On 04/30/2014 11:38 PM, charujing123 wrote: > Hi FS experts and users > I have done the each subjects' surface regestration on fsaverage > surface, and merge all of them into a *.mgh. Group analysis is also > completed. > Now I have two questions: > 1,I want to extract the VtxMax vertex number thickness for all > subjects. The VtxMax vertex number can be got in the > *.sig.cluster.summary file. And it represents the most significant > vertex in that cluster. I search my question in google and find these > scripts which maybe helpful: > for i in `seq 1 $numsubject` > do > mri_convert --frame $i y.mgh > $SUBJECTS_DIR/fsaverage/surf/lh.$i.mgh > mris_convert -c $i.mgh > $SUBJECTS_DIR/fsaverage/surf/lh.inflated lh.$i.asc > done > I got the lh.*.asc file and open it. there are five columes in this > file: I guess that: first colume is vertex number, the 2nd-4th columes > represent MNI coordinates in surface, and the 5th colume is thickness > of this vertex. If I want to deal with my 1st question, all I need to > get the lh.*.asc file and search the specific vertex number in this > file. All of above, is there anything wrong? I don't think so although I've never done it myself. I would probably use something like
mri_segstats --i y.mgh --vox vertexno 0 0 --avgwf file.dat This will save all of the subjects' data from vertex vertexno in file.dat > 2, I created a surface mask, and want to extract the average thickness > value in this mask for every subject. How can I complete it? mri_segstats --i lh.thickness --seg mask.mgh --id 1 --sum averagethickness.summary doug > Any reply will be highly appreaciated. > Thanks > All the best. > Rujing Zha > 2014-05-01 > ------------------------------------------------------------------------ > charujing123 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
