Hi Yuanyuan
this is really more of a batch processing/shell scripting question than a FreeSurfer one. Something like (in tcsh)
set SUBJECTS = (N001 N002...) foreach s ($SUBJECTS) mris_anatomical_stats -l lh.precentral.label -t lh.thickness -b \ -f $s/stats/lh.precentral.stats $s lh end
should do the trick
On Sat, 14 Dec 2019, ?????? wrote:
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Dear FreeSurfer developers,
I used Freesurfer QDEC for group comparisons and identified clusters with significance cortical thickness between the Patient group and the Control group. Then I created several ROIs manually, saved them as labels, and mapped them onto each subject.
I have learned how to get the cortical thickness of certain label (e.g., lh.precentral.label) from one subject (e.g. N001) using this command "mris_anatomical_stats -l lh.precentral.label -t lh.thickness -b -f N001/stats/lh.precentral.stats N001 lh".
But using this command for each label and each subject (one by one) to extract cortical thickness is rather time-consuming, I am wondering if there this a batch processing command for this (for all subjects, do the aforementioned command automatically, so that I can extract the cortical thickness values of the lh.precentral.label of all subjects)?
I've searched the freesurfer wiki and the question list but found no help. Excuse me for this basic question.
Thanks in advance.
Best regards,
Yuanyuan Yin