Apply registration on fiducials

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Apply registration on fiducials

Ganesh Narayanasamy-2

I have registered 2 CT images using Rigid + BSpline registrations. Now, I want to transform the coordinates of the tumor surface from the fixed image to that in the moving image. I tried using Resample scalar/vector volume module, but could not go much further. Can you suggest ways?
We are familiar with clicking at the images and recording these fiducial points. As there are 1000s of coordinates, I have saved them in excel/text file format. How would I read them in the Fiducial module in Slicer3D?

Thanks,
Ganesh


************************************************************************

"What the mind of man can conceive and believe, It can achieve" - Napolean Hill
-Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
************************************************************************


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Re: Apply registration on fiducials

inorton
Hi Ganesh,
 
I tried using Resample scalar/vector volume module, but could not go much further. Can you suggest ways?

1. If you have a labelmap volume for the tumor segmentation then try applying "Resample..." module to the lbmap and then re-create the model from the resampled labelmap.
2. Otherwise if you only have a vtk model, there is a module called "ModelIntoLabelVolume" under "Surface Models" menu. This will create an outline labelmap along the edges of your model. To fill-in, try the recommendations about filling volumes on the mailing list earlier this week (YMMV if the tumor surface is complicated). Then try #1

The bspline could probably be applied to the model directly (at least given a space-defining image for the model). But I don't know if this is implemented anywhere in Slicer yet

We are familiar with clicking at the images and recording these fiducial points. As there are 1000s of coordinates, I have saved them in excel/text file format.

I don't exactly understand the goal here, but the fiducial module may have trouble with 1000s of coordinates.
 
How would I read them in the Fiducial module in Slicer3D?
 
Create a few fiducials in Slicer, then save the scene. The fiducial list will be saved as a "fidulistname.fcsv". Check this file for the format, transform your excel table to match, then save as .fcsv and re-import into Slicer.

HTH,
-Isaiah


On Fri, May 20, 2011 at 1:15 PM, Ganesh Narayanasamy <[hidden email]> wrote:

I have registered 2 CT images using Rigid + BSpline registrations. Now, I want to transform the coordinates of the tumor surface from the fixed image to that in the moving image. I tried using Resample scalar/vector volume module, but could not go much further. Can you suggest ways?
We are familiar with clicking at the images and recording these fiducial points. As there are 1000s of coordinates, I have saved them in excel/text file format. How would I read them in the Fiducial module in Slicer3D?

Thanks,
Ganesh


************************************************************************

"What the mind of man can conceive and believe, It can achieve" - Napolean Hill
-Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
************************************************************************


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Re: Apply registration on fiducials

Andrey Fedorov
Ganesh,

I had the same problem, and (Incidentally!) I had to prepare this as
an extension for a collaborator just yesterday! This mapping cannot be
done directly, because the B-spline transform provides mapping from
fixed to moving image, while your points are defined in the moving
image space.

Please read the instructions that I prepared for my collaborator
below, and give this extension a try. This is a command-line module,
and you can use it either from GUI of from command line. Note that
Slicer does not support loading fiducials list produced by a CLI
module. You will need to manually load the fcsv file if you run it
from GUI. If you run it from command line, you will need to make sure
the .fcsv file is in the proper format, as described in the Fiducials
module documentation.

Hope this helps

AF




I put the extension on NAMIC Sandbox for you. Go to
http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
download the .s3ext file and save it in Slicer3/Extensions folder.
Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
the binary, which will be placed to
Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.

To use the module from command line

TransformFiducialList --fiducialsfile <input.fcsv> --inputtransform
<tfm> --outputfiducialsfile <output.fcsv> --movingimage <moving>
--fixedimage <fixed>

I did some last minor cosmetic fixes last minute, which I didn't test,
please try and let me know if you have problems.

On Fri, May 20, 2011 at 2:54 PM, Isaiah Norton <[hidden email]> wrote:

> Hi Ganesh,
>
>>
>> I tried using Resample scalar/vector volume module, but could not go much
>> further. Can you suggest ways?
>
> 1. If you have a labelmap volume for the tumor segmentation then try
> applying "Resample..." module to the lbmap and then re-create the model from
> the resampled labelmap.
> 2. Otherwise if you only have a vtk model, there is a module called
> "ModelIntoLabelVolume" under "Surface Models" menu. This will create an
> outline labelmap along the edges of your model. To fill-in, try the
> recommendations about filling volumes on the mailing list earlier this week
> (YMMV if the tumor surface is complicated). Then try #1
>
> The bspline could probably be applied to the model directly (at least given
> a space-defining image for the model). But I don't know if this is
> implemented anywhere in Slicer yet
>
>> We are familiar with clicking at the images and recording these fiducial
>> points. As there are 1000s of coordinates, I have saved them in excel/text
>> file format.
>
> I don't exactly understand the goal here, but the fiducial module may have
> trouble with 1000s of coordinates.
>
>>
>> How would I read them in the Fiducial module in Slicer3D?
>
>
> Create a few fiducials in Slicer, then save the scene. The fiducial list
> will be saved as a "fidulistname.fcsv". Check this file for the format,
> transform your excel table to match, then save as .fcsv and re-import into
> Slicer.
>
> HTH,
> -Isaiah
>
>
> On Fri, May 20, 2011 at 1:15 PM, Ganesh Narayanasamy <[hidden email]>
> wrote:
>>
>> I have registered 2 CT images using Rigid + BSpline registrations. Now, I
>> want to transform the coordinates of the tumor surface from the fixed image
>> to that in the moving image. I tried using Resample scalar/vector volume
>> module, but could not go much further. Can you suggest ways?
>> We are familiar with clicking at the images and recording these fiducial
>> points. As there are 1000s of coordinates, I have saved them in excel/text
>> file format. How would I read them in the Fiducial module in Slicer3D?
>>
>> Thanks,
>> Ganesh
>>
>>
>> ************************************************************************
>> "What the mind of man can conceive and believe, It can achieve" - Napolean
>> Hill
>> -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
>> ************************************************************************
>>
>>
>> _______________________________________________
>> 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: Apply registration on fiducials

Ganesh Narayanasamy-2


Thank you for the suggestions.
AF, I have the fiducial points (coordinates of the tumor surface in 3D) defined in the fixed image. I am trying to convert it into the coordinates of the tumor surface in the moving image, after deformation. I am trying to derive the new tumor surface (in the moving image) using the deformation and the original contour in the fixed image. This saves the physician from drawing the contour again.
Would that change anything ?

Yes, I am able to read in the fiducials from .fcsv file using the example in the documentation.

Thanks,
Ganesh


> Date: Fri, 20 May 2011 15:22:39 -0400
> Subject: Re: [slicer-users] Apply registration on fiducials
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
>
> Ganesh,
>
> I had the same problem, and (Incidentally!) I had to prepare this as
> an extension for a collaborator just yesterday! This mapping cannot be
> done directly, because the B-spline transform provides mapping from
> fixed to moving image, while your points are defined in the moving
> image space.
>
> Please read the instructions that I prepared for my collaborator
> below, and give this extension a try. This is a command-line module,
> and you can use it either from GUI of from command line. Note that
> Slicer does not support loading fiducials list produced by a CLI
> module. You will need to manually load the fcsv file if you run it
> from GUI. If you run it from command line, you will need to make sure
> the .fcsv file is in the proper format, as described in the Fiducials
> module documentation.
>
> Hope this helps
>
> AF
>
>
>
>
> I put the extension on NAMIC Sandbox for you. Go to
> http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
> download the .s3ext file and save it in Slicer3/Extensions folder.
> Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
> the binary, which will be placed to
> Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.
>
> To use the module from command line
>
> TransformFiducialList --fiducialsfile <input.fcsv> --inputtransform
> <tfm> --outputfiducialsfile <output.fcsv> --movingimage <moving>
> --fixedimage <fixed>
>
> I did some last minor cosmetic fixes last minute, which I didn't test,
> please try and let me know if you have problems.
>
> On Fri, May 20, 2011 at 2:54 PM, Isaiah Norton <[hidden email]> wrote:
> > Hi Ganesh,
> >
> >>
> >> I tried using Resample scalar/vector volume module, but could not go much
> >> further. Can you suggest ways?
> >
> > 1. If you have a labelmap volume for the tumor segmentation then try
> > applying "Resample..." module to the lbmap and then re-create the model from
> > the resampled labelmap.
> > 2. Otherwise if you only have a vtk model, there is a module called
> > "ModelIntoLabelVolume" under "Surface Models" menu. This will create an
> > outline labelmap along the edges of your model. To fill-in, try the
> > recommendations about filling volumes on the mailing list earlier this week
> > (YMMV if the tumor surface is complicated). Then try #1
> >
> > The bspline could probably be applied to the model directly (at least given
> > a space-defining image for the model). But I don't know if this is
> > implemented anywhere in Slicer yet
> >
> >> We are familiar with clicking at the images and recording these fiducial
> >> points. As there are 1000s of coordinates, I have saved them in excel/text
> >> file format.
> >
> > I don't exactly understand the goal here, but the fiducial module may have
> > trouble with 1000s of coordinates.
> >
> >>
> >> How would I read them in the Fiducial module in Slicer3D?
> >
> >
> > Create a few fiducials in Slicer, then save the scene. The fiducial list
> > will be saved as a "fidulistname.fcsv". Check this file for the format,
> > transform your excel table to match, then save as .fcsv and re-import into
> > Slicer.
> >
> > HTH,
> > -Isaiah
> >

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Re: Apply registration on fiducials

Andrey Fedorov
On Fri, May 20, 2011 at 5:19 PM, Ganesh Narayanasamy
<[hidden email]> wrote:
> AF, I have the fiducial points (coordinates of the tumor surface in 3D)
> defined in the fixed image. I am trying to convert it into the coordinates
> of the tumor surface in the moving image, after deformation. I am trying to
> derive the new tumor surface (in the moving image) using the deformation and
> the original contour in the fixed image. This saves the physician from
> drawing the contour again.
> Would that change anything ?
>

Ganesh, the module I mentioned will transform fiducials from the space
of moving image to the fixed image. If you need to go in the other
direction, it will not help you. Also, it will not work with surfaces,
just with fiducials. Sorry if I misunderstood your initial email.

> Yes, I am able to read in the fiducials from .fcsv file using the example in
> the documentation.
>
> Thanks,
> Ganesh
>
>
>> Date: Fri, 20 May 2011 15:22:39 -0400
>> Subject: Re: [slicer-users] Apply registration on fiducials
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Ganesh,
>>
>> I had the same problem, and (Incidentally!) I had to prepare this as
>> an extension for a collaborator just yesterday! This mapping cannot be
>> done directly, because the B-spline transform provides mapping from
>> fixed to moving image, while your points are defined in the moving
>> image space.
>>
>> Please read the instructions that I prepared for my collaborator
>> below, and give this extension a try. This is a command-line module,
>> and you can use it either from GUI of from command line. Note that
>> Slicer does not support loading fiducials list produced by a CLI
>> module. You will need to manually load the fcsv file if you run it
>> from GUI. If you run it from command line, you will need to make sure
>> the .fcsv file is in the proper format, as described in the Fiducials
>> module documentation.
>>
>> Hope this helps
>>
>> AF
>>
>>
>>
>>
>> I put the extension on NAMIC Sandbox for you. Go to
>>
>> http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
>> download the .s3ext file and save it in Slicer3/Extensions folder.
>> Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
>> the binary, which will be placed to
>>
>> Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.
>>
>> To use the module from command line
>>
>> TransformFiducialList --fiducialsfile <input.fcsv> --inputtransform
>> <tfm> --outputfiducialsfile <output.fcsv> --movingimage <moving>
>> --fixedimage <fixed>
>>
>> I did some last minor cosmetic fixes last minute, which I didn't test,
>> please try and let me know if you have problems.
>>
>> On Fri, May 20, 2011 at 2:54 PM, Isaiah Norton <[hidden email]>
>> wrote:
>> > Hi Ganesh,
>> >
>> >>
>> >> I tried using Resample scalar/vector volume module, but could not go
>> >> much
>> >> further. Can you suggest ways?
>> >
>> > 1. If you have a labelmap volume for the tumor segmentation then try
>> > applying "Resample..." module to the lbmap and then re-create the model
>> > from
>> > the resampled labelmap.
>> > 2. Otherwise if you only have a vtk model, there is a module called
>> > "ModelIntoLabelVolume" under "Surface Models" menu. This will create an
>> > outline labelmap along the edges of your model. To fill-in, try the
>> > recommendations about filling volumes on the mailing list earlier this
>> > week
>> > (YMMV if the tumor surface is complicated). Then try #1
>> >
>> > The bspline could probably be applied to the model directly (at least
>> > given
>> > a space-defining image for the model). But I don't know if this is
>> > implemented anywhere in Slicer yet
>> >
>> >> We are familiar with clicking at the images and recording these
>> >> fiducial
>> >> points. As there are 1000s of coordinates, I have saved them in
>> >> excel/text
>> >> file format.
>> >
>> > I don't exactly understand the goal here, but the fiducial module may
>> > have
>> > trouble with 1000s of coordinates.
>> >
>> >>
>> >> How would I read them in the Fiducial module in Slicer3D?
>> >
>> >
>> > Create a few fiducials in Slicer, then save the scene. The fiducial list
>> > will be saved as a "fidulistname.fcsv". Check this file for the format,
>> > transform your excel table to match, then save as .fcsv and re-import
>> > into
>> > Slicer.
>> >
>> > HTH,
>> > -Isaiah
>> >
>
> _______________________________________________
> 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: Apply registration on fiducials

Ganesh Narayanasamy-2
In reply to this post by Ganesh Narayanasamy-2

As I am interested in transforming surface between the fixed & moving images that are registered using non-rigid Bspline method, I have broken the surface into 1000s of points. Now, I wanted to apply the transformation onto these points and get the transformed coordinates of the structure. It is true that this is a round about manner, I cannot find anything wrong with this method.

AF, If your method transforms fiducials from moving image into the fixed image space, all I have to do is interchange the two images which should not be a problem. However, I have never run code in the command line mode.. how would I start this?

Thanks,
Ganesh


>
> Message: 1
> Date: Fri, 20 May 2011 21:45:34 -0400
> From: Andriy Fedorov <[hidden email]>
> Subject: Re: [slicer-users] Apply registration on fiducials
> To: Ganesh Narayanasamy <[hidden email]>
> Cc: [hidden email]
> Message-ID: <BANLkTim6eu5bAau=x=[hidden email]>
> Content-Type: text/plain; charset=UTF-8
>
> On Fri, May 20, 2011 at 5:19 PM, Ganesh Narayanasamy
> <[hidden email]> wrote:
> > AF, I have the fiducial points (coordinates of the tumor surface in 3D)
> > defined in the fixed image. I am trying to convert it into the coordinates
> > of the tumor surface in the moving image, after deformation. I am trying to
> > derive the new tumor surface (in the moving image) using the deformation and
> > the original contour in the fixed image. This saves the physician from
> > drawing the contour again.
> > Would that change anything ?
> >
>
> Ganesh, the module I mentioned will transform fiducials from the space
> of moving image to the fixed image. If you need to go in the other
> direction, it will not help you. Also, it will not work with surfaces,
> just with fiducials. Sorry if I misunderstood your initial email.
>
> > Yes, I am able to read in the fiducials from .fcsv file using the example in
> > the documentation.
> >
> > Thanks,
> > Ganesh
> >
> >
> >> Date: Fri, 20 May 2011 15:22:39 -0400
> >> Subject: Re: [slicer-users] Apply registration on fiducials
> >> From: [hidden email]
> >> To: [hidden email]
> >> CC: [hidden email]
> >>
> >> Ganesh,
> >>
> >> I had the same problem, and (Incidentally!) I had to prepare this as
> >> an extension for a collaborator just yesterday! This mapping cannot be
> >> done directly, because the B-spline transform provides mapping from
> >> fixed to moving image, while your points are defined in the moving
> >> image space.
> >>
> >> Please read the instructions that I prepared for my collaborator
> >> below, and give this extension a try. This is a command-line module,
> >> and you can use it either from GUI of from command line. Note that
> >> Slicer does not support loading fiducials list produced by a CLI
> >> module. You will need to manually load the fcsv file if you run it
> >> from GUI. If you run it from command line, you will need to make sure
> >> the .fcsv file is in the proper format, as described in the Fiducials
> >> module documentation.
> >>
> >> Hope this helps
> >>
> >> AF
> >>
> >>
> >>
> >>
> >> I put the extension on NAMIC Sandbox for you. Go to
> >>
> >> http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
> >> download the .s3ext file and save it in Slicer3/Extensions folder.
> >> Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
> >> the binary, which will be placed to
> >>
> >> Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.
> >>
> >> To use the module from command line
> >>
> >> TransformFiducialList --fiducialsfile <input.fcsv> --inputtransform
> >> <tfm> --outputfiducialsfile <output.fcsv> --movingimage <moving>
> >> --fixedimage <fixed>
> >>
> >> I did some last minor cosmetic fixes last minute, which I didn't test,
> >> please try and let me know if you have problems.
> >>
> >> On Fri, May 20, 2011 at 2:54 PM, Isaiah Norton <[hidden email]>
> >> wrote:
> >> > Hi Ganesh,
> >> >
> >> >>
> >> >> I tried using Resample scalar/vector volume module, but could not go
> >> >> much
> >> >> further. Can you suggest ways?
> >> >
> >> > 1. If you have a labelmap volume for the tumor segmentation then try
> >> > applying "Resample..." module to the lbmap and then re-create the model
> >> > from
> >> > the resampled labelmap.
> >> > 2. Otherwise if you only have a vtk model, there is a module called
> >> > "ModelIntoLabelVolume" under "Surface Models" menu. This will create an
> >> > outline labelmap along the edges of your model. To fill-in, try the
> >> > recommendations about filling volumes on the mailing list earlier this
> >> > week
> >> > (YMMV if the tumor surface is complicated). Then try #1
> >> >
> >> > The bspline could probably be applied to the model directly (at least
> >> > given
> >> > a space-defining image for the model). But I don't know if this is
> >> > implemented anywhere in Slicer yet
> >> >
> >> >> We are familiar with clicking at the images and recording these
> >> >> fiducial
> >> >> points. As there are 1000s of coordinates, I have saved them in
> >> >> excel/text
> >> >> file format.
> >> >
> >> > I don't exactly understand the goal here, but the fiducial module may
> >> > have
> >> > trouble with 1000s of coordinates.
> >> >
> >> >>
> >> >> How would I read them in the Fiducial module in Slicer3D?
> >> >
> >> >
> >> > Create a few fiducials in Slicer, then save the scene. The fiducial list
> >> > will be saved as a "fidulistname.fcsv". Check this file for the format,
> >> > transform your excel table to match, then save as .fcsv and re-import
> >> > into
> >> > Slicer.
> >> >
> >> > HTH,
> >> > -Isaiah
> >> >
> >


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Re: Apply registration on fiducials

Andrey Fedorov
On Mon, May 23, 2011 at 3:40 PM, Ganesh Narayanasamy
<[hidden email]> wrote:

>
> As I am interested in transforming surface between the fixed & moving images
> that are registered using non-rigid Bspline method, I have broken the
> surface into 1000s of points. Now, I wanted to apply the transformation onto
> these points and get the transformed coordinates of the structure. It is
> true that this is a round about manner, I cannot find anything wrong with
> this method.
>
> AF, If your method transforms fiducials from moving image into the fixed
> image space, all I have to do is interchange the two images which should not
> be a problem. However, I have never run code in the command line mode.. how
> would I start this?
>

You can also run it in the GUI mode. Just specify the name of the file
for the output fiducials, and then load it back into Slicer as you
would for any other fiducial file. The extension of the output file
should be fcsv.

> Thanks,
> Ganesh
>
>
>>
>> Message: 1
>> Date: Fri, 20 May 2011 21:45:34 -0400
>> From: Andriy Fedorov <[hidden email]>
>> Subject: Re: [slicer-users] Apply registration on fiducials
>> To: Ganesh Narayanasamy <[hidden email]>
>> Cc: [hidden email]
>> Message-ID: <BANLkTim6eu5bAau=x=[hidden email]>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Fri, May 20, 2011 at 5:19 PM, Ganesh Narayanasamy
>> <[hidden email]> wrote:
>> > AF, I have the fiducial points (coordinates of the tumor surface in 3D)
>> > defined in the fixed image. I am trying to convert it into the
>> > coordinates
>> > of the tumor surface in the moving image, after deformation. I am trying
>> > to
>> > derive the new tumor surface (in the moving image) using the deformation
>> > and
>> > the original contour in the fixed image. This saves the physician from
>> > drawing the contour again.
>> > Would that change anything ?
>> >
>>
>> Ganesh, the module I mentioned will transform fiducials from the space
>> of moving image to the fixed image. If you need to go in the other
>> direction, it will not help you. Also, it will not work with surfaces,
>> just with fiducials. Sorry if I misunderstood your initial email.
>>
>> > Yes, I am able to read in the fiducials from .fcsv file using the
>> > example in
>> > the documentation.
>> >
>> > Thanks,
>> > Ganesh
>> >
>> >
>> >> Date: Fri, 20 May 2011 15:22:39 -0400
>> >> Subject: Re: [slicer-users] Apply registration on fiducials
>> >> From: [hidden email]
>> >> To: [hidden email]
>> >> CC: [hidden email]
>> >>
>> >> Ganesh,
>> >>
>> >> I had the same problem, and (Incidentally!) I had to prepare this as
>> >> an extension for a collaborator just yesterday! This mapping cannot be
>> >> done directly, because the B-spline transform provides mapping from
>> >> fixed to moving image, while your points are defined in the moving
>> >> image space.
>> >>
>> >> Please read the instructions that I prepared for my collaborator
>> >> below, and give this extension a try. This is a command-line module,
>> >> and you can use it either from GUI of from command line. Note that
>> >> Slicer does not support loading fiducials list produced by a CLI
>> >> module. You will need to manually load the fcsv file if you run it
>> >> from GUI. If you run it from command line, you will need to make sure
>> >> the .fcsv file is in the proper format, as described in the Fiducials
>> >> module documentation.
>> >>
>> >> Hope this helps
>> >>
>> >> AF
>> >>
>> >>
>> >>
>> >>
>> >> I put the extension on NAMIC Sandbox for you. Go to
>> >>
>> >>
>> >> http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
>> >> download the .s3ext file and save it in Slicer3/Extensions folder.
>> >> Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
>> >> the binary, which will be placed to
>> >>
>> >>
>> >> Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.
>> >>
>> >> To use the module from command line
>> >>
>> >> TransformFiducialList --fiducialsfile <input.fcsv> --inputtransform
>> >> <tfm> --outputfiducialsfile <output.fcsv> --movingimage <moving>
>> >> --fixedimage <fixed>
>> >>
>> >> I did some last minor cosmetic fixes last minute, which I didn't test,
>> >> please try and let me know if you have problems.
>> >>
>> >> On Fri, May 20, 2011 at 2:54 PM, Isaiah Norton
>> >> <[hidden email]>
>> >> wrote:
>> >> > Hi Ganesh,
>> >> >
>> >> >>
>> >> >> I tried using Resample scalar/vector volume module, but could not go
>> >> >> much
>> >> >> further. Can you suggest ways?
>> >> >
>> >> > 1. If you have a labelmap volume for the tumor segmentation then try
>> >> > applying "Resample..." module to the lbmap and then re-create the
>> >> > model
>> >> > from
>> >> > the resampled labelmap.
>> >> > 2. Otherwise if you only have a vtk model, there is a module called
>> >> > "ModelIntoLabelVolume" under "Surface Models" menu. This will create
>> >> > an
>> >> > outline labelmap along the edges of your model. To fill-in, try the
>> >> > recommendations about filling volumes on the mailing list earlier
>> >> > this
>> >> > week
>> >> > (YMMV if the tumor surface is complicated). Then try #1
>> >> >
>> >> > The bspline could probably be applied to the model directly (at least
>> >> > given
>> >> > a space-defining image for the model). But I don't know if this is
>> >> > implemented anywhere in Slicer yet
>> >> >
>> >> >> We are familiar with clicking at the images and recording these
>> >> >> fiducial
>> >> >> points. As there are 1000s of coordinates, I have saved them in
>> >> >> excel/text
>> >> >> file format.
>> >> >
>> >> > I don't exactly understand the goal here, but the fiducial module may
>> >> > have
>> >> > trouble with 1000s of coordinates.
>> >> >
>> >> >>
>> >> >> How would I read them in the Fiducial module in Slicer3D?
>> >> >
>> >> >
>> >> > Create a few fiducials in Slicer, then save the scene. The fiducial
>> >> > list
>> >> > will be saved as a "fidulistname.fcsv". Check this file for the
>> >> > format,
>> >> > transform your excel table to match, then save as .fcsv and re-import
>> >> > into
>> >> > Slicer.
>> >> >
>> >> > HTH,
>> >> > -Isaiah
>> >> >
>> >
>
>
> _______________________________________________
> 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: Apply registration on fiducials

Ganesh Narayanasamy-2
In reply to this post by Andrey Fedorov


AF: Can you elaborate on downloading your plugin a little bit more?
I do not know where to save the TransformFiducialList.s3ext file. As such, when I open the Extension Management Wizard, it does not appear in the list with other extensions. Can you guide me through the process.

Thanks,
Ganesh


> Date: Fri, 20 May 2011 15:22:39 -0400
> Subject: Re: [slicer-users] Apply registration on fiducials
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
>
> Ganesh,
>
> I had the same problem, and (Incidentally!) I had to prepare this as
> an extension for a collaborator just yesterday! This mapping cannot be
> done directly, because the B-spline transform provides mapping from
> fixed to moving image, while your points are defined in the moving
> image space.
>
> Please read the instructions that I prepared for my collaborator
> below, and give this extension a try. This is a command-line module,
> and you can use it either from GUI of from command line. Note that
> Slicer does not support loading fiducials list produced by a CLI
> module. You will need to manually load the fcsv file if you run it
> from GUI. If you run it from command line, you will need to make sure
> the .fcsv file is in the proper format, as described in the Fiducials
> module documentation.
>
> Hope this helps
>
> AF
>
>
>
>
> I put the extension on NAMIC Sandbox for you. Go to
> http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
> download the .s3ext file and save it in Slicer3/Extensions folder.
> Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
> the binary, which will be placed to
> Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.
>
> To use the module from command line
>
> TransformFiducialList --fiducialsfile <input.fcsv> --inputtransform
> <tfm> --outputfiducialsfile <output.fcsv> --movingimage <moving>
> --fixedimage <fixed>
>
> I did some last minor cosmetic fixes last minute, which I didn't test,
> please try and let me know if you have problems.
>
> On Fri, May 20, 2011 at 2:54 PM, Isaiah Norton <[hidden email]> wrote:
> > Hi Ganesh,
> >
> >>
> >> I tried using Resample scalar/vector volume module, but could not go much
> >> further. Can you suggest ways?
> >
> > 1. If you have a labelmap volume for the tumor segmentation then try
> > applying "Resample..." module to the lbmap and then re-create the model from
> > the resampled labelmap.
> > 2. Otherwise if you only have a vtk model, there is a module called
> > "ModelIntoLabelVolume" under "Surface Models" menu. This will create an
> > outline labelmap along the edges of your model. To fill-in, try the
> > recommendations about filling volumes on the mailing list earlier this week
> > (YMMV if the tumor surface is complicated). Then try #1
> >
> > The bspline could probably be applied to the model directly (at least given
> > a space-defining image for the model). But I don't know if this is
> > implemented anywhere in Slicer yet
> >
> >> We are familiar with clicking at the images and recording these fiducial
> >> points. As there are 1000s of coordinates, I have saved them in excel/text
> >> file format.
> >
> > I don't exactly understand the goal here, but the fiducial module may have
> > trouble with 1000s of coordinates.
> >
> >>
> >> How would I read them in the Fiducial module in Slicer3D?
> >
> >
> > Create a few fiducials in Slicer, then save the scene. The fiducial list
> > will be saved as a "fidulistname.fcsv". Check this file for the format,
> > transform your excel table to match, then save as .fcsv and re-import into
> > Slicer.
> >
> > HTH,
> > -Isaiah
> >
> >
> > On Fri, May 20, 2011 at 1:15 PM, Ganesh Narayanasamy <[hidden email]>
> > wrote:
> >>
> >> I have registered 2 CT images using Rigid + BSpline registrations. Now, I
> >> want to transform the coordinates of the tumor surface from the fixed image
> >> to that in the moving image. I tried using Resample scalar/vector volume
> >> module, but could not go much further. Can you suggest ways?
> >> We are familiar with clicking at the images and recording these fiducial
> >> points. As there are 1000s of coordinates, I have saved them in excel/text
> >> file format. How would I read them in the Fiducial module in Slicer3D?
> >>
> >> Thanks,
> >> Ganesh
> >>
> >>
> >> ************************************************************************
> >> "What the mind of man can conceive and believe, It can achieve" - Napolean
> >> Hill
> >> -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
> >> ************************************************************************
> >>
> >>
> >> _______________________________________________
> >> 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: Apply registration on fiducials

Andrey Fedorov
On Wed, May 25, 2011 at 3:42 PM, Ganesh Narayanasamy
<[hidden email]> wrote:
>
>
> AF: Can you elaborate on downloading your plugin a little bit more?
> I do not know where to save the TransformFiducialList.s3ext file. As such,
> when I open the Extension Management Wizard, it does not appear in the list
> with other extensions. Can you guide me through the process.
>

Ganesh, I included the instructions in my first email. Here they are again:

1) Go to http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
2) download the .s3ext file and save it in
SLICER_HOME/Slicer3/Extensions folder.
3) Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
the binary, which will be placed to
SLICER_HOME/Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.

SLICER_HOME corresponds to the directory where Slicer3 source tree is located.

If the module does not show up in GUI after you complete these steps,
add SLICER_HOME/Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins
directory to the list of module paths using View->Application
settings->Module settings dialog.

Hope this helps.

> Thanks,
> Ganesh
>
>
>> Date: Fri, 20 May 2011 15:22:39 -0400
>> Subject: Re: [slicer-users] Apply registration on fiducials
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Ganesh,
>>
>> I had the same problem, and (Incidentally!) I had to prepare this as
>> an extension for a collaborator just yesterday! This mapping cannot be
>> done directly, because the B-spline transform provides mapping from
>> fixed to moving image, while your points are defined in the moving
>> image space.
>>
>> Please read the instructions that I prepared for my collaborator
>> below, and give this extension a try. This is a command-line module,
>> and you can use it either from GUI of from command line. Note that
>> Slicer does not support loading fiducials list produced by a CLI
>> module. You will need to manually load the fcsv file if you run it
>> from GUI. If you run it from command line, you will need to make sure
>> the .fcsv file is in the proper format, as described in the Fiducials
>> module documentation.
>>
>> Hope this helps
>>
>> AF
>>
>>
>>
>>
>> I put the extension on NAMIC Sandbox for you. Go to
>>
>> http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
>> download the .s3ext file and save it in Slicer3/Extensions folder.
>> Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
>> the binary, which will be placed to
>>
>> Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.
>>
>> To use the module from command line
>>
>> TransformFiducialList --fiducialsfile <input.fcsv> --inputtransform
>> <tfm> --outputfiducialsfile <output.fcsv> --movingimage <moving>
>> --fixedimage <fixed>
>>
>> I did some last minor cosmetic fixes last minute, which I didn't test,
>> please try and let me know if you have problems.
>>
>> On Fri, May 20, 2011 at 2:54 PM, Isaiah Norton <[hidden email]>
>> wrote:
>> > Hi Ganesh,
>> >
>> >>
>> >> I tried using Resample scalar/vector volume module, but could not go
>> >> much
>> >> further. Can you suggest ways?
>> >
>> > 1. If you have a labelmap volume for the tumor segmentation then try
>> > applying "Resample..." module to the lbmap and then re-create the model
>> > from
>> > the resampled labelmap.
>> > 2. Otherwise if you only have a vtk model, there is a module called
>> > "ModelIntoLabelVolume" under "Surface Models" menu. This will create an
>> > outline labelmap along the edges of your model. To fill-in, try the
>> > recommendations about filling volumes on the mailing list earlier this
>> > week
>> > (YMMV if the tumor surface is complicated). Then try #1
>> >
>> > The bspline could probably be applied to the model directly (at least
>> > given
>> > a space-defining image for the model). But I don't know if this is
>> > implemented anywhere in Slicer yet
>> >
>> >> We are familiar with clicking at the images and recording these
>> >> fiducial
>> >> points. As there are 1000s of coordinates, I have saved them in
>> >> excel/text
>> >> file format.
>> >
>> > I don't exactly understand the goal here, but the fiducial module may
>> > have
>> > trouble with 1000s of coordinates.
>> >
>> >>
>> >> How would I read them in the Fiducial module in Slicer3D?
>> >
>> >
>> > Create a few fiducials in Slicer, then save the scene. The fiducial list
>> > will be saved as a "fidulistname.fcsv". Check this file for the format,
>> > transform your excel table to match, then save as .fcsv and re-import
>> > into
>> > Slicer.
>> >
>> > HTH,
>> > -Isaiah
>> >
>> >
>> > On Fri, May 20, 2011 at 1:15 PM, Ganesh Narayanasamy
>> > <[hidden email]>
>> > wrote:
>> >>
>> >> I have registered 2 CT images using Rigid + BSpline registrations. Now,
>> >> I
>> >> want to transform the coordinates of the tumor surface from the fixed
>> >> image
>> >> to that in the moving image. I tried using Resample scalar/vector
>> >> volume
>> >> module, but could not go much further. Can you suggest ways?
>> >> We are familiar with clicking at the images and recording these
>> >> fiducial
>> >> points. As there are 1000s of coordinates, I have saved them in
>> >> excel/text
>> >> file format. How would I read them in the Fiducial module in Slicer3D?
>> >>
>> >> Thanks,
>> >> Ganesh
>> >>
>> >>
>> >>
>> >> ************************************************************************
>> >> "What the mind of man can conceive and believe, It can achieve" -
>> >> Napolean
>> >> Hill
>> >> -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer
>> >> Center
>> >>
>> >> ************************************************************************
>> >>
>> >>
>> >> _______________________________________________
>> >> 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: Apply registration on fiducials

Andrey Fedorov
Ganesh,

I am very sorry -- I just realized that I assumed your Slicer is built
from source! The extension I mentioned is not part of the
stable/nightly Slicer releases. You will need to build Slicer from
source following the instructions here to try it out:

http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions

Sorry for the confusion

AF



On Wed, May 25, 2011 at 5:20 PM, Andriy Fedorov <[hidden email]> wrote:

> On Wed, May 25, 2011 at 3:42 PM, Ganesh Narayanasamy
> <[hidden email]> wrote:
>>
>>
>> AF: Can you elaborate on downloading your plugin a little bit more?
>> I do not know where to save the TransformFiducialList.s3ext file. As such,
>> when I open the Extension Management Wizard, it does not appear in the list
>> with other extensions. Can you guide me through the process.
>>
>
> Ganesh, I included the instructions in my first email. Here they are again:
>
> 1) Go to http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
> 2) download the .s3ext file and save it in
> SLICER_HOME/Slicer3/Extensions folder.
> 3) Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
> the binary, which will be placed to
> SLICER_HOME/Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.
>
> SLICER_HOME corresponds to the directory where Slicer3 source tree is located.
>
> If the module does not show up in GUI after you complete these steps,
> add SLICER_HOME/Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins
> directory to the list of module paths using View->Application
> settings->Module settings dialog.
>
> Hope this helps.
>
>> Thanks,
>> Ganesh
>>
>>
>>> Date: Fri, 20 May 2011 15:22:39 -0400
>>> Subject: Re: [slicer-users] Apply registration on fiducials
>>> From: [hidden email]
>>> To: [hidden email]
>>> CC: [hidden email]
>>>
>>> Ganesh,
>>>
>>> I had the same problem, and (Incidentally!) I had to prepare this as
>>> an extension for a collaborator just yesterday! This mapping cannot be
>>> done directly, because the B-spline transform provides mapping from
>>> fixed to moving image, while your points are defined in the moving
>>> image space.
>>>
>>> Please read the instructions that I prepared for my collaborator
>>> below, and give this extension a try. This is a command-line module,
>>> and you can use it either from GUI of from command line. Note that
>>> Slicer does not support loading fiducials list produced by a CLI
>>> module. You will need to manually load the fcsv file if you run it
>>> from GUI. If you run it from command line, you will need to make sure
>>> the .fcsv file is in the proper format, as described in the Fiducials
>>> module documentation.
>>>
>>> Hope this helps
>>>
>>> AF
>>>
>>>
>>>
>>>
>>> I put the extension on NAMIC Sandbox for you. Go to
>>>
>>> http://viewvc.slicer.org/viewvc.cgi/NAMICSandBox/trunk/TransformFiducialList/,
>>> download the .s3ext file and save it in Slicer3/Extensions folder.
>>> Then run ./Slicer3/Scripts/extend.tcl TransformFiducialList to build
>>> the binary, which will be placed to
>>>
>>> Slicer3-ext/TransformFiducialList-instal/lib/Slicer3/Plugins/TransformFiducialList.
>>>
>>> To use the module from command line
>>>
>>> TransformFiducialList --fiducialsfile <input.fcsv> --inputtransform
>>> <tfm> --outputfiducialsfile <output.fcsv> --movingimage <moving>
>>> --fixedimage <fixed>
>>>
>>> I did some last minor cosmetic fixes last minute, which I didn't test,
>>> please try and let me know if you have problems.
>>>
>>> On Fri, May 20, 2011 at 2:54 PM, Isaiah Norton <[hidden email]>
>>> wrote:
>>> > Hi Ganesh,
>>> >
>>> >>
>>> >> I tried using Resample scalar/vector volume module, but could not go
>>> >> much
>>> >> further. Can you suggest ways?
>>> >
>>> > 1. If you have a labelmap volume for the tumor segmentation then try
>>> > applying "Resample..." module to the lbmap and then re-create the model
>>> > from
>>> > the resampled labelmap.
>>> > 2. Otherwise if you only have a vtk model, there is a module called
>>> > "ModelIntoLabelVolume" under "Surface Models" menu. This will create an
>>> > outline labelmap along the edges of your model. To fill-in, try the
>>> > recommendations about filling volumes on the mailing list earlier this
>>> > week
>>> > (YMMV if the tumor surface is complicated). Then try #1
>>> >
>>> > The bspline could probably be applied to the model directly (at least
>>> > given
>>> > a space-defining image for the model). But I don't know if this is
>>> > implemented anywhere in Slicer yet
>>> >
>>> >> We are familiar with clicking at the images and recording these
>>> >> fiducial
>>> >> points. As there are 1000s of coordinates, I have saved them in
>>> >> excel/text
>>> >> file format.
>>> >
>>> > I don't exactly understand the goal here, but the fiducial module may
>>> > have
>>> > trouble with 1000s of coordinates.
>>> >
>>> >>
>>> >> How would I read them in the Fiducial module in Slicer3D?
>>> >
>>> >
>>> > Create a few fiducials in Slicer, then save the scene. The fiducial list
>>> > will be saved as a "fidulistname.fcsv". Check this file for the format,
>>> > transform your excel table to match, then save as .fcsv and re-import
>>> > into
>>> > Slicer.
>>> >
>>> > HTH,
>>> > -Isaiah
>>> >
>>> >
>>> > On Fri, May 20, 2011 at 1:15 PM, Ganesh Narayanasamy
>>> > <[hidden email]>
>>> > wrote:
>>> >>
>>> >> I have registered 2 CT images using Rigid + BSpline registrations. Now,
>>> >> I
>>> >> want to transform the coordinates of the tumor surface from the fixed
>>> >> image
>>> >> to that in the moving image. I tried using Resample scalar/vector
>>> >> volume
>>> >> module, but could not go much further. Can you suggest ways?
>>> >> We are familiar with clicking at the images and recording these
>>> >> fiducial
>>> >> points. As there are 1000s of coordinates, I have saved them in
>>> >> excel/text
>>> >> file format. How would I read them in the Fiducial module in Slicer3D?
>>> >>
>>> >> Thanks,
>>> >> Ganesh
>>> >>
>>> >>
>>> >>
>>> >> ************************************************************************
>>> >> "What the mind of man can conceive and believe, It can achieve" -
>>> >> Napolean
>>> >> Hill
>>> >> -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer
>>> >> Center
>>> >>
>>> >> ************************************************************************
>>> >>
>>> >>
>>> >> _______________________________________________
>>> >> 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
>>
>
_______________________________________________
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