You can use mri_segstats with the annotation (--annot) and the cluster sig map as a mask (--mask , --maskthresh, --masksign), use the --y input to mri_glmfit as the input (--i) to mri_segstats, and specify --avgwf roiaverages.txt --sum roi.sum.txt

roi.sum.txt will have the list of parcellations with each one getting a number. roiaverages.txt will have a row for each subject and a column for each parcellation. Some of the parcellationos will be zero of course

doug

On 11/26/14 12:04 AM, Scott Hayes wrote:

Hi, Is there a way to generate an intersection between a cortical thickness stats map (e.g., sig.mgh) in fsaverage space and native space neuroanatomy using FS parcellations (e.g., lh.apac.anot.)? We would like to plot cortical thickness of the significant clusters for each subject, but separate the significant clusters by the parcellations, e.g., if the significant cluster spans parahippocampal and fusiform cortex, I would like those plotted separately (preferably w/o drawing ROIs--and again, not using the entire PHC or fusiform parcellation--only the portion that is significant in the group analysis).

It seems like this might be possible to accomplish w/ a single command, but we have not been able to pinpoint the exact command w/ the necessary flags. Any guidance would be appreciated.

Thanks, Scott

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer