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Dear expert，
I saw a paper mentioned this ：
By using the *deformation field* from nonlinear registration, we can
build the correspondence between voxels in the template and each linearly-aligned image. For instance, for each voxel (x, y, z) in the template image, we can find its corresponding voxel (x + dx, y + dy, z + dz) in each linearly-aligned image, where (dx, dy, dz) is the *displacement* from the template image to the linearly-aligned image defined by the deformation field.
So, I want to get the deformation field from the template to the linearly registered image(flirt_T1).
Can Freesurfer do this? Which file is a linearly registered image that does not contain an affine transformation? How can I get this deformation field?
Your help is greatly appreciated.
Best, ping
External Email - Use Caution
Could you explain what you are trying to achieve and which transformation you are referring to? I don't get: 1) what are the input and output files of the registration for which you want the deformation field? 2) What command did you use to perform the registration? 3) Is it linear or nonlinear?
(The file <subject>/mri/transforms/talairach.m3z stores a transformation field of a nonlinear registration, but I'm not sure whether it is what you want.)
I find the quoted part a bit confusing (but that may just be me). The first sentence talks about nonlinear registration, and the others talk about linear registration -- but still mention a deformation field. Maybe some more context would help.
For a linear registration, an affine matrix should be all you need.
Tim
On August 28, 2019 at 9:55 AM ping cao pingcao.cp@gmail.com wrote:
External Email - Use CautionDear expert，
I saw a paper mentioned this ：
By using the *deformation field* from nonlinear registration, we can
build the correspondence between voxels in the template and each linearly-aligned image. For instance, for each voxel (x, y, z) in the template image, we can find its corresponding voxel (x + dx, y + dy, z + dz) in each linearly-aligned image, where (dx, dy, dz) is the *displacement* from the template image to the linearly-aligned image defined by the deformation field.
So, I want to get the deformation field from the template to the linearly registered image(flirt_T1).
Can Freesurfer do this? Which file is a linearly registered image that does not contain an affine transformation? How can I get this deformation field?
Your help is greatly appreciated.
Best, ping _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Tim,
Thank you for your reply! 1) I want the the deformation field is the displacement from the template image to the linearly-aligned image defined. 2) I just use the recon-all to generate the file. 3) What I want is to first linearly register to template to obtain a linearly registered image, and then perform nonlinear registration to obtain the deformation field from the origin image to the template.
I don't know which image is linearly registered in freesurfer, which one is after nonlinear registration, and the deformation field file is 128*128*128*3, I can't think of it as displacement I want .
Best, ping
Tim Schäfer ts+ml@rcmd.org 于2019年8月28日周三 下午4:30写道：
External Email - Use CautionCould you explain what you are trying to achieve and which transformation you are referring to? I don't get:
- what are the input and output files of the registration for which you
want the deformation field? 2) What command did you use to perform the registration? 3) Is it linear or nonlinear?
(The file <subject>/mri/transforms/talairach.m3z stores a transformation field of a nonlinear registration, but I'm not sure whether it is what you want.)
I find the quoted part a bit confusing (but that may just be me). The first sentence talks about nonlinear registration, and the others talk about linear registration -- but still mention a deformation field. Maybe some more context would help.
For a linear registration, an affine matrix should be all you need.
Tim
On August 28, 2019 at 9:55 AM ping cao pingcao.cp@gmail.com wrote:
External Email - Use CautionDear expert，
I saw a paper mentioned this ：
By using the *deformation field* from nonlinear registration, we can
build the correspondence between voxels in the template and each linearly-aligned image. For instance, for each voxel (x, y, z) in the template image, we can find its corresponding voxel (x + dx, y + dy, z
dz) in each linearly-aligned image, where (dx, dy, dz) is the *displacement* from the template image to the linearly-aligned image defined by the deformation field.
So, I want to get the deformation field from the template to the linearly registered image(flirt_T1).
Can Freesurfer do this? Which file is a linearly registered image that does not contain an affine transformation? How can I get this deformation field?
Your help is greatly appreciated.
Best, ping _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Forschung - Klinische Bildgebung Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters Universitätsklinikum Frankfurt / Haus 93, Raum A 305 Deutschordenstr. 50, 60528 Frankfurt am Main Tel.: +49 (0)69 6301 85832
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ping
we don't apply the linear registration to any image - we use it to initialize the nonlinear warp. And yes, the nonlinear warp is stored as a 128^3 array with 2 voxel spacing and interpolation between them. You can visualize the .m3z directly in freeview as a 3-frame displacement volume or mri_convert it I believe.
cheers Bruce
On Thu, 29 Aug 2019, ping cao wrote:
External Email - Use Caution
Dear Tim, Thank you for your reply!
- I want the the deformation field is the displacement from the template
image to the linearly-aligned image defined. 2) I just use the recon-all to generate the file. 3) What I want is to first linearly register to template to obtain a linearly registered image, and then perform nonlinear registration to obtain the deformation field from the origin image to the template.
I don't know which image is linearly registered in freesurfer, which one is after nonlinear registration, and the deformation field file is 128*128*128*3, I can't think of it as displacement I want .
Best, ping
Tim Schäfer ts+ml@rcmd.org 于2019年8月28日周三 下午4:30写道： External Email - Use Caution
Could you explain what you are trying to achieve and which transformation you are referring to? I don't get: 1) what are the input and output files of the registration for which you want the deformation field? 2) What command did you use to perform the registration? 3) Is it linear or nonlinear? (The file <subject>/mri/transforms/talairach.m3z stores a transformation field of a nonlinear registration, but I'm not sure whether it is what you want.) I find the quoted part a bit confusing (but that may just be me). The first sentence talks about nonlinear registration, and the others talk about linear registration -- but still mention a deformation field. Maybe some more context would help. For a linear registration, an affine matrix should be all you need. Tim > On August 28, 2019 at 9:55 AM ping cao <pingcao.cp@gmail.com> wrote: > > > External Email - Use Caution > > Dear expert， > > I saw a paper mentioned this ： > > By using the *deformation field* from nonlinear registration, we can > > build the correspondence between voxels in the template and each > > linearly-aligned image. For instance, for each voxel (x, y, z) in the > > template image, we can find its corresponding voxel (x + dx, y + dy, z + > > dz) in each linearly-aligned image, where (dx, dy, dz) is the > > *displacement* from the template image to the linearly-aligned image > > defined by the deformation field. > > > > So, I want to get the deformation field from the template to the linearly > registered image(flirt_T1). > > Can Freesurfer do this? Which file is a linearly registered image that > does not contain an affine transformation? How can I get this deformation > field? > > > Your help is greatly appreciated. > > > Best, > ping > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Forschung - Klinische Bildgebung Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters Universitätsklinikum Frankfurt / Haus 93, Raum A 305 Deutschordenstr. 50, 60528 Frankfurt am Main Tel.: +49 (0)69 6301 85832 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Ping
the displacement fields are stored in m3z format in the file talairach.m3z. They are a vector field over the atlas that maps points in the atlas to points in the original (not linearly aligned) space.
cheers Bruce
On Wed, 28 Aug 2019, ping cao wrote:
External Email - Use Caution
Dear expert， I saw a paper mentioned this ：
By using the deformation field from nonlinear registration, we can build the correspondence between voxels in the template and each linearly-aligned image. For instance, for each voxel (x, y, z) in the template image, we can find its corresponding voxel (x + dx, y + dy, z + dz) in each linearly-aligned image, where (dx, dy, dz) is the displacement from the template image to the linearly-aligned image defined by the deformation field. So, I want to get the deformation field from the template to the linearly registered image(flirt_T1).Can Freesurfer do this? Which file is a linearly registered image that does not contain an affine transformation? How can I get this deformation field?
Your help is greatly appreciated.Best, ping
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
ping cao -
Tim Schäfer