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Just had a chance to try the command. Thanks, it worked!
I was struggling to also have the surface projections in the same space, but found a way to do that. For anyone else who might need this:
tkregister2 --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz --targ $SUBJECTS_DIR/subject/mri/orig.mgz --ixfm $SUBJECTS_DIR/subject/mri/transforms/talairach.xfm -outxfm $SUBJECTS_DIR/subject/mri/transforms/talairach.xfm --reg deleteme.reg --s subject --surfs
Best, Lindsay
On Wed, Jan 16, 2019 at 10:04 AM lindsay hanford lindsay.hanford@gmail.com wrote:
Hi, I just wanted to follow up on this post. Is there a way to load the command below, but with a different atlas? tkregister2 --s 180523_HTP02168_ANAT5_init2base --fstal --surfs
Again, I have tried other options but am unable to the get the surfs in the same space.
Thanks, Lindsay
On Wed, Dec 19, 2018 at 10:36 AM lindsay hanford < lindsay.hanford@gmail.com> wrote:
Hello Freesurfer Community,
I am interested in seeing how well my subject scan registered to a custom atlas after being run through recon-all. From Freesurfer Wiki, although it is possible to see this in freeview, tkregister2 seems to be the best method as manual edits can be made if the registration went badly. I am however running into issues trying to load the subject image, atlas image, and surfaces in the same space.
If I understand correctly, when I ran my recon-all specifying a custom atlas (-custom-tal-atlas RLB700_atlas_as_orig) the transform files (talairach.xfm) are to the custom atlas rather than the talairach atlas.
If I load: tkregister2 --s 180523_HTP02168_ANAT5_init2base --fstal --surfs the subject scan, talairach atlas and surfaces load just fine. It is clear the talairach atlas was not used.
I have tried running multiple variations of the following, and in all cases, the atlas is in a different space. tkregister2 --mov RLB700.nii.gz --s 180523_HTP02168_ANAT5_init2base --regheader --reg 180523_HTP02168_ANAT5_init2base/mri/transforms/talairach.xfm --surfs
Resources used: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview https://surfer.nmr.mgh.harvard.edu/fswiki/MulitModalIntegration
Any suggestions? Thanks, Lindsay
-- *Lindsay Hanford, PhD* *The Buckner Laboratory* *|* *Harvard University* 280 Northwest Laboratory, 52 Oxford St *|* Cambridge, MA 02138 412-218-4368 *|* lindsay.hanford@gmail.com