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...@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...@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
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