You can always get info by running the command with --help.
mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz
This assumes that the atlas is in registration with the mni152 (you can test with tkregister --mov atlas.nii.gz --s subject --regheader --reg deleteme.dat, the two volumes should be in registration)
You can take lh.atlas.nii.gz and use it as input to mri_surf2surf to transfer to an individual. Make sure to use --mapmethod nnf
On 06/13/2018 06:59 PM, Ryan Flores wrote:
External Email - Use Caution
Hello all,
I am hoping to obtain structural information (e.g., cortical thickness, surface area, and volume) based on the n30r83 (aka Hammersmith) atlas, which is in MNI space. The atlas differentiates between the hemispheres by using odd/even numbers in the labels.
After looking through the archives I found a potential solution, which entails using the mri_vol2surf & mri_surf2surf commands. I’ve recon-ed the MNI brain to obtain the proper space; however, I’m unsure of how exactly to implement the commands and which flags are relevant. Any advice would be greatly appreciated.
Thank you for your time. I look forward to hearing from you.
Best,
Ryan
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Ryan Flores
Clinical Research Coordinator
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer