The easiest way to to re-run mris_preproc without the --paired-diff to get a stack of all your data, then run
mri_segstats --i stackwithalldata.smoothed.mgh --seg ocn.mgh --excludeid 0 --avgwf ocn.dat
ocn.mgh is the ocn file (output cluster number), and ocn.dat will be a table with each input from diff.fsgd on the rows and each cluster on the columns
On 10/6/16 2:23 AM, Anders Hougaard wrote:
Dear Freesurfers,
This is probably a very basic question, but I was unable to find an answer in the mailing list:
I did a paired cortical thickness group analysis:
mris_preproc --fsgd /home/paired.fsgd --target fsaverage --hemi lh --meas thickness --out lh.paired.00.mgh --paired-diff
(smoothing)
mri_glmfit --