
>>
>> Hi Vickie,
>>
>> Can you please tell me your OS, Slicer Version, and
>> extension version (extension URL)?
>>
>> Thank you,
>> Greg
>>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Zhang, Yi
>> Sent: Thursday, February 17, 2011 12:26 AM
>> To: [hidden email]
>> Subject: [slicer-users] Plastimatch error
>>
>> Hi,
>>
>> I have encountered following error while trying to peform B-spline
>> deformable registration on Plastmatch:
>>
>> ERROR: In
>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>> line 1575
>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>> process was null when state was queried, result (1) = Error.
>>
>> Please help.
>> Thanks!
>> Vickie
>>
>> --
>> Greg Sharp, PhD
>> Department of Radiation Oncology
>> Massachusetts General Hospital
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
>>
>>
>
>
> --
> Greg Sharp, PhD
> Department of Radiation Oncology
> Massachusetts General Hospital

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Re: Plastimatch error

pieper
Administrator
Hi Vickie -

The slicer nightly builds are made with ubuntu 8.04, but apparently
those binaries don't run on centos/redhat 5.5.

You can try the near-final versions of the next release here:

http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/

The plastimatch extension should work with those builds (linux or mac),
but let us know if it doesn't.

-Steve

On 03/01/2011 07:55 PM, Zhang, Yi wrote:

> Hi Greg,
>
> I tried to upgrade Slicer to 2010-11-3 on our linux network. However, I got an error running Slicer3 - "/usr/lib64/libstdc++.so.6: version 'GLIBCXX_3.4.9' not found"
> So I think our network does not have the updated GLIBC to run most updated Slicer3.
> I downloaded the mac version of Slicer3 to my mac computer - Slicer3-3.6.2-2010-11-03-darwin-x86 and Slicer3 is running. I cannot locate plastimatch from the extension manager (path: http://ext.slicer.org/ext/Slicer-3-6/15432-darwin-x86).
>
> Do you have a working plastimatch on a mac version of Slicer3? If you do, what is the path to find that plastimatch?
>
> Thanks,
> Vickie
>
> On Feb 25, 2011, at 6:25 AM, Gregory Sharp wrote:
>
>>
>> Hi Vickie,
>>
>> Oops, my bad.  You are right.  That version is not compatible.
>>
>> Would you consider upgrading your Slicer version to 2010-11-03?
>>
>> Greg
>>
>>
>> On Thu, 24 Feb 2011 20:11:31 -0800
>> "Zhang, Yi"<[hidden email]>  wrote:
>>
>>> Hi Greg,
>>>
>>> After downloading plastimatch from
>>> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/<http://ext.slicer.org/ext/Slicer-3-6/16102-linux-x86_64/>
>>> <http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/>I don't see
>>> plastimatch under Modules anymore. It seems to have disappeared from
>>> Slicer3. Any ideas?
>>>
>>> Vickie
>>> On Feb 24, 2011, at 6:30 PM, Sharp, Gregory C. wrote:
>>>
>>>
>>> Hi Vickie,
>>>
>>> Thanks for your patience and persistence!
>>>
>>> You have hit a bug in plastimatch which thankfully is already fixed.
>>> Can you try to update your plastimatch?  You will need to point the
>>> extensions "Where to search" URL to a different location:
>>>
>>> For 32-bit linux it is here:
>>>
>>> http://ext.slicer.org/ext/Slicer-3-6/16108%2dlinux%2dx86/
>>>
>>> For 64-bit linux it is here:
>>>
>>> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/
>>>
>>> Greg
>>>
>>> -----Original Message-----
>>> From: Zhang, Yi [mailto:[hidden email]]
>>> Sent: Thu 2/24/2011 6:24 PM
>>> To: Sharp, Gregory C.
>>> Cc: [hidden email]
>>> Subject: Re: [slicer-users] Plastimatch error
>>>
>>> Hi Greg,
>>>
>>> Sorry I was out of the office last few days.
>>> I tried 5 or 10 mm grid size, but still I'm getting errors.
>>> again, both volumes are:
>>> Image matrix: 256 by 256 by 22
>>> Image resolution: 0.15625 by 0.15625 by 1.25mm
>>>
>>> Stage 1:
>>> subsampling rate: 1,1,1
>>> Grid size (mm): 10
>>> Max iterations: 30
>>>
>>> result: completed with errors: (B-spline deformable registration), 20.91s
>>> Error log:
>>> ERROR: In
>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>>> ic.cxx, line 1522
>>> vtkCommandLineModuleLogic (0x1270af00): B-spline deformable registration
>>> completed with errors
>>> "Information":
>>> B-spline deformable registration standard output:
>>>
>>> fixed
>>> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeC.nrrd
>>> Loading fixed image...
>>> done!
>>> moving
>>> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeB.nrrd
>>> Loading moving image...
>>> done!
>>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>>> Converting fixed
>>> Converting moving
>>> Done.
>>> SUBSAMPLE: (1 1 1), (1 1 1)
>>> moving_ss size = 256 256 22
>>> fixed_ss size = 256 256 22
>>> bspline_xform_initialize
>>> rdims = (4,4,3)
>>> vox_per_rgn = (64,64,8)
>>> cdims = (7 7 6)
>>> xform_any_to_gpuit_bsp complete
>>> BSPLINE PARMS
>>> max_its = 30
>>> BSPLINE XFORM HEADER
>>> vox_per_rgn = 64 64 8
>>> roi_offset = 0 0 0
>>> roi_dim = 256 256 22
>>> Setting NMAX, MMAX = 882 49
>>> START
>>> RUNNING THE L-BFGS-B CODE
>>>
>>>           * * *
>>>
>>> Machine precision = 2.220E-16
>>> N =  882    M =  49
>>> This problem is unconstrained.
