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

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charujing123

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