Problem using Resample Scalar/Vector/DWI

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Problem using Resample Scalar/Vector/DWI

stan-2
Hi all,

I'm trying to rotate a dwi volume by using the module Resample
Scalar/Vector/DWI volume
What I do is the following:

1. I load the dwi sequence
2. Create a transform node from the Data menu
3. I use these objects to set Input Volume, Reference Volume, and
Transform Node in the module.

After pushing the Appy button, I get a strange image (attached) and the
following error in the error
log window:

ERROR: In
/home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx, line 278
vtkImageLogic (0x7f5604503130): Execute: input1
NumberOfScalarComponents, 62, must match out input2
NumberOfScalarComponents 1

What I'm doing wrong?

thanks!

stan




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Re: Problem using Resample Scalar/Vector/DWI

stan-2
Thanks François, that's was my mistake, I didn't notice that there was
an option
to create specific DW volumes.

Now, when I try to estimate the diffusion tensor from the resampled dwi
sequence I get another error:

ERROR: In
/home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
line 1575
vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
terminated with an unknown exception.

However, I don't have this error when computing the tensor of the
original DWI sequence. Any ideas?

Thanks!

stan

Le 17/11/2010 17:14, Francois Budin a écrit :

> Hi Estanislao,
>
> What did you select as the output volume? Did you select "Create New
> Volume" or "Create New DiffusionWeighted Volume" or something else?
> Sincerely,
>
> Francois
>
> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao Oubel<[hidden email]>  wrote:
>    
>> Hi all,
>>
>> I'm trying to rotate a dwi volume by using the module Resample
>> Scalar/Vector/DWI volume
>> What I do is the following:
>>
>> 1. I load the dwi sequence
>> 2. Create a transform node from the Data menu
>> 3. I use these objects to set Input Volume, Reference Volume, and Transform
>> Node in the module.
>>
>> After pushing the Appy button, I get a strange image (attached) and the
>> following error in the error
>> log window:
>>
>> ERROR: In /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>> line 278
>> vtkImageLogic (0x7f5604503130): Execute: input1 NumberOfScalarComponents,
>> 62, must match out input2 NumberOfScalarComponents 1
>>
>> What I'm doing wrong?
>>
>> thanks!
>>
>> stan
>>
>>
>>
>>
>> _______________________________________________
>> 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: Problem using Resample Scalar/Vector/DWI

Francois Budin-2
I tried to find where the problem was from and here is what I found:
-If I run the module outside of Slicer it works
-If I do it inside Slicer, I get the following error:
ERROR: In /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
line 1575
vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
terminated with a fault.
When I save the transformed DWI on the disk, the vector [0 0 0] is
[NaN NaN NaN]. I am trying to figure out why.

Francois

On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel <[hidden email]> wrote:

> Thanks François, that's was my mistake, I didn't notice that there was an
> option
> to create specific DW volumes.
>
> Now, when I try to estimate the diffusion tensor from the resampled dwi
> sequence I get another error:
>
> ERROR: In
> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
> line 1575
> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
> terminated with an unknown exception.
>
> However, I don't have this error when computing the tensor of the original
> DWI sequence. Any ideas?
>
> Thanks!
>
> stan
>
> Le 17/11/2010 17:14, Francois Budin a écrit :
>>
>> Hi Estanislao,
>>
>> What did you select as the output volume? Did you select "Create New
>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>> Sincerely,
>>
>> Francois
>>
>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao Oubel<[hidden email]>
>>  wrote:
>>
>>>
>>> Hi all,
>>>
>>> I'm trying to rotate a dwi volume by using the module Resample
>>> Scalar/Vector/DWI volume
>>> What I do is the following:
>>>
>>> 1. I load the dwi sequence
>>> 2. Create a transform node from the Data menu
>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>> Transform
>>> Node in the module.
>>>
>>> After pushing the Appy button, I get a strange image (attached) and the
>>> following error in the error
>>> log window:
>>>
>>> ERROR: In
>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>> line 278
>>> vtkImageLogic (0x7f5604503130): Execute: input1 NumberOfScalarComponents,
>>> 62, must match out input2 NumberOfScalarComponents 1
>>>
>>> What I'm doing wrong?
>>>
>>> thanks!
>>>
>>> stan
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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: Problem using Resample Scalar/Vector/DWI

stan-2
OK, Thanks! Please keep me updated.

stan




Le 18/11/2010 16:34, Francois Budin a écrit :

> I tried to find where the problem was from and here is what I found:
> -If I run the module outside of Slicer it works
> -If I do it inside Slicer, I get the following error:
> ERROR: In /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
> line 1575
> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
> terminated with a fault.
> When I save the transformed DWI on the disk, the vector [0 0 0] is
> [NaN NaN NaN]. I am trying to figure out why.
>
> Francois
>
> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<[hidden email]>  wrote:
>    
>> Thanks François, that's was my mistake, I didn't notice that there was an
>> option
>> to create specific DW volumes.
>>
>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>> sequence I get another error:
>>
>> ERROR: In
>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>> line 1575
>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>> terminated with an unknown exception.
>>
>> However, I don't have this error when computing the tensor of the original
>> DWI sequence. Any ideas?
>>
>> Thanks!
>>
>> stan
>>
>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>      
>>> Hi Estanislao,
>>>
>>> What did you select as the output volume? Did you select "Create New
>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>> Sincerely,
>>>
>>> Francois
>>>
>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao Oubel<[hidden email]>
>>>   wrote:
>>>
>>>        
>>>> Hi all,
>>>>
>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>> Scalar/Vector/DWI volume
>>>> What I do is the following:
>>>>
>>>> 1. I load the dwi sequence
>>>> 2. Create a transform node from the Data menu
>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>> Transform
>>>> Node in the module.
>>>>
>>>> After pushing the Appy button, I get a strange image (attached) and the
>>>> following error in the error
>>>> log window:
>>>>
>>>> ERROR: In
>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>> line 278
>>>> vtkImageLogic (0x7f5604503130): Execute: input1 NumberOfScalarComponents,
>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>
>>>> What I'm doing wrong?
>>>>
>>>> thanks!
>>>>
>>>> stan
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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: Problem using Resample Scalar/Vector/DWI

Dominik Meier
In reply to this post by Francois Budin-2
Hi Stan,

Francois is correct, I think. I've encountered a similar issue occasionally when resampling DWI:  the baseline vector that should be [0 0 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes module and the diffusion editor and manually enter 0 where you see an NaN. That worked for me.