>>> MSE[   0] 172793.406 NV 1430550 GM  3440.164 GN 40055.410 [    0.699 secs]
>>>                    CMIN   0.00 CAVG   0.00 CMAX   0.00
>>> MSE[   1] 168788.625 NV 1436510 GM -14022.742 GN 44458.961 [    0.701 secs]
>>>                    CMIN  -0.26 CAVG  -0.00 CMAX   0.27
>>> MSE[   2] 156002.094 NV 1427438 GM -9776.679 GN 38473.344 [    0.721 secs]
>>>                    CMIN  -1.29 CAVG  -0.01 CMAX   1.36
>>> MSE[   3] 113203.945 NV 1376563 GM -1506.240 GN 36962.977 [    0.701 secs]
>>>                    CMIN  -5.42 CAVG  -0.02 CMAX   5.73
>>> MSE[   4] 182364.469 NV 1221763 GM  8802.257 GN 44880.477 [    0.665 secs]
>>>                    CMIN -16.33 CAVG  -0.06 CMAX  23.58
>>> MSE[   5] 88962.250 NV 1334618 GM  2365.741 GN 29213.508 [    0.686 secs]
>>>                    CMIN  -8.32 CAVG  -0.03 CMAX  10.47
>>> MSE[   6] 74965.664 NV 1301347 GM -3784.107 GN 22351.080 [    0.680 secs]
>>>                    CMIN  -8.87 CAVG  -0.05 CMAX  11.16
>>> MSE[   7] 68752.648 NV 1261210 GM -9005.963 GN 20776.543 [    0.672 secs]
>>>                    CMIN  -9.90 CAVG  -0.05 CMAX  10.98
>>> MSE[   8] 62334.117 NV 1253569 GM   -84.478 GN 13559.529 [    0.670 secs]
>>>                    CMIN -10.70 CAVG  -0.03 CMAX  11.15
>>> MSE[   9] 59037.574 NV 1242716 GM  9142.486 GN 15676.164 [    0.669 secs]
>>>                    CMIN -11.83 CAVG  -0.02 CMAX  11.41
>>> MSE[  10] 56116.086 NV 1223911 GM  5785.482 GN 11916.921 [    0.665 secs]
>>>                    CMIN -13.08 CAVG  -0.03 CMAX  12.40
>>> MSE[  11] 51500.602 NV 1178880 GM  1053.619 GN 11454.988 [    0.656 secs]
>>>                    CMIN -16.59 CAVG  -0.05 CMAX  14.58
>>> MSE[  12] 48438.137 NV 1149236 GM -3097.842 GN  9308.528 [    0.649 secs]
>>>                    CMIN -19.33 CAVG  -0.08 CMAX  16.23
>>> MSE[  13] 45976.199 NV 1122297 GM -1455.273 GN  7629.981 [    0.644 secs]
>>>                    CMIN -22.45 CAVG  -0.09 CMAX  17.95
>>> MSE[  14] 44144.320 NV 1106619 GM -1121.861 GN  6836.752 [    0.641 secs]
>>>                    CMIN -24.13 CAVG  -0.09 CMAX  19.08
>>> MSE[  15] 42542.715 NV 1052552 GM -2756.149 GN  8741.547 [    0.630 secs]
>>>                    CMIN -30.40 CAVG  -0.08 CMAX  25.25
>>> MSE[  16] 40959.645 NV 1040040 GM  2106.021 GN 11453.347 [    0.627 secs]
>>>                    CMIN -31.82 CAVG  -0.05 CMAX  27.37
>>> MSE[  17] 38835.320 NV 1047948 GM   171.968 GN  5861.133 [    0.629 secs]
>>>                    CMIN -30.59 CAVG  -0.05 CMAX  26.64
>>> MSE[  18] 38289.160 NV 1033359 GM  2835.816 GN  6007.721 [    0.634 secs]
>>>                    CMIN -31.34 CAVG  -0.05 CMAX  28.26
>>> MSE[  19] 37757.949 NV 1022548 GM   764.146 GN  5460.470 [    0.624 secs]
>>>                    CMIN -32.10 CAVG  -0.05 CMAX  29.80
>>> MSE[  20] 36572.082 NV 990523 GM  -990.091 GN  5187.105 [    0.618 secs]
>>>                    CMIN -34.10 CAVG  -0.06 CMAX  34.08
>>> MSE[  21] 35282.254 NV 952616 GM -3800.624 GN  7294.177 [    0.618 secs]
>>>                    CMIN -35.25 CAVG  -0.07 CMAX  38.78
>>> MSE[  22] 33919.004 NV 938209 GM  -242.454 GN  5740.723 [    0.608 secs]
>>>                    CMIN -33.92 CAVG  -0.08 CMAX  40.26
>>> MSE[  23] 33370.039 NV 916397 GM  1086.198 GN  5384.354 [    0.603 secs]
>>>                    CMIN -34.06 CAVG  -0.07 CMAX  42.59
>>> MSE[  24] 32082.525 NV 927453 GM   492.501 GN  5629.464 [    0.605 secs]
>>>                    CMIN -31.95 CAVG  -0.07 CMAX  41.66
>>> MSE[  25] 31317.986 NV 923391 GM   430.064 GN  3504.146 [    0.604 secs]
>>>                    CMIN -31.63 CAVG  -0.07 CMAX  42.50
>>> MSE[  26] 30691.617 NV 920224 GM    70.180 GN  3819.907 [    0.610 secs]
>>>                    CMIN -31.26 CAVG  -0.07 CMAX  43.41
>>> MSE[  27] 30035.088 NV 914436 GM  -474.841 GN  4630.180 [    0.603 secs]
>>>                    CMIN -30.58 CAVG  -0.06 CMAX  44.40
>>> MSE[  28] 29283.193 NV 902584 GM  -565.189 GN  6579.526 [    0.600 secs]
>>>                    CMIN -29.99 CAVG  -0.06 CMAX  46.43
>>> MSE[  29] 28504.350 NV 899740 GM   403.089 GN  5322.814 [    0.599 secs]
>>>                    CMIN -30.24 CAVG  -0.06 CMAX  47.21
>>> MSE[  30] 27685.469 NV 880915 GM  -360.044 GN  6465.846 [    0.595 secs]
>>>                    CMIN -32.59 CAVG  -0.06 CMAX  49.30
>>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>>> Warping...
>>> Running: plm_warp_native
>>> Converting input image...
>>> Converting xform...
>>> bspline_xform_initialize
>>> rdims = (4,4,3)
>>> vox_per_rgn = (64,64,8)
>>> cdims = (7 7 6)
>>> Input pih
>>> Origin
>>> [-20, -20, -13]
>>> Spacing
>>> [0.15625, 0.15625, 1.25]
>>> Region
>>> ImageRegion (0x7fffd0b054d0)
>>> Dimension: 3
>>> Index: [0, 0, 0]
>>> Size: [256, 256, 22]
>>> Running: gpuit_bsp_to_itk_bsp_raw
>>> Setting bsp_spacing
>>> [10, 10, 10]
>>> Setting bsp_origin
>>> [-30, -30, -23]
>>> Setting bsp_region
>>> ImageRegion (0x7fffd0b04ee0)
>>> Dimension: 3
>>> Index: [0, 0, 0]
>>> Size: [7, 7, 6]
>>> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
>>> Running: xform_itk_bsp_to_itk_bsp
>>> Setting bsp_spacing
>>> [10, 10, 10]
>>> Setting bsp_origin
>>> [-30, -30, -23]
>>> Setting bsp_region
>>> ImageRegion (0x7fffd0b04c30)
>>> Dimension: 3
>>> Index: [0, 0, 0]
>>> Size: [7, 7, 6]
>>> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
>>> Completed: xform_itk_bsp_to_itk_bsp
>>> Creating output volume...
>>> Unhandled image type in Plm_image::convert (14 ->  4)
>>>
>>>
>>> Thanks,
>>> Vickie
>>> On Feb 21, 2011, at 9:04 AM, Sharp, Gregory C. wrote:
>>>
>>>
>>> Hi Vickie,
>>>
>>> Please try setting the "Grid Size" parameter to something
>>> smaller than the image size.  For a smoother deformation,
>>> you may try 10 mm or 20 mm.  For a wigglier deformation, you
>>> may try something like 1 mm or 5 mm.
>>>
>>> Greg
>>>
>>>
>>> -----Original Message-----
>>> From: Zhang, Yi [mailto:[hidden email]]
>>> Sent: Sun 2/20/2011 10:28 PM
>>> To: Sharp, Gregory C.
>>> Cc: [hidden email]
>>> Subject: Re: [slicer-users] Plastimatch error
>>>
>>> Image matrix: 256 by 256 by 22
>>> image resolution: 0.15625 by 0.15625 by 1.25mm
>>> FOV: 40 by 40 by 27.5 mm
>>> Thanks,
>>> Vickie
>>> On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:
>>>
>>>
>>> Hi Vickie,
>>>
>>> This is very helpful.  It looks like the registration code
>>> is running out of memory building the lookup table.
>>>
>>> I think this can be solved by changing the grid spacing.
>>> Can you tell me your image resolution and voxel spacing?
>>> Then I will suggest some modified settings.
>>>
>>> Greg
>>>
>>> -----Original Message-----
>>> From: Zhang, Yi [mailto:[hidden email]]
>>> Sent: Fri 2/18/2011 4:54 PM
>>> To: Sharp, Gregory C.
>>> Cc: [hidden email]
>>> Subject: Re: [slicer-users] Plastimatch error
>>>
>>> Hi Greg,
>>>
>>> I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
>>> installed Plastimatch from
>>> http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
>>> Tested with 2 3D images.
>>> It ran for 75.42 secs and completed with errors.
>>>
>>> ERROR: In
>>>
>>>
>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>>> ic.cxx, line 1522
>>> vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
>>> completed with errors
>>>
>>> I have two 3D mask images in nrrd format, same resolution, same matrix size
>>> and
>>> FOV.
>>> Using Plastimatch B-spline Registration, I left stage 0 and stage 2
>>> unchecked.
>>> For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max
>>> iterations
>>> =
>>> 50
>>> Afer 75.42 seconds, it completed with following error:
>>>
>>> Looks like the linux is working better, but still gives errors. Any
>>> suggestions?
>>>
>>> Thanks,
>>> Vickie
>>>
>>> FYI: output from "Information"
>>>
>>> B-spline deformable registration standard output:
>>>
>>> fixed
>>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
>>> Loading fixed image...
>>> done!
>>> moving
>>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
>>> Loading moving image...
>>> done!
>>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>>> Converting fixed
>>> Converting moving
>>> Done.
>>> SUBSAMPLE: (1 1 1), (1 1 1)
>>> moving_ss size = 256 256 22
>>> fixed_ss size = 256 256 22
>>> bspline_xform_initialize
>>> rdims = (1,1,1)
>>> vox_per_rgn = (640,640,80)
>>> cdims = (4 4 4)
>>> xform_any_to_gpuit_bsp complete
>>> BSPLINE PARMS
>>> max_its = 50
>>> BSPLINE XFORM HEADER
>>> vox_per_rgn = 640 640 80
>>> roi_offset = 0 0 0
>>> roi_dim = 256 256 22
>>> Setting NMAX, MMAX = 192 33
>>> START
>>> RUNNING THE L-BFGS-B CODE
>>>
>>>         * * *
>>>
>>> Machine precision = 2.220E-16
>>> N =  192    M =  33
>>> This problem is unconstrained.
>>> MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
>>>                  CMIN   0.00 CAVG   0.00 CMAX   0.00
>>> MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
>>>                  CMIN  -0.47 CAVG  -0.00 CMAX   0.55
>>> MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
>>>                  CMIN  -2.33 CAVG  -0.01 CMAX   2.75
>>> MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
>>>                  CMIN  -3.54 CAVG  -0.02 CMAX   4.65
>>> MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
>>>                  CMIN  -8.39 CAVG  -0.02 CMAX  12.27
>>> MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
>>>                  CMIN  -4.44 CAVG  -0.02 CMAX   6.07
>>> MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
>>>                  CMIN  -5.12 CAVG  -0.02 CMAX   7.14
>>> MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
>>>                  CMIN -27.43 CAVG  -0.06 CMAX  45.42
>>> MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
>>>                  CMIN  -5.81 CAVG  -0.02 CMAX   8.33
>>> MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
>>>                  CMIN  -5.21 CAVG  -0.02 CMAX   7.29
>>> MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
>>>                  CMIN  -5.14 CAVG  -0.02 CMAX   7.16
>>> MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
>>>                  CMIN  -5.18 CAVG  -0.02 CMAX   7.25
>>> MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
>>>                  CMIN  -5.14 CAVG  -0.02 CMAX   7.18
>>> MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
>>>                  CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>>> MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.18
>>> MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
>>>                  CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>>> MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
>>>                  CMIN  -5.87 CAVG  -0.04 CMAX   8.12
>>> MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
>>>                  CMIN  -5.29 CAVG  -0.02 CMAX   7.37
>>> MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
>>>                  CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>>> MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
>>>                  CMIN  -8.56 CAVG  -0.09 CMAX  11.31
>>> MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
>>>                  CMIN  -5.63 CAVG  -0.03 CMAX   7.77
>>> MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
>>>                  CMIN  -5.23 CAVG  -0.02 CMAX   7.28
>>> MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
>>>                  CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>>> MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
>>>                  CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>> MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
>>>                  CMIN  -5.63 CAVG  -0.04 CMAX   7.56
>>> MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
>>>                  CMIN  -5.26 CAVG  -0.02 CMAX   7.27
>>> MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
>>>                  CMIN  -5.11 CAVG  -0.04 CMAX   7.84
>>> MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
>>>                  CMIN  -5.03 CAVG  -0.05 CMAX   8.18
>>> MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
>>>                  CMIN  -7.75 CAVG  -0.06 CMAX   9.52
>>> MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
>>>                  CMIN -19.57 CAVG  -0.14 CMAX  15.94
>>> MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
>>>                  CMIN -14.77 CAVG  -0.12 CMAX  13.34
>>> MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
>>>                  CMIN -10.03 CAVG   0.00 CMAX  11.79
>>> MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
>>>                  CMIN -12.47 CAVG  -0.11 CMAX  12.07
>>> MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
>>>                  CMIN -13.62 CAVG  -0.12 CMAX  12.84
>>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>>> Warping...
>>> Running: plm_warp_native
>>> Converting input image...
>>> Converting xform...
>>> bspline_xform_initialize
>>> Error allocating memory for q_lut
>>>
>>> On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:
>>>
>>>
>>> Hi Vickie,
>>>
>>> Unfortunately I couldn't reproduce the problem.  You are using a good
>>> configuration of versions which is supposed to work.
>>>
>>> We should test if the problem is with Parallels.  Can you please try
>>> downloading and running another extension, such as ExampleCommandLine?
>>> (By the way, why do you run Slicer on Parallels instead of the OSX native
>>> version?)
>>>
>>> Also, can you tell me if there is any output in the "standard output"
>>> part of the error log?
>>>
>>> An alternative route is to run plastimatch independent of Slicer, then
>>> loading the results into Slicer for further analysis.  Let me know if you
>>> like to pursue that route and I can walk you through.
>>>
>>> Greg
>>>
>>>
>>> On Thu, 17 Feb 2011 10:22:33 -0800
>>> "Zhang, Yi"<[hidden email]>  wrote:
>>>
>>> Sorry,
>>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>>> using the Parallels Desktop since I don't own a PC. (do you think that
>>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>>> extension version:
>>>
>>>
>>>
>>> http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010
>>> -06-10-win32
>>>
>>> Actually, not only B-spline, but other two functionalities give me the same
>>> error - DICOM/DICOM RT import and landmark deformable registration.
>>>
>>> Thanks,
>>> Vickie
>>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>>
>>>
>>> Hi Vickie,
>>>
>>> Can you please tell me your OS, Slicer Version, and
>>> extension version (extension URL)?
>>>
>>> Thank you,
>>> Greg
>>>
>>> -----Original Message-----
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Zhang, Yi
>>> Sent: Thursday, February 17, 2011 12:26 AM
>>> To: [hidden email]
>>> Subject: [slicer-users] Plastimatch error
>>>
>>> Hi,
>>>
>>> I have encountered following error while trying to peform B-spline
>>> deformable registration on Plastmatch:
>>>
>>> ERROR: In
>>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>>> line 1575
>>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>>> process was null when state was queried, result (1) = Error.
>>>
>>> Please help.
>>> Thanks!
>>> Vickie
>>>
>>> --
>>> Greg Sharp, PhD
>>> Department of Radiation Oncology
>>> Massachusetts General Hospital
>>>
>>>
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>>> error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>> --
>> Greg Sharp, PhD
>> Department of Radiation Oncology
>> Massachusetts General Hospital
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: Plastimatch error

Zhang, Yi
Thank you Steve and Greg for all of your help!
Plastimatch is running well with the new release.

Vickie
On Mar 2, 2011, at 6:10 AM, Steve Pieper wrote:

> Hi Vickie -
>
> The slicer nightly builds are made with ubuntu 8.04, but apparently
> those binaries don't run on centos/redhat 5.5.
>
> You can try the near-final versions of the next release here:
>
> http://boggs.bwh.harvard.edu/slicer/3.6.3-RC2/
>
> The plastimatch extension should work with those builds (linux or mac),
> but let us know if it doesn't.
>
> -Steve
>
> On 03/01/2011 07:55 PM, Zhang, Yi wrote:
>> Hi Greg,
>>
>> I tried to upgrade Slicer to 2010-11-3 on our linux network. However, I got an error running Slicer3 - "/usr/lib64/libstdc++.so.6: version 'GLIBCXX_3.4.9' not found"
>> So I think our network does not have the updated GLIBC to run most updated Slicer3.
>> I downloaded the mac version of Slicer3 to my mac computer - Slicer3-3.6.2-2010-11-03-darwin-x86 and Slicer3 is running. I cannot locate plastimatch from the extension manager (path: http://ext.slicer.org/ext/Slicer-3-6/15432-darwin-x86).
>>
>> Do you have a working plastimatch on a mac version of Slicer3? If you do, what is the path to find that plastimatch?
>>
>> Thanks,
>> Vickie
>>
>> On Feb 25, 2011, at 6:25 AM, Gregory Sharp wrote:
>>
>>>
>>> Hi Vickie,
>>>
>>> Oops, my bad.  You are right.  That version is not compatible.
>>>
>>> Would you consider upgrading your Slicer version to 2010-11-03?
>>>
>>> Greg
>>>
>>>
>>> On Thu, 24 Feb 2011 20:11:31 -0800
>>> "Zhang, Yi"<[hidden email]>  wrote:
>>>
>>>> Hi Greg,
>>>>
>>>> After downloading plastimatch from
>>>> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/<http://ext.slicer.org/ext/Slicer-3-6/16102-linux-x86_64/>
>>>> <http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/>I don't see
>>>> plastimatch under Modules anymore. It seems to have disappeared from
>>>> Slicer3. Any ideas?
>>>>
>>>> Vickie
>>>> On Feb 24, 2011, at 6:30 PM, Sharp, Gregory C. wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Thanks for your patience and persistence!
>>>>
>>>> You have hit a bug in plastimatch which thankfully is already fixed.
>>>> Can you try to update your plastimatch?  You will need to point the
>>>> extensions "Where to search" URL to a different location:
>>>>
>>>> For 32-bit linux it is here:
>>>>
>>>> http://ext.slicer.org/ext/Slicer-3-6/16108%2dlinux%2dx86/
>>>>
>>>> For 64-bit linux it is here:
>>>>
>>>> http://ext.slicer.org/ext/Slicer-3-6/16102%2dlinux%2dx86_64/
>>>>
>>>> Greg
>>>>
>>>> -----Original Message-----
>>>> From: Zhang, Yi [mailto:[hidden email]]
>>>> Sent: Thu 2/24/2011 6:24 PM
>>>> To: Sharp, Gregory C.
>>>> Cc: [hidden email]
>>>> Subject: Re: [slicer-users] Plastimatch error
>>>>
>>>> Hi Greg,
>>>>
>>>> Sorry I was out of the office last few days.
>>>> I tried 5 or 10 mm grid size, but still I'm getting errors.
>>>> again, both volumes are:
>>>> Image matrix: 256 by 256 by 22
>>>> Image resolution: 0.15625 by 0.15625 by 1.25mm
>>>>
>>>> Stage 1:
>>>> subsampling rate: 1,1,1
>>>> Grid size (mm): 10
>>>> Max iterations: 30
>>>>
>>>> result: completed with errors: (B-spline deformable registration), 20.91s
>>>> Error log:
>>>> ERROR: In
>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>>>> ic.cxx, line 1522
>>>> vtkCommandLineModuleLogic (0x1270af00): B-spline deformable registration
>>>> completed with errors
>>>> "Information":
>>>> B-spline deformable registration standard output:
>>>>
>>>> fixed
>>>> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeC.nrrd
>>>> Loading fixed image...
>>>> done!
>>>> moving
>>>> image=/home/vzhang/SlicerData/extension/BHAHD_vtkMRMLScalarVolumeNodeB.nrrd
>>>> Loading moving image...
>>>> done!
>>>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>>>> Converting fixed
>>>> Converting moving
>>>> Done.
>>>> SUBSAMPLE: (1 1 1), (1 1 1)
>>>> moving_ss size = 256 256 22
>>>> fixed_ss size = 256 256 22
>>>> bspline_xform_initialize
>>>> rdims = (4,4,3)
>>>> vox_per_rgn = (64,64,8)
>>>> cdims = (7 7 6)
>>>> xform_any_to_gpuit_bsp complete
>>>> BSPLINE PARMS
>>>> max_its = 30
>>>> BSPLINE XFORM HEADER
>>>> vox_per_rgn = 64 64 8
>>>> roi_offset = 0 0 0
>>>> roi_dim = 256 256 22
>>>> Setting NMAX, MMAX = 882 49
>>>> START
>>>> RUNNING THE L-BFGS-B CODE
>>>>
>>>>          * * *
>>>>
>>>> Machine precision = 2.220E-16
>>>> N =  882    M =  49
>>>> This problem is unconstrained.
>>>> MSE[   0] 172793.406 NV 1430550 GM  3440.164 GN 40055.410 [    0.699 secs]
>>>>                   CMIN   0.00 CAVG   0.00 CMAX   0.00
>>>> MSE[   1] 168788.625 NV 1436510 GM -14022.742 GN 44458.961 [    0.701 secs]
>>>>                   CMIN  -0.26 CAVG  -0.00 CMAX   0.27
>>>> MSE[   2] 156002.094 NV 1427438 GM -9776.679 GN 38473.344 [    0.721 secs]
>>>>                   CMIN  -1.29 CAVG  -0.01 CMAX   1.36
>>>> MSE[   3] 113203.945 NV 1376563 GM -1506.240 GN 36962.977 [    0.701 secs]
>>>>                   CMIN  -5.42 CAVG  -0.02 CMAX   5.73
>>>> MSE[   4] 182364.469 NV 1221763 GM  8802.257 GN 44880.477 [    0.665 secs]
>>>>                   CMIN -16.33 CAVG  -0.06 CMAX  23.58
>>>> MSE[   5] 88962.250 NV 1334618 GM  2365.741 GN 29213.508 [    0.686 secs]
>>>>                   CMIN  -8.32 CAVG  -0.03 CMAX  10.47
>>>> MSE[   6] 74965.664 NV 1301347 GM -3784.107 GN 22351.080 [    0.680 secs]
>>>>                   CMIN  -8.87 CAVG  -0.05 CMAX  11.16
>>>> MSE[   7] 68752.648 NV 1261210 GM -9005.963 GN 20776.543 [    0.672 secs]
>>>>                   CMIN  -9.90 CAVG  -0.05 CMAX  10.98
>>>> MSE[   8] 62334.117 NV 1253569 GM   -84.478 GN 13559.529 [    0.670 secs]
>>>>                   CMIN -10.70 CAVG  -0.03 CMAX  11.15
>>>> MSE[   9] 59037.574 NV 1242716 GM  9142.486 GN 15676.164 [    0.669 secs]
>>>>                   CMIN -11.83 CAVG  -0.02 CMAX  11.41
>>>> MSE[  10] 56116.086 NV 1223911 GM  5785.482 GN 11916.921 [    0.665 secs]
>>>>                   CMIN -13.08 CAVG  -0.03 CMAX  12.40
>>>> MSE[  11] 51500.602 NV 1178880 GM  1053.619 GN 11454.988 [    0.656 secs]
>>>>                   CMIN -16.59 CAVG  -0.05 CMAX  14.58
>>>> MSE[  12] 48438.137 NV 1149236 GM -3097.842 GN  9308.528 [    0.649 secs]
>>>>                   CMIN -19.33 CAVG  -0.08 CMAX  16.23
>>>> MSE[  13] 45976.199 NV 1122297 GM -1455.273 GN  7629.981 [    0.644 secs]
>>>>                   CMIN -22.45 CAVG  -0.09 CMAX  17.95
>>>> MSE[  14] 44144.320 NV 1106619 GM -1121.861 GN  6836.752 [    0.641 secs]
>>>>                   CMIN -24.13 CAVG  -0.09 CMAX  19.08
>>>> MSE[  15] 42542.715 NV 1052552 GM -2756.149 GN  8741.547 [    0.630 secs]
>>>>                   CMIN -30.40 CAVG  -0.08 CMAX  25.25
>>>> MSE[  16] 40959.645 NV 1040040 GM  2106.021 GN 11453.347 [    0.627 secs]
>>>>                   CMIN -31.82 CAVG  -0.05 CMAX  27.37
>>>> MSE[  17] 38835.320 NV 1047948 GM   171.968 GN  5861.133 [    0.629 secs]
>>>>                   CMIN -30.59 CAVG  -0.05 CMAX  26.64
>>>> MSE[  18] 38289.160 NV 1033359 GM  2835.816 GN  6007.721 [    0.634 secs]
>>>>                   CMIN -31.34 CAVG  -0.05 CMAX  28.26
>>>> MSE[  19] 37757.949 NV 1022548 GM   764.146 GN  5460.470 [    0.624 secs]
>>>>                   CMIN -32.10 CAVG  -0.05 CMAX  29.80
>>>> MSE[  20] 36572.082 NV 990523 GM  -990.091 GN  5187.105 [    0.618 secs]
>>>>                   CMIN -34.10 CAVG  -0.06 CMAX  34.08
>>>> MSE[  21] 35282.254 NV 952616 GM -3800.624 GN  7294.177 [    0.618 secs]
>>>>                   CMIN -35.25 CAVG  -0.07 CMAX  38.78
>>>> MSE[  22] 33919.004 NV 938209 GM  -242.454 GN  5740.723 [    0.608 secs]
>>>>                   CMIN -33.92 CAVG  -0.08 CMAX  40.26
>>>> MSE[  23] 33370.039 NV 916397 GM  1086.198 GN  5384.354 [    0.603 secs]
>>>>                   CMIN -34.06 CAVG  -0.07 CMAX  42.59
>>>> MSE[  24] 32082.525 NV 927453 GM   492.501 GN  5629.464 [    0.605 secs]
>>>>                   CMIN -31.95 CAVG  -0.07 CMAX  41.66
>>>> MSE[  25] 31317.986 NV 923391 GM   430.064 GN  3504.146 [    0.604 secs]
>>>>                   CMIN -31.63 CAVG  -0.07 CMAX  42.50
>>>> MSE[  26] 30691.617 NV 920224 GM    70.180 GN  3819.907 [    0.610 secs]
>>>>                   CMIN -31.26 CAVG  -0.07 CMAX  43.41
>>>> MSE[  27] 30035.088 NV 914436 GM  -474.841 GN  4630.180 [    0.603 secs]
>>>>                   CMIN -30.58 CAVG  -0.06 CMAX  44.40
>>>> MSE[  28] 29283.193 NV 902584 GM  -565.189 GN  6579.526 [    0.600 secs]
>>>>                   CMIN -29.99 CAVG  -0.06 CMAX  46.43
>>>> MSE[  29] 28504.350 NV 899740 GM   403.089 GN  5322.814 [    0.599 secs]
>>>>                   CMIN -30.24 CAVG  -0.06 CMAX  47.21
>>>> MSE[  30] 27685.469 NV 880915 GM  -360.044 GN  6465.846 [    0.595 secs]
>>>>                   CMIN -32.59 CAVG  -0.06 CMAX  49.30
>>>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>>>> Warping...
>>>> Running: plm_warp_native
>>>> Converting input image...
>>>> Converting xform...
>>>> bspline_xform_initialize
>>>> rdims = (4,4,3)
>>>> vox_per_rgn = (64,64,8)
>>>> cdims = (7 7 6)
>>>> Input pih
>>>> Origin
>>>> [-20, -20, -13]
>>>> Spacing
>>>> [0.15625, 0.15625, 1.25]
>>>> Region
>>>> ImageRegion (0x7fffd0b054d0)
>>>> Dimension: 3
>>>> Index: [0, 0, 0]
>>>> Size: [256, 256, 22]
>>>> Running: gpuit_bsp_to_itk_bsp_raw
>>>> Setting bsp_spacing
>>>> [10, 10, 10]
>>>> Setting bsp_origin
>>>> [-30, -30, -23]
>>>> Setting bsp_region
>>>> ImageRegion (0x7fffd0b04ee0)
>>>> Dimension: 3
>>>> Index: [0, 0, 0]
>>>> Size: [7, 7, 6]
>>>> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
>>>> Running: xform_itk_bsp_to_itk_bsp
>>>> Setting bsp_spacing
>>>> [10, 10, 10]
>>>> Setting bsp_origin
>>>> [-30, -30, -23]
>>>> Setting bsp_region
>>>> ImageRegion (0x7fffd0b04c30)
>>>> Dimension: 3
>>>> Index: [0, 0, 0]
>>>> Size: [7, 7, 6]
>>>> Setting bsp_direction = 1 0 0 0 1 0 0 0 1
>>>> Completed: xform_itk_bsp_to_itk_bsp
>>>> Creating output volume...
>>>> Unhandled image type in Plm_image::convert (14 ->  4)
>>>>
>>>>
>>>> Thanks,
>>>> Vickie
>>>> On Feb 21, 2011, at 9:04 AM, Sharp, Gregory C. wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Please try setting the "Grid Size" parameter to something
>>>> smaller than the image size.  For a smoother deformation,
>>>> you may try 10 mm or 20 mm.  For a wigglier deformation, you
>>>> may try something like 1 mm or 5 mm.
>>>>
>>>> Greg
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Zhang, Yi [mailto:[hidden email]]
>>>> Sent: Sun 2/20/2011 10:28 PM
>>>> To: Sharp, Gregory C.
>>>> Cc: [hidden email]
>>>> Subject: Re: [slicer-users] Plastimatch error
>>>>
>>>> Image matrix: 256 by 256 by 22
>>>> image resolution: 0.15625 by 0.15625 by 1.25mm
>>>> FOV: 40 by 40 by 27.5 mm
>>>> Thanks,
>>>> Vickie
>>>> On Feb 20, 2011, at 7:00 PM, Sharp, Gregory C. wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> This is very helpful.  It looks like the registration code
>>>> is running out of memory building the lookup table.
>>>>
>>>> I think this can be solved by changing the grid spacing.
>>>> Can you tell me your image resolution and voxel spacing?
>>>> Then I will suggest some modified settings.
>>>>
>>>> Greg
>>>>
>>>> -----Original Message-----
>>>> From: Zhang, Yi [mailto:[hidden email]]
>>>> Sent: Fri 2/18/2011 4:54 PM
>>>> To: Sharp, Gregory C.
>>>> Cc: [hidden email]
>>>> Subject: Re: [slicer-users] Plastimatch error
>>>>
>>>> Hi Greg,
>>>>
>>>> I downloaded Slicer3-3.6-2010-06-10-linux-x86_64 to our linux network. And
>>>> installed Plastimatch from
>>>> http://ext.slicer.org/ext/Slicer-3-6/13744-linux-x86_64
>>>> Tested with 2 3D images.
>>>> It ran for 75.42 secs and completed with errors.
>>>>
>>>> ERROR: In
>>>>
>>>>
>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLog
>>>> ic.cxx, line 1522
>>>> vtkCommandLineModuleLogic (0x1d5d97a0): B-spline deformable registration
>>>> completed with errors
>>>>
>>>> I have two 3D mask images in nrrd format, same resolution, same matrix size
>>>> and
>>>> FOV.
>>>> Using Plastimatch B-spline Registration, I left stage 0 and stage 2
>>>> unchecked.
>>>> For stage 1, I put subsampling rate = [1,1,1], Grid size = 100, max
>>>> iterations
>>>> =
>>>> 50
>>>> Afer 75.42 seconds, it completed with following error:
>>>>
>>>> Looks like the linux is working better, but still gives errors. Any
>>>> suggestions?
>>>>
>>>> Thanks,
>>>> Vickie
>>>>
>>>> FYI: output from "Information"
>>>>
>>>> B-spline deformable registration standard output:
>>>>
>>>> fixed
>>>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeC.nrrd
>>>> Loading fixed image...
>>>> done!
>>>> moving
>>>> image=/home/vzhang/SlicerData/extension/BBHFJ_vtkMRMLScalarVolumeNodeB.nrrd
>>>> Loading moving image...
>>>> done!
>>>> [1] xf_in->m_type = 0, xf_out->m_type = 0
>>>> Converting fixed
>>>> Converting moving
>>>> Done.
>>>> SUBSAMPLE: (1 1 1), (1 1 1)
>>>> moving_ss size = 256 256 22
>>>> fixed_ss size = 256 256 22
>>>> bspline_xform_initialize
>>>> rdims = (1,1,1)
>>>> vox_per_rgn = (640,640,80)
>>>> cdims = (4 4 4)
>>>> xform_any_to_gpuit_bsp complete
>>>> BSPLINE PARMS
>>>> max_its = 50
>>>> BSPLINE XFORM HEADER
>>>> vox_per_rgn = 640 640 80
>>>> roi_offset = 0 0 0
>>>> roi_dim = 256 256 22
>>>> Setting NMAX, MMAX = 192 33
>>>> START
>>>> RUNNING THE L-BFGS-B CODE
>>>>
>>>>        * * *
>>>>
>>>> Machine precision = 2.220E-16
>>>> N =  192    M =  33
>>>> This problem is unconstrained.
>>>> MSE[   0] 172793.406 NV 1430550 GM  3439.737 GN 30124.119 [   10.775 secs]
>>>>                 CMIN   0.00 CAVG   0.00 CMAX   0.00
>>>> MSE[   1] 168275.266 NV 1424940 GM -5014.567 GN 30481.576 [    0.820 secs]
>>>>                 CMIN  -0.47 CAVG  -0.00 CMAX   0.55
>>>> MSE[   2] 157821.125 NV 1364025 GM   490.165 GN 10444.228 [    0.824 secs]
>>>>                 CMIN  -2.33 CAVG  -0.01 CMAX   2.75
>>>> MSE[   3] 150639.672 NV 1322945 GM -3168.723 GN  8878.263 [    0.819 secs]
>>>>                 CMIN  -3.54 CAVG  -0.02 CMAX   4.65
>>>> MSE[   4] 188038.469 NV 1104705 GM  5709.269 GN 35672.590 [    0.779 secs]
>>>>                 CMIN  -8.39 CAVG  -0.02 CMAX  12.27
>>>> MSE[   5] 148842.766 NV 1243158 GM  1997.787 GN 20606.512 [    0.810 secs]
>>>>                 CMIN  -4.44 CAVG  -0.02 CMAX   6.07
>>>> MSE[   6] 148750.625 NV 1209877 GM  2647.233 GN 16888.412 [    0.790 secs]
>>>>                 CMIN  -5.12 CAVG  -0.02 CMAX   7.14
>>>> MSE[   7] 806886.812 NV 381837 GM 21044.473 GN 23951.367 [    0.614 secs]
>>>>                 CMIN -27.43 CAVG  -0.06 CMAX  45.42
>>>> MSE[   8] 152320.859 NV 1185717 GM  5175.555 GN 16294.637 [    0.780 secs]
>>>>                 CMIN  -5.81 CAVG  -0.02 CMAX   8.33
>>>> MSE[   9] 148912.469 NV 1207340 GM  1072.352 GN 17781.539 [    0.781 secs]
>>>>                 CMIN  -5.21 CAVG  -0.02 CMAX   7.29
>>>> MSE[  10] 148732.609 NV 1209789 GM  3026.238 GN 16650.699 [    0.782 secs]
>>>>                 CMIN  -5.14 CAVG  -0.02 CMAX   7.16
>>>> MSE[  11] 148842.719 NV 1208203 GM  2533.625 GN 16642.928 [    0.780 secs]
>>>>                 CMIN  -5.18 CAVG  -0.02 CMAX   7.25
>>>> MSE[  12] 148723.188 NV 1209753 GM  3064.563 GN 16639.996 [    0.781 secs]
>>>>                 CMIN  -5.14 CAVG  -0.02 CMAX   7.18
>>>> MSE[  13] 148801.906 NV 1208722 GM  2787.533 GN 16551.098 [    0.780 secs]
>>>>                 CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>>>> MSE[  14] 148718.281 NV 1209738 GM  3013.684 GN 16662.023 [    0.780 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.18
>>>> MSE[  15] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.785 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  16] 148759.312 NV 1209209 GM  2952.867 GN 16575.090 [    0.783 secs]
>>>>                 CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>>>> MSE[  17] 148717.328 NV 1209686 GM  3028.778 GN 16613.072 [    0.787 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  18] 148714.375 NV 1209727 GM  3016.455 GN 16630.223 [    0.779 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  19] 150613.188 NV 1190233 GM   995.946 GN 13185.175 [    0.783 secs]
>>>>                 CMIN  -5.87 CAVG  -0.04 CMAX   8.12
>>>> MSE[  20] 148911.750 NV 1206059 GM   596.928 GN 16508.850 [    0.790 secs]
>>>>                 CMIN  -5.29 CAVG  -0.02 CMAX   7.37
>>>> MSE[  21] 148749.172 NV 1208980 GM  2882.243 GN 16270.943 [    0.847 secs]
>>>>                 CMIN  -5.17 CAVG  -0.02 CMAX   7.22
>>>> MSE[  22] 148719.094 NV 1209605 GM  2989.419 GN 16580.570 [    0.797 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  23] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.834 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  24] 148717.031 NV 1209645 GM  2999.337 GN 16592.098 [    0.798 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  25] 148714.031 NV 1209707 GM  3021.097 GN 16605.896 [    0.786 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  26] 148713.828 NV 1209715 GM  3023.048 GN 16609.420 [    0.789 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  27] 148713.766 NV 1209717 GM  3013.073 GN 16615.166 [    0.775 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  28] 175370.141 NV 1071035 GM  -907.450 GN 33266.391 [    0.749 secs]
>>>>                 CMIN  -8.56 CAVG  -0.09 CMAX  11.31
>>>> MSE[  29] 149951.703 NV 1198289 GM   410.754 GN 15046.626 [    0.774 secs]
>>>>                 CMIN  -5.63 CAVG  -0.03 CMAX   7.77
>>>> MSE[  30] 148812.062 NV 1207861 GM  1381.749 GN 16895.891 [    0.772 secs]
>>>>                 CMIN  -5.23 CAVG  -0.02 CMAX   7.28
>>>> MSE[  31] 148737.641 NV 1209338 GM  2954.447 GN 16500.389 [    0.773 secs]
>>>>                 CMIN  -5.16 CAVG  -0.02 CMAX   7.20
>>>> MSE[  32] 148717.484 NV 1209658 GM  2991.898 GN 16609.189 [    0.773 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  33] 148713.969 NV 1209711 GM  3016.083 GN 16610.049 [    0.772 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  34] 148713.906 NV 1209715 GM  3019.795 GN 16611.596 [    0.772 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  35] 148713.750 NV 1209717 GM  3013.334 GN 16615.154 [    0.779 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  36] 148713.812 NV 1209716 GM  3019.594 GN 16611.320 [    0.775 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  37] 148713.734 NV 1209717 GM  3015.496 GN 16613.883 [    0.775 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  38] 148713.703 NV 1209717 GM  3019.348 GN 16611.369 [    0.780 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  39] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.792 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  40] 148713.703 NV 1209717 GM  3020.359 GN 16610.771 [    0.785 secs]
>>>>                 CMIN  -5.15 CAVG  -0.02 CMAX   7.19
>>>> MSE[  41] 149230.156 NV 1202567 GM -3212.984 GN 13317.635 [    0.787 secs]
>>>>                 CMIN  -5.63 CAVG  -0.04 CMAX   7.56
>>>> MSE[  42] 148573.141 NV 1209045 GM  1713.927 GN 15354.268 [    0.769 secs]
>>>>                 CMIN  -5.26 CAVG  -0.02 CMAX   7.27
>>>> MSE[  43] 143860.938 NV 1209402 GM  -855.199 GN  6535.604 [    0.779 secs]
>>>>                 CMIN  -5.11 CAVG  -0.04 CMAX   7.84
>>>> MSE[  44] 139446.422 NV 1215427 GM -1688.968 GN  8863.167 [    0.781 secs]
>>>>                 CMIN  -5.03 CAVG  -0.05 CMAX   8.18
>>>> MSE[  45] 127585.609 NV 1177313 GM  2248.406 GN  6065.925 [    0.775 secs]
>>>>                 CMIN  -7.75 CAVG  -0.06 CMAX   9.52
>>>> MSE[  46] 127429.797 NV 985327 GM 21602.986 GN 23426.008 [    0.740 secs]
>>>>                 CMIN -19.57 CAVG  -0.14 CMAX  15.94
>>>> MSE[  47] 118871.992 NV 1057706 GM 15481.925 GN 19304.348 [    0.762 secs]
>>>>                 CMIN -14.77 CAVG  -0.12 CMAX  13.34
>>>> MSE[  48] 213189.203 NV 1073180 GM -12869.133 GN 23120.221 [    0.754 secs]
>>>>                 CMIN -10.03 CAVG   0.00 CMAX  11.79
>>>> MSE[  49] 116845.352 NV 1075250 GM 11625.675 GN 14186.798 [    0.771 secs]
>>>>                 CMIN -12.47 CAVG  -0.11 CMAX  12.07
>>>> MSE[  50] 115312.266 NV 1067161 GM 10351.102 GN 15636.233 [    0.764 secs]
>>>>                 CMIN -13.62 CAVG  -0.12 CMAX  12.84
>>>> [2] xf_out->m_type = 8, xf_in->m_type = 0
>>>> Warping...
>>>> Running: plm_warp_native
>>>> Converting input image...
>>>> Converting xform...
>>>> bspline_xform_initialize
>>>> Error allocating memory for q_lut
>>>>
>>>> On Feb 18, 2011, at 10:44 AM, Gregory Sharp wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Unfortunately I couldn't reproduce the problem.  You are using a good
>>>> configuration of versions which is supposed to work.
>>>>
>>>> We should test if the problem is with Parallels.  Can you please try
>>>> downloading and running another extension, such as ExampleCommandLine?
>>>> (By the way, why do you run Slicer on Parallels instead of the OSX native
>>>> version?)
>>>>
>>>> Also, can you tell me if there is any output in the "standard output"
>>>> part of the error log?
>>>>
>>>> An alternative route is to run plastimatch independent of Slicer, then
>>>> loading the results into Slicer for further analysis.  Let me know if you
>>>> like to pursue that route and I can walk you through.
>>>>
>>>> Greg
>>>>
>>>>
>>>> On Thu, 17 Feb 2011 10:22:33 -0800
>>>> "Zhang, Yi"<[hidden email]>  wrote:
>>>>
>>>> Sorry,
>>>> OS: windows xp. However, my computer is a MacBook Pro with Mac OS X. I'm
>>>> using the Parallels Desktop since I don't own a PC. (do you think that
>>>> could be the problem?) Slicer version: Slicer3-3.6-2010-06-10-win32
>>>> extension version:
>>>>
>>>>
>>>>
>>>> http://ext.slicer.org/ext/Slicer-3-6/13750-win32/plastimatch-slicer-svn1339-2010
>>>> -06-10-win32
>>>>
>>>> Actually, not only B-spline, but other two functionalities give me the same
>>>> error - DICOM/DICOM RT import and landmark deformable registration.
>>>>
>>>> Thanks,
>>>> Vickie
>>>> On Feb 17, 2011, at 8:27 AM, Sharp, Gregory C. wrote:
>>>>
>>>>
>>>> Hi Vickie,
>>>>
>>>> Can you please tell me your OS, Slicer Version, and
>>>> extension version (extension URL)?
>>>>
>>>> Thank you,
>>>> Greg
>>>>
>>>> -----Original Message-----
>>>> From: [hidden email]
>>>> [mailto:[hidden email]] On Behalf Of Zhang, Yi
>>>> Sent: Thursday, February 17, 2011 12:26 AM
>>>> To: [hidden email]
>>>> Subject: [slicer-users] Plastimatch error
>>>>
>>>> Hi,
>>>>
>>>> I have encountered following error while trying to peform B-spline
>>>> deformable registration on Plastmatch:
>>>>
>>>> ERROR: In
>>>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
>>>> line 1575
>>>> vtkCommandLineModuleLogic (13B19540): B-spline deformable registration
>>>> process was null when state was queried, result (1) = Error.
>>>>
>>>> Please help.
>>>> Thanks!
>>>> Vickie
>>>>
>>>> --
>>>> Greg Sharp, PhD
>>>> Department of Radiation Oncology
>>>> Massachusetts General Hospital
>>>>
>>>>
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>> e-mail contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>>>> error
>>>> but does not contain patient information, please contact the sender and
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Greg Sharp, PhD
>>> Department of Radiation Oncology
>>> Massachusetts General Hospital
>>
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