Hi Freesurfers,
My processing stream involves moving the parcellated functional networks of Yeo and Choi to original subject domain to do connectivity analyses. While my process works very well for the Yeo networks I'm rather unsatisfied by the results of the Choi translations.
I'm hoping someone has some suggestions for improving things so that the Choi ROIs map onto individual subjects nearly as well as the general Freesurfer striatal segmentations.
NB - I work with AD patients, so I'm sure part of the problem is atrophy-based. However, I'm sure there are ways to improve things...
*My current pipeline involves two steps:* *mri_vol2vol * *--mov Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz * *--targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader * *--o FSL_choi_17Net_MNI152_tight_parcellation.nii.gz --no-save-reg --interp nearest*
*mri_label2vol * *--seg FSL_choi_17Net_MNI152_tight_parcellation.nii.gz * *--reg $SUBJECTS_DIR/{$subj}/mri/transforms/reg.mni152.2mm.dat * *--invertmtx * *--o Choi_17Network_tight_striatum_orig.nii.gz * *--temp $SUBJECTS_DIR/{$subj}/mri/orig.mgz*
I suspect one way to improve things would be to do a recon-all based procedure, but I have no clue what commands within the recon-all domain that would involve.
Thanks for your suggestions.