Re: [Freesurfer] ROI analysis with manually created labels
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: External Email - Use Caution 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ROI analysis with manually created labels
External Email - Use Caution 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 thelh.precentral.label ofall 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___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
External Email - Use Caution Here the results: pwd: /Users/boris/Desktop/MirLIND_test/1122/mri ls -l BN_Atlas_subcotex.mgz: -rwxrwxrwx 1 boris staff 37013 13 Aug 23:30 BN_Atlas_subcotex.mgz Best, Boris > Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. > : > > pwd ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