Dominik

On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:

> I tried to find where the problem was from and here is what I found:
> -If I run the module outside of Slicer it works
> -If I do it inside Slicer, I get the following error:
> ERROR: In /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
> line 1575
> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
> terminated with a fault.
> When I save the transformed DWI on the disk, the vector [0 0 0] is
> [NaN NaN NaN]. I am trying to figure out why.
>
> Francois
>
> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel <[hidden email]> wrote:
>> Thanks François, that's was my mistake, I didn't notice that there was an
>> option
>> to create specific DW volumes.
>>
>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>> sequence I get another error:
>>
>> ERROR: In
>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>> line 1575
>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>> terminated with an unknown exception.
>>
>> However, I don't have this error when computing the tensor of the original
>> DWI sequence. Any ideas?
>>
>> Thanks!
>>
>> stan
>>
>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>
>>> Hi Estanislao,
>>>
>>> What did you select as the output volume? Did you select "Create New
>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>> Sincerely,
>>>
>>> Francois
>>>
>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao Oubel<[hidden email]>
>>>  wrote:
>>>
>>>>
>>>> Hi all,
>>>>
>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>> Scalar/Vector/DWI volume
>>>> What I do is the following:
>>>>
>>>> 1. I load the dwi sequence
>>>> 2. Create a transform node from the Data menu
>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>> Transform
>>>> Node in the module.
>>>>
>>>> After pushing the Appy button, I get a strange image (attached) and the
>>>> following error in the error
>>>> log window:
>>>>
>>>> ERROR: In
>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>> line 278
>>>> vtkImageLogic (0x7f5604503130): Execute: input1 NumberOfScalarComponents,
>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>
>>>> What I'm doing wrong?
>>>>
>>>> thanks!
>>>>
>>>> stan
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>>
>>>>
>>
>>
> _______________________________________________
> 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: Problem using Resample Scalar/Vector/DWI

stan-2
Hi Dominik,

Good idea! Thanks!

stan




Le 19/11/2010 14:53, Dominik Meier a écrit :

> Hi Stan,
>
> Francois is correct, I think. I've encountered a similar issue occasionally when resampling DWI:  the baseline vector that should be [0 0 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes module and the diffusion editor and manually enter 0 where you see an NaN. That worked for me.
>
> Dominik
>
> On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:
>
>    
>> I tried to find where the problem was from and here is what I found:
>> -If I run the module outside of Slicer it works
>> -If I do it inside Slicer, I get the following error:
>> ERROR: In /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>> line 1575
>> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
>> terminated with a fault.
>> When I save the transformed DWI on the disk, the vector [0 0 0] is
>> [NaN NaN NaN]. I am trying to figure out why.
>>
>> Francois
>>
>> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<[hidden email]>  wrote:
>>      
>>> Thanks François, that's was my mistake, I didn't notice that there was an
>>> option
>>> to create specific DW volumes.
>>>
>>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>>> sequence I get another error:
>>>
>>> ERROR: In
>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>> line 1575
>>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>>> terminated with an unknown exception.
>>>
>>> However, I don't have this error when computing the tensor of the original
>>> DWI sequence. Any ideas?
>>>
>>> Thanks!
>>>
>>> stan
>>>
>>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>        
>>>> Hi Estanislao,
>>>>
>>>> What did you select as the output volume? Did you select "Create New
>>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>>> Sincerely,
>>>>
>>>> Francois
>>>>
>>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao Oubel<[hidden email]>
>>>>   wrote:
>>>>
>>>>          
>>>>> Hi all,
>>>>>
>>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>>> Scalar/Vector/DWI volume
>>>>> What I do is the following:
>>>>>
>>>>> 1. I load the dwi sequence
>>>>> 2. Create a transform node from the Data menu
>>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>>> Transform
>>>>> Node in the module.
>>>>>
>>>>> After pushing the Appy button, I get a strange image (attached) and the
>>>>> following error in the error
>>>>> log window:
>>>>>
>>>>> ERROR: In
>>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>>> line 278
>>>>> vtkImageLogic (0x7f5604503130): Execute: input1 NumberOfScalarComponents,
>>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>>
>>>>> What I'm doing wrong?
>>>>>
>>>>> thanks!
>>>>>
>>>>> stan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>>
>>>>>
>>>>>            
>>>
>>>        
>> _______________________________________________
>> 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: Problem using Resample Scalar/Vector/DWI

Francois Budin-2
I really have no idea where the problem is coming from. I tried to
print out the values that are saved as NaN and they are 0,0,0 while
the module is running. If somebody has any idea that would be very
helpful.

Francois

On Fri, Nov 19, 2010 at 9:17 AM, Estanislao Oubel <[hidden email]> wrote:

> Hi Dominik,
>
> Good idea! Thanks!
>
> stan
>
>
>
>
> Le 19/11/2010 14:53, Dominik Meier a écrit :
>>
>> Hi Stan,
>>
>> Francois is correct, I think. I've encountered a similar issue
>> occasionally when resampling DWI:  the baseline vector that should be [0 0
>> 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes
>> module and the diffusion editor and manually enter 0 where you see an NaN.
>> That worked for me.
>>
>> Dominik
>>
>> On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:
>>
>>
>>>
>>> I tried to find where the problem was from and here is what I found:
>>> -If I run the module outside of Slicer it works
>>> -If I do it inside Slicer, I get the following error:
>>> ERROR: In
>>> /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>> line 1575
>>> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
>>> terminated with a fault.
>>> When I save the transformed DWI on the disk, the vector [0 0 0] is
>>> [NaN NaN NaN]. I am trying to figure out why.
>>>
>>> Francois
>>>
>>> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<[hidden email]>
>>>  wrote:
>>>
>>>>
>>>> Thanks François, that's was my mistake, I didn't notice that there was
>>>> an
>>>> option
>>>> to create specific DW volumes.
>>>>
>>>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>>>> sequence I get another error:
>>>>
>>>> ERROR: In
>>>>
>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>> line 1575
>>>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>>>> terminated with an unknown exception.
>>>>
>>>> However, I don't have this error when computing the tensor of the
>>>> original
>>>> DWI sequence. Any ideas?
>>>>
>>>> Thanks!
>>>>
>>>> stan
>>>>
>>>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>>
>>>>>
>>>>> Hi Estanislao,
>>>>>
>>>>> What did you select as the output volume? Did you select "Create New
>>>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>>>> Sincerely,
>>>>>
>>>>> Francois
>>>>>
>>>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao
>>>>> Oubel<[hidden email]>
>>>>>  wrote:
>>>>>
>>>>>
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>>>> Scalar/Vector/DWI volume
>>>>>> What I do is the following:
>>>>>>
>>>>>> 1. I load the dwi sequence
>>>>>> 2. Create a transform node from the Data menu
>>>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>>>> Transform
>>>>>> Node in the module.
>>>>>>
>>>>>> After pushing the Appy button, I get a strange image (attached) and
>>>>>> the
>>>>>> following error in the error
>>>>>> log window:
>>>>>>
>>>>>> ERROR: In
>>>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>>>> line 278
>>>>>> vtkImageLogic (0x7f5604503130): Execute: input1
>>>>>> NumberOfScalarComponents,
>>>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>>>
>>>>>> What I'm doing wrong?
>>>>>>
>>>>>> thanks!
>>>>>>
>>>>>> stan
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> 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: Problem using Resample Scalar/Vector/DWI

Francois Budin-2
Hi everyone,

The problem only appears when the module is loaded in Slicer as a
shared object. If the module is compiled only as an executable file,
then the output is correct, even when used directly in Slicer. I am
not sure if it is a problem with Slicer or with my module.

Francois

On Fri, Nov 19, 2010 at 4:37 PM, Francois Budin <[hidden email]> wrote:

> I really have no idea where the problem is coming from. I tried to
> print out the values that are saved as NaN and they are 0,0,0 while
> the module is running. If somebody has any idea that would be very
> helpful.
>
> Francois
>
> On Fri, Nov 19, 2010 at 9:17 AM, Estanislao Oubel <[hidden email]> wrote:
>> Hi Dominik,
>>
>> Good idea! Thanks!
>>
>> stan
>>
>>
>>
>>
>> Le 19/11/2010 14:53, Dominik Meier a écrit :
>>>
>>> Hi Stan,
>>>
>>> Francois is correct, I think. I've encountered a similar issue
>>> occasionally when resampling DWI:  the baseline vector that should be [0 0
>>> 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes
>>> module and the diffusion editor and manually enter 0 where you see an NaN.
>>> That worked for me.
>>>
>>> Dominik
>>>
>>> On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:
>>>
>>>
>>>>
>>>> I tried to find where the problem was from and here is what I found:
>>>> -If I run the module outside of Slicer it works
>>>> -If I do it inside Slicer, I get the following error:
>>>> ERROR: In
>>>> /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>> line 1575
>>>> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
>>>> terminated with a fault.
>>>> When I save the transformed DWI on the disk, the vector [0 0 0] is
>>>> [NaN NaN NaN]. I am trying to figure out why.
>>>>
>>>> Francois
>>>>
>>>> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<[hidden email]>
>>>>  wrote:
>>>>
>>>>>
>>>>> Thanks François, that's was my mistake, I didn't notice that there was
>>>>> an
>>>>> option
>>>>> to create specific DW volumes.
>>>>>
>>>>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>>>>> sequence I get another error:
>>>>>
>>>>> ERROR: In
>>>>>
>>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>> line 1575
>>>>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>>>>> terminated with an unknown exception.
>>>>>
>>>>> However, I don't have this error when computing the tensor of the
>>>>> original
>>>>> DWI sequence. Any ideas?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> stan
>>>>>
>>>>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>>>
>>>>>>
>>>>>> Hi Estanislao,
>>>>>>
>>>>>> What did you select as the output volume? Did you select "Create New
>>>>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>>>>> Sincerely,
>>>>>>
>>>>>> Francois
>>>>>>
>>>>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao
>>>>>> Oubel<[hidden email]>
>>>>>>  wrote:
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>>>>> Scalar/Vector/DWI volume
>>>>>>> What I do is the following:
>>>>>>>
>>>>>>> 1. I load the dwi sequence
>>>>>>> 2. Create a transform node from the Data menu
>>>>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>>>>> Transform
>>>>>>> Node in the module.
>>>>>>>
>>>>>>> After pushing the Appy button, I get a strange image (attached) and
>>>>>>> the
>>>>>>> following error in the error
>>>>>>> log window:
>>>>>>>
>>>>>>> ERROR: In
>>>>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>>>>> line 278
>>>>>>> vtkImageLogic (0x7f5604503130): Execute: input1
>>>>>>> NumberOfScalarComponents,
>>>>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>>>>
>>>>>>> What I'm doing wrong?
>>>>>>>
>>>>>>> thanks!
>>>>>>>
>>>>>>> stan
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> 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: Problem using Resample Scalar/Vector/DWI

pieper
Administrator
Hi Francois -

I'm cc'ing Jim Miller on this - he may have an idea why passing the DWI
data to/from a shared library module is different than going via a
command line.

One possibility, it seems to me, is that the pointer might be on the
stack and it could be go out of scope before it gets loaded back to the
scene - can you send the info on the file and line number where you set
the data and where the writer is invoked?

-Steve

On 11/22/2010 01:56 PM, Francois Budin wrote:

> Hi everyone,
>
> The problem only appears when the module is loaded in Slicer as a
> shared object. If the module is compiled only as an executable file,
> then the output is correct, even when used directly in Slicer. I am
> not sure if it is a problem with Slicer or with my module.
>
> Francois
>
> On Fri, Nov 19, 2010 at 4:37 PM, Francois Budin<[hidden email]>  wrote:
>> I really have no idea where the problem is coming from. I tried to
>> print out the values that are saved as NaN and they are 0,0,0 while
>> the module is running. If somebody has any idea that would be very
>> helpful.
>>
>> Francois
>>
>> On Fri, Nov 19, 2010 at 9:17 AM, Estanislao Oubel<[hidden email]>  wrote:
>>> Hi Dominik,
>>>
>>> Good idea! Thanks!
>>>
>>> stan
>>>
>>>
>>>
>>>
>>> Le 19/11/2010 14:53, Dominik Meier a écrit :
>>>>
>>>> Hi Stan,
>>>>
>>>> Francois is correct, I think. I've encountered a similar issue
>>>> occasionally when resampling DWI:  the baseline vector that should be [0 0
>>>> 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes
>>>> module and the diffusion editor and manually enter 0 where you see an NaN.
>>>> That worked for me.
>>>>
>>>> Dominik
>>>>
>>>> On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:
>>>>
>>>>
>>>>>
>>>>> I tried to find where the problem was from and here is what I found:
>>>>> -If I run the module outside of Slicer it works
>>>>> -If I do it inside Slicer, I get the following error:
>>>>> ERROR: In
>>>>> /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>> line 1575
>>>>> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
>>>>> terminated with a fault.
>>>>> When I save the transformed DWI on the disk, the vector [0 0 0] is
>>>>> [NaN NaN NaN]. I am trying to figure out why.
>>>>>
>>>>> Francois
>>>>>
>>>>> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<[hidden email]>
>>>>>   wrote:
>>>>>
>>>>>>
>>>>>> Thanks François, that's was my mistake, I didn't notice that there was
>>>>>> an
>>>>>> option
>>>>>> to create specific DW volumes.
>>>>>>
>>>>>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>>>>>> sequence I get another error:
>>>>>>
>>>>>> ERROR: In
>>>>>>
>>>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>> line 1575
>>>>>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>>>>>> terminated with an unknown exception.
>>>>>>
>>>>>> However, I don't have this error when computing the tensor of the
>>>>>> original
>>>>>> DWI sequence. Any ideas?
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> stan
>>>>>>
>>>>>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>>>>
>>>>>>>
>>>>>>> Hi Estanislao,
>>>>>>>
>>>>>>> What did you select as the output volume? Did you select "Create New
>>>>>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>>>>>> Sincerely,
>>>>>>>
>>>>>>> Francois
>>>>>>>
>>>>>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao
>>>>>>> Oubel<[hidden email]>
>>>>>>>   wrote:
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> Hi all,
>>>>>>>>
>>>>>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>>>>>> Scalar/Vector/DWI volume
>>>>>>>> What I do is the following:
>>>>>>>>
>>>>>>>> 1. I load the dwi sequence
>>>>>>>> 2. Create a transform node from the Data menu
>>>>>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>>>>>> Transform
>>>>>>>> Node in the module.
>>>>>>>>
>>>>>>>> After pushing the Appy button, I get a strange image (attached) and
>>>>>>>> the
>>>>>>>> following error in the error
>>>>>>>> log window:
>>>>>>>>
>>>>>>>> ERROR: In
>>>>>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>>>>>> line 278
>>>>>>>> vtkImageLogic (0x7f5604503130): Execute: input1
>>>>>>>> NumberOfScalarComponents,
>>>>>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>>>>>
>>>>>>>> What I'm doing wrong?
>>>>>>>>
>>>>>>>> thanks!
>>>>>>>>
>>>>>>>> stan
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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: Problem using Resample Scalar/Vector/DWI

Demian Wassermann-2
Hi All,

I had reported this error at some point. It came from the fact that ResampleDTI was dividing the gradient directions by its norm at some point in order to reorient the direction of the gradients. Maybe some new fix brought the bug back.

Cheers
Demian

--
Demian Wassermann, PhD
[hidden email]
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Nov 22, 2010, at 6:18 PM, Steve Pieper wrote:

> Hi Francois -
>
> I'm cc'ing Jim Miller on this - he may have an idea why passing the DWI
> data to/from a shared library module is different than going via a
> command line.
>
> One possibility, it seems to me, is that the pointer might be on the
> stack and it could be go out of scope before it gets loaded back to the
> scene - can you send the info on the file and line number where you set
> the data and where the writer is invoked?
>
> -Steve
>
> On 11/22/2010 01:56 PM, Francois Budin wrote:
>> Hi everyone,
>>
>> The problem only appears when the module is loaded in Slicer as a
>> shared object. If the module is compiled only as an executable file,
>> then the output is correct, even when used directly in Slicer. I am
>> not sure if it is a problem with Slicer or with my module.
>>
>> Francois
>>
>> On Fri, Nov 19, 2010 at 4:37 PM, Francois Budin<[hidden email]>  wrote:
>>> I really have no idea where the problem is coming from. I tried to
>>> print out the values that are saved as NaN and they are 0,0,0 while
>>> the module is running. If somebody has any idea that would be very
>>> helpful.
>>>
>>> Francois
>>>
>>> On Fri, Nov 19, 2010 at 9:17 AM, Estanislao Oubel<[hidden email]>  wrote:
>>>> Hi Dominik,
>>>>
>>>> Good idea! Thanks!
>>>>
>>>> stan
>>>>
>>>>
>>>>
>>>>
>>>> Le 19/11/2010 14:53, Dominik Meier a écrit :
>>>>>
>>>>> Hi Stan,
>>>>>
>>>>> Francois is correct, I think. I've encountered a similar issue
>>>>> occasionally when resampling DWI:  the baseline vector that should be [0 0
>>>>> 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes
>>>>> module and the diffusion editor and manually enter 0 where you see an NaN.
>>>>> That worked for me.
>>>>>
>>>>> Dominik
>>>>>
>>>>> On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:
>>>>>
>>>>>
>>>>>>
>>>>>> I tried to find where the problem was from and here is what I found:
>>>>>> -If I run the module outside of Slicer it works
>>>>>> -If I do it inside Slicer, I get the following error:
>>>>>> ERROR: In
>>>>>> /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>> line 1575
>>>>>> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
>>>>>> terminated with a fault.
>>>>>> When I save the transformed DWI on the disk, the vector [0 0 0] is
>>>>>> [NaN NaN NaN]. I am trying to figure out why.
>>>>>>
>>>>>> Francois
>>>>>>
>>>>>> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<[hidden email]>
>>>>>>  wrote:
>>>>>>
>>>>>>>
>>>>>>> Thanks François, that's was my mistake, I didn't notice that there was
>>>>>>> an
>>>>>>> option
>>>>>>> to create specific DW volumes.
>>>>>>>
>>>>>>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>>>>>>> sequence I get another error:
>>>>>>>
>>>>>>> ERROR: In
>>>>>>>
>>>>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>>> line 1575
>>>>>>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>>>>>>> terminated with an unknown exception.
>>>>>>>
>>>>>>> However, I don't have this error when computing the tensor of the
>>>>>>> original
>>>>>>> DWI sequence. Any ideas?
>>>>>>>
>>>>>>> Thanks!
>>>>>>>
>>>>>>> stan
>>>>>>>
>>>>>>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>>>>>
>>>>>>>>
>>>>>>>> Hi Estanislao,
>>>>>>>>
>>>>>>>> What did you select as the output volume? Did you select "Create New
>>>>>>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>>>>>>> Sincerely,
>>>>>>>>
>>>>>>>> Francois
>>>>>>>>
>>>>>>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao
>>>>>>>> Oubel<[hidden email]>
>>>>>>>>  wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>
>>>>>>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>>>>>>> Scalar/Vector/DWI volume
>>>>>>>>> What I do is the following:
>>>>>>>>>
>>>>>>>>> 1. I load the dwi sequence
>>>>>>>>> 2. Create a transform node from the Data menu
>>>>>>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>>>>>>> Transform
>>>>>>>>> Node in the module.
>>>>>>>>>
>>>>>>>>> After pushing the Appy button, I get a strange image (attached) and
>>>>>>>>> the
>>>>>>>>> following error in the error
>>>>>>>>> log window:
>>>>>>>>>
>>>>>>>>> ERROR: In
>>>>>>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>>>>>>> line 278
>>>>>>>>> vtkImageLogic (0x7f5604503130): Execute: input1
>>>>>>>>> NumberOfScalarComponents,
>>>>>>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>>>>>>
>>>>>>>>> What I'm doing wrong?
>>>>>>>>>
>>>>>>>>> thanks!
>>>>>>>>>
>>>>>>>>> stan
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
> _______________________________________________
> 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: Problem using Resample Scalar/Vector/DWI

Francois Budin-2
Steve and Jim, the file that is suppose the write the file out is
ResampleVolume2.cxx (Slicer3/Applications/CLI). It is updating the
writer line 1205.
I am modifying the MetaDataDictionary around line 981.
Demian, I see the bug you are talking about but it has been corrected
and it is slightly different this time. Last time there was a problem
of dividing the norm by 0 if I remember correctly. This time this case
is handled properly, but for some reason, when starting the module in
Slicer as a shared module, something is not written back properly in
Slicer at the end.

Francois

On Mon, Nov 22, 2010 at 4:23 PM, Demian Wassermann
<[hidden email]> wrote:

> Hi All,
>
> I had reported this error at some point. It came from the fact that ResampleDTI was dividing the gradient directions by its norm at some point in order to reorient the direction of the gradients. Maybe some new fix brought the bug back.
>
> Cheers
> Demian
>
> --
> Demian Wassermann, PhD
> [hidden email]
> LMI / PNL / SPL Labs
> Harvard Medical School
> Brigham and Women's Hospital
> 1249 Boylston, Boston, MA, USA
>
> On Nov 22, 2010, at 6:18 PM, Steve Pieper wrote:
>
>> Hi Francois -
>>
>> I'm cc'ing Jim Miller on this - he may have an idea why passing the DWI
>> data to/from a shared library module is different than going via a
>> command line.
>>
>> One possibility, it seems to me, is that the pointer might be on the
>> stack and it could be go out of scope before it gets loaded back to the
>> scene - can you send the info on the file and line number where you set
>> the data and where the writer is invoked?
>>
>> -Steve
>>
>> On 11/22/2010 01:56 PM, Francois Budin wrote:
>>> Hi everyone,
>>>
>>> The problem only appears when the module is loaded in Slicer as a
>>> shared object. If the module is compiled only as an executable file,
>>> then the output is correct, even when used directly in Slicer. I am
>>> not sure if it is a problem with Slicer or with my module.
>>>
>>> Francois
>>>
>>> On Fri, Nov 19, 2010 at 4:37 PM, Francois Budin<[hidden email]>  wrote:
>>>> I really have no idea where the problem is coming from. I tried to
>>>> print out the values that are saved as NaN and they are 0,0,0 while
>>>> the module is running. If somebody has any idea that would be very
>>>> helpful.
>>>>
>>>> Francois
>>>>
>>>> On Fri, Nov 19, 2010 at 9:17 AM, Estanislao Oubel<[hidden email]>  wrote:
>>>>> Hi Dominik,
>>>>>
>>>>> Good idea! Thanks!
>>>>>
>>>>> stan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Le 19/11/2010 14:53, Dominik Meier a écrit :
>>>>>>
>>>>>> Hi Stan,
>>>>>>
>>>>>> Francois is correct, I think. I've encountered a similar issue
>>>>>> occasionally when resampling DWI:  the baseline vector that should be [0 0
>>>>>> 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes
>>>>>> module and the diffusion editor and manually enter 0 where you see an NaN.
>>>>>> That worked for me.
>>>>>>
>>>>>> Dominik
>>>>>>
>>>>>> On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> I tried to find where the problem was from and here is what I found:
>>>>>>> -If I run the module outside of Slicer it works
>>>>>>> -If I do it inside Slicer, I get the following error:
>>>>>>> ERROR: In
>>>>>>> /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>>> line 1575
>>>>>>> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
>>>>>>> terminated with a fault.
>>>>>>> When I save the transformed DWI on the disk, the vector [0 0 0] is
>>>>>>> [NaN NaN NaN]. I am trying to figure out why.
>>>>>>>
>>>>>>> Francois
>>>>>>>
>>>>>>> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<[hidden email]>
>>>>>>>  wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> Thanks François, that's was my mistake, I didn't notice that there was
>>>>>>>> an
>>>>>>>> option
>>>>>>>> to create specific DW volumes.
>>>>>>>>
>>>>>>>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>>>>>>>> sequence I get another error:
>>>>>>>>
>>>>>>>> ERROR: In
>>>>>>>>
>>>>>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>>>> line 1575
>>>>>>>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>>>>>>>> terminated with an unknown exception.
>>>>>>>>
>>>>>>>> However, I don't have this error when computing the tensor of the
>>>>>>>> original
>>>>>>>> DWI sequence. Any ideas?
>>>>>>>>
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>> stan
>>>>>>>>
>>>>>>>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Estanislao,
>>>>>>>>>
>>>>>>>>> What did you select as the output volume? Did you select "Create New
>>>>>>>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>>>>>>>> Sincerely,
>>>>>>>>>
>>>>>>>>> Francois
>>>>>>>>>
>>>>>>>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao
>>>>>>>>> Oubel<[hidden email]>
>>>>>>>>>  wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Hi all,
>>>>>>>>>>
>>>>>>>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>>>>>>>> Scalar/Vector/DWI volume
>>>>>>>>>> What I do is the following:
>>>>>>>>>>
>>>>>>>>>> 1. I load the dwi sequence
>>>>>>>>>> 2. Create a transform node from the Data menu
>>>>>>>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>>>>>>>> Transform
>>>>>>>>>> Node in the module.
>>>>>>>>>>
>>>>>>>>>> After pushing the Appy button, I get a strange image (attached) and
>>>>>>>>>> the
>>>>>>>>>> following error in the error
>>>>>>>>>> log window:
>>>>>>>>>>
>>>>>>>>>> ERROR: In
>>>>>>>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>>>>>>>> line 278
>>>>>>>>>> vtkImageLogic (0x7f5604503130): Execute: input1
>>>>>>>>>> NumberOfScalarComponents,
>>>>>>>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>>>>>>>
>>>>>>>>>> What I'm doing wrong?
>>>>>>>>>>
>>>>>>>>>> thanks!
>>>>>>>>>>
>>>>>>>>>> stan
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>> _______________________________________________
>> 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: Problem using Resample Scalar/Vector/DWI

pieper
Administrator
Hmm, I don't see anything obviously wrong with it, but the next place to
look I think is MRMLIDImageIO::SetDWNodeValues at line 726 of
Libs/MRMLIDImageIO/itkMRMLIDImageIO.cxx.  This is where the dwi
gradients get converted from ITK to MRML when running as a shared
library module.

Anybody see an issue there?

-Steve

On 11/22/2010 04:49 PM, Francois Budin wrote:

> Steve and Jim, the file that is suppose the write the file out is
> ResampleVolume2.cxx (Slicer3/Applications/CLI). It is updating the
> writer line 1205.
> I am modifying the MetaDataDictionary around line 981.
> Demian, I see the bug you are talking about but it has been corrected
> and it is slightly different this time. Last time there was a problem
> of dividing the norm by 0 if I remember correctly. This time this case
> is handled properly, but for some reason, when starting the module in
> Slicer as a shared module, something is not written back properly in
> Slicer at the end.
>
> Francois
>
> On Mon, Nov 22, 2010 at 4:23 PM, Demian Wassermann
> <[hidden email]>  wrote:
>> Hi All,
>>
>> I had reported this error at some point. It came from the fact that ResampleDTI was dividing the gradient directions by its norm at some point in order to reorient the direction of the gradients. Maybe some new fix brought the bug back.
>>
>> Cheers
>> Demian
>>
>> --
>> Demian Wassermann, PhD
>> [hidden email]
>> LMI / PNL / SPL Labs
>> Harvard Medical School
>> Brigham and Women's Hospital
>> 1249 Boylston, Boston, MA, USA
>>
>> On Nov 22, 2010, at 6:18 PM, Steve Pieper wrote:
>>
>>> Hi Francois -
>>>
>>> I'm cc'ing Jim Miller on this - he may have an idea why passing the DWI
>>> data to/from a shared library module is different than going via a
>>> command line.
>>>
>>> One possibility, it seems to me, is that the pointer might be on the
>>> stack and it could be go out of scope before it gets loaded back to the
>>> scene - can you send the info on the file and line number where you set
>>> the data and where the writer is invoked?
>>>
>>> -Steve
>>>
>>> On 11/22/2010 01:56 PM, Francois Budin wrote:
>>>> Hi everyone,
>>>>
>>>> The problem only appears when the module is loaded in Slicer as a
>>>> shared object. If the module is compiled only as an executable file,
>>>> then the output is correct, even when used directly in Slicer. I am
>>>> not sure if it is a problem with Slicer or with my module.
>>>>
>>>> Francois
>>>>
>>>> On Fri, Nov 19, 2010 at 4:37 PM, Francois Budin<[hidden email]>    wrote:
>>>>> I really have no idea where the problem is coming from. I tried to
>>>>> print out the values that are saved as NaN and they are 0,0,0 while
>>>>> the module is running. If somebody has any idea that would be very
>>>>> helpful.
>>>>>
>>>>> Francois
>>>>>
>>>>> On Fri, Nov 19, 2010 at 9:17 AM, Estanislao Oubel<[hidden email]>    wrote:
>>>>>> Hi Dominik,
>>>>>>
>>>>>> Good idea! Thanks!
>>>>>>
>>>>>> stan
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Le 19/11/2010 14:53, Dominik Meier a écrit :
>>>>>>>
>>>>>>> Hi Stan,
>>>>>>>
>>>>>>> Francois is correct, I think. I've encountered a similar issue
>>>>>>> occasionally when resampling DWI:  the baseline vector that should be [0 0
>>>>>>> 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes
>>>>>>> module and the diffusion editor and manually enter 0 where you see an NaN.
>>>>>>> That worked for me.
>>>>>>>
>>>>>>> Dominik
>>>>>>>
>>>>>>> On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:
>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>> I tried to find where the problem was from and here is what I found:
>>>>>>>> -If I run the module outside of Slicer it works
>>>>>>>> -If I do it inside Slicer, I get the following error:
>>>>>>>> ERROR: In
>>>>>>>> /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>>>> line 1575
>>>>>>>> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
>>>>>>>> terminated with a fault.
>>>>>>>> When I save the transformed DWI on the disk, the vector [0 0 0] is
>>>>>>>> [NaN NaN NaN]. I am trying to figure out why.
>>>>>>>>
>>>>>>>> Francois
>>>>>>>>
>>>>>>>> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<[hidden email]>
>>>>>>>>   wrote:
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks François, that's was my mistake, I didn't notice that there was
>>>>>>>>> an
>>>>>>>>> option
>>>>>>>>> to create specific DW volumes.
>>>>>>>>>
>>>>>>>>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>>>>>>>>> sequence I get another error:
>>>>>>>>>
>>>>>>>>> ERROR: In
>>>>>>>>>
>>>>>>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>>>>> line 1575
>>>>>>>>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>>>>>>>>> terminated with an unknown exception.
>>>>>>>>>
>>>>>>>>> However, I don't have this error when computing the tensor of the
>>>>>>>>> original
>>>>>>>>> DWI sequence. Any ideas?
>>>>>>>>>
>>>>>>>>> Thanks!
>>>>>>>>>
>>>>>>>>> stan
>>>>>>>>>
>>>>>>>>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Hi Estanislao,
>>>>>>>>>>
>>>>>>>>>> What did you select as the output volume? Did you select "Create New
>>>>>>>>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>>>>>>>>> Sincerely,
>>>>>>>>>>
>>>>>>>>>> Francois
>>>>>>>>>>
>>>>>>>>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao
>>>>>>>>>> Oubel<[hidden email]>
>>>>>>>>>>   wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Hi all,
>>>>>>>>>>>
>>>>>>>>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>>>>>>>>> Scalar/Vector/DWI volume
>>>>>>>>>>> What I do is the following:
>>>>>>>>>>>
>>>>>>>>>>> 1. I load the dwi sequence
>>>>>>>>>>> 2. Create a transform node from the Data menu
>>>>>>>>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>>>>>>>>> Transform
>>>>>>>>>>> Node in the module.
>>>>>>>>>>>
>>>>>>>>>>> After pushing the Appy button, I get a strange image (attached) and
>>>>>>>>>>> the
>>>>>>>>>>> following error in the error
>>>>>>>>>>> log window:
>>>>>>>>>>>
>>>>>>>>>>> ERROR: In
>>>>>>>>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>>>>>>>>> line 278
>>>>>>>>>>> vtkImageLogic (0x7f5604503130): Execute: input1
>>>>>>>>>>> NumberOfScalarComponents,
>>>>>>>>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>>>>>>>>
>>>>>>>>>>> What I'm doing wrong?
>>>>>>>>>>>
>>>>>>>>>>> thanks!
>>>>>>>>>>>
>>>>>>>>>>> stan
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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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>>> 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: Problem using Resample Scalar/Vector/DWI

Francois Budin-2
In reply to this post by Demian Wassermann-2
The bug has been fixed in the trunk and in Slicer 3.6

Francois

On Mon, Nov 22, 2010 at 4:23 PM, Demian Wassermann
<[hidden email]> wrote:

> Hi All,
>
> I had reported this error at some point. It came from the fact that ResampleDTI was dividing the gradient directions by its norm at some point in order to reorient the direction of the gradients. Maybe some new fix brought the bug back.
>
> Cheers
> Demian
>
> --
> Demian Wassermann, PhD
> [hidden email]
> LMI / PNL / SPL Labs
> Harvard Medical School
> Brigham and Women's Hospital
> 1249 Boylston, Boston, MA, USA
>
> On Nov 22, 2010, at 6:18 PM, Steve Pieper wrote:
>
>> Hi Francois -
>>
>> I'm cc'ing Jim Miller on this - he may have an idea why passing the DWI
>> data to/from a shared library module is different than going via a
>> command line.
>>
>> One possibility, it seems to me, is that the pointer might be on the
>> stack and it could be go out of scope before it gets loaded back to the
>> scene - can you send the info on the file and line number where you set
>> the data and where the writer is invoked?
>>
>> -Steve
>>
>> On 11/22/2010 01:56 PM, Francois Budin wrote:
>>> Hi everyone,
>>>
>>> The problem only appears when the module is loaded in Slicer as a
>>> shared object. If the module is compiled only as an executable file,
>>> then the output is correct, even when used directly in Slicer. I am
>>> not sure if it is a problem with Slicer or with my module.
>>>
>>> Francois
>>>
>>> On Fri, Nov 19, 2010 at 4:37 PM, Francois Budin<[hidden email]>  wrote:
>>>> I really have no idea where the problem is coming from. I tried to
>>>> print out the values that are saved as NaN and they are 0,0,0 while
>>>> the module is running. If somebody has any idea that would be very
>>>> helpful.
>>>>
>>>> Francois
>>>>
>>>> On Fri, Nov 19, 2010 at 9:17 AM, Estanislao Oubel<[hidden email]>  wrote:
>>>>> Hi Dominik,
>>>>>
>>>>> Good idea! Thanks!
>>>>>
>>>>> stan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Le 19/11/2010 14:53, Dominik Meier a écrit :
>>>>>>
>>>>>> Hi Stan,
>>>>>>
>>>>>> Francois is correct, I think. I've encountered a similar issue
>>>>>> occasionally when resampling DWI:  the baseline vector that should be [0 0
>>>>>> 0] is somehow corrupted into NaN.  You can do a manual fix via the Volumes
>>>>>> module and the diffusion editor and manually enter 0 where you see an NaN.
>>>>>> That worked for me.
>>>>>>
>>>>>> Dominik
>>>>>>
>>>>>> On Nov 18, 2010, at 10:34 AM, Francois Budin wrote:
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> I tried to find where the problem was from and here is what I found:
>>>>>>> -If I run the module outside of Slicer it works
>>>>>>> -If I do it inside Slicer, I get the following error:
>>>>>>> ERROR: In
>>>>>>> /home/hayes/Slicer3-release-gbt/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>>> line 1575
>>>>>>> vtkCommandLineModuleLogic (0x157b6740): Diffusion Tensor Estimation
>>>>>>> terminated with a fault.
>>>>>>> When I save the transformed DWI on the disk, the vector [0 0 0] is
>>>>>>> [NaN NaN NaN]. I am trying to figure out why.
>>>>>>>
>>>>>>> Francois
>>>>>>>
>>>>>>> On Wed, Nov 17, 2010 at 12:37 PM, Estanislao Oubel<[hidden email]>
>>>>>>>  wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> Thanks François, that's was my mistake, I didn't notice that there was
>>>>>>>> an
>>>>>>>> option
>>>>>>>> to create specific DW volumes.
>>>>>>>>
>>>>>>>> Now, when I try to estimate the diffusion tensor from the resampled dwi
>>>>>>>> sequence I get another error:
>>>>>>>>
>>>>>>>> ERROR: In
>>>>>>>>
>>>>>>>> /home/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
>>>>>>>> line 1575
>>>>>>>> vtkCommandLineModuleLogic (0x75cca10): Diffusion Tensor Estimation
>>>>>>>> terminated with an unknown exception.
>>>>>>>>
>>>>>>>> However, I don't have this error when computing the tensor of the
>>>>>>>> original
>>>>>>>> DWI sequence. Any ideas?
>>>>>>>>
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>> stan
>>>>>>>>
>>>>>>>> Le 17/11/2010 17:14, Francois Budin a écrit :
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi Estanislao,
>>>>>>>>>
>>>>>>>>> What did you select as the output volume? Did you select "Create New
>>>>>>>>> Volume" or "Create New DiffusionWeighted Volume" or something else?
>>>>>>>>> Sincerely,
>>>>>>>>>
>>>>>>>>> Francois
>>>>>>>>>
>>>>>>>>> On Wed, Nov 17, 2010 at 10:17 AM, Estanislao
>>>>>>>>> Oubel<[hidden email]>
>>>>>>>>>  wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Hi all,
>>>>>>>>>>
>>>>>>>>>> I'm trying to rotate a dwi volume by using the module Resample
>>>>>>>>>> Scalar/Vector/DWI volume
>>>>>>>>>> What I do is the following:
>>>>>>>>>>
>>>>>>>>>> 1. I load the dwi sequence
>>>>>>>>>> 2. Create a transform node from the Data menu
>>>>>>>>>> 3. I use these objects to set Input Volume, Reference Volume, and
>>>>>>>>>> Transform
>>>>>>>>>> Node in the module.
>>>>>>>>>>
>>>>>>>>>> After pushing the Appy button, I get a strange image (attached) and
>>>>>>>>>> the
>>>>>>>>>> following error in the error
>>>>>>>>>> log window:
>>>>>>>>>>
>>>>>>>>>> ERROR: In
>>>>>>>>>> /home/hayes/Slicer-3-6/Slicer3-lib/VTK/Imaging/vtkImageLogic.cxx,
>>>>>>>>>> line 278
>>>>>>>>>> vtkImageLogic (0x7f5604503130): Execute: input1
>>>>>>>>>> NumberOfScalarComponents,
>>>>>>>>>> 62, must match out input2 NumberOfScalarComponents 1
>>>>>>>>>>
>>>>>>>>>> What I'm doing wrong?
>>>>>>>>>>
>>>>>>>>>> thanks!
>>>>>>>>>>
>>>>>>>>>> stan
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>> _______________________________________________
>> 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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