Not sure what you are trying to do, but if you want to check the tal reg of a typical analysis, you can run 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 This gives the same thing as your tkregsiter2 command line. Maybe you can customize it to your own result

On 1/16/19 10:04 AM, lindsay hanford wrote:

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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.commailto: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.commailto:lindsay.hanford@gmail.com

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