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
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