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:
External Email - Use Caution
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.hanf...@gmail.com<mailto:lindsay.hanf...@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.hanf...@gmail.com<mailto:lindsay.hanf...@gmail.com>
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