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