On 3/17/2022 12:53 PM, Hua, Jessica wrote:

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Hi Dr. Greve,

You are right, it does not make sense to try to pull the CC subregions into surface space as they are volume labels. You recommended: /"As for getting them into MNI152, you could just run recon-all on the MNI152."/ I am not following, can you elaborate on how I would run recon-all on the MNI152?

Just run recon-all -s mni152 -i $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz -all

And once I do that, how would I extract the CC subregions to be used in FSL?

mri_binarize --i aparc+aseg.mgz --match 251 252 253 254 255 --o cc.nii.gz

For background, what I would like to do is take the CC subregions in FreeSurfer and convert them into MNI space to be used as ROIs in FSL DTI analyses. We found some volumetric differences of FreeSurfer CC ROIs, and now we want to pull those same ROIs into FSL for our DTI analyses.

Best,

Jessica

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*From:* Hua, Jessica *Sent:* Tuesday, March 8, 2022 10:00 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Cc:* Straub, Kelsey (MU-Student) ktsfk2@mail.missouri.edu *Subject:* Extraction of CC Labels and Conversion to FSL MNI Space Hi FreeSurfer,

I am trying to extract CC subregion labels from aparc+aseg.mgz (ids: 251-255) into a format that is compatible with MNI space in FSL. I was planning on extracting CC labels and then converting the labels from fsaverage space to MNI space. I first tried to extract the 5 separate CC labels using the command: /mri_vol2label --c aparc+aseg.mgz --id 255 --l 255.label/. When viewed in FreeView, the labels were spotty looking. Did I do this mgz to label extraction correctly?

And also do you have a recommended code to convert FreeSurfer CC subregions into MNI space ROIs for FSL?

Best,

Jessica

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