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Hi FreeSurfer,
The FreeSurfer atlas includes 5 corpus callosum regions. I am trying to create ROIs of those 5 regions and transfer them to FSL in .nii format to be used in DTI analyses. However, I have been unable to figure out how to put these ROIs in MNI152 space and transfer them to FSL. It was recommended that I run recon-all on the MNI template. Here is my code:
recon-all -s John1 -i MNI152_T1_2mm_brain.nii -all -qcache -3T
However when I try to run recon-all, I get the below message. Do you know why recon-all is not working (note: I tried this is 6.0 and 7.2)? And do you know how I can get FreeSurfer CC ROIS into MNI152 space and then convert them to FSL .nii files?
#@# Curv .H and .K lh Mon Apr 25 18:54:14 PDT 2022
/Users/jessicahua/Box/John/John1/surf
\n mris_curvature -w -seed 1234 lh.white.preaparc \n
setting seed for random number generator to 1234
total integrated curvature = 16.045*4pi (201.629) --> -15 handles
ICI = 107.1, FI = 655.1, variation=11743.051
writing Gaussian curvature to /Users/jessicahua/Box/John/John1/surf/lh.white.preaparc.K...done.
writing mean curvature to /Users/jessicahua/Box/John/John1/surf/lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: lh.white.H: Function not implemented
Darwin Jessicas-MacBook-Pro-2.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 30 13:34:27 PDT 2020; root:xnu-4570.71.82.8~1/RELEASE_X86_64 x86_64
recon-all -s John1 exited with ERRORS at Mon Apr 25 18:54:17 PDT 2022
Thank you,
Jessica