Map the annotation into the indididual subject space with mris_apply_reg. Then create a segmentation from the annotation using mri_aparc2aseg. Look inside any recon-all.log file for an example command line. You will need to change the annot and the output. Then run fcseed-config specifying the new name of the seg with -seg and the segid you want. After that, everything is the same.

On 4/13/18 8:32 PM, Sims, Sara A wrote:

Hello,

I am trying to use Glasser’s parcellation to create a correlation matrix that compares all parcels to all parcels.

I am new to FSFAST, but so far I have gotten the data preprocessed and ready to go. But I am unsure how to proceed.

I have rh and lh annotation files of the parcellation in fsaverage space and I am not sure what to do to them to get to the point that I can use “fcseed-sess”? Should I convert them to labels and then put them on each subject? But what do I do after that?

Help please,

Sara Sims

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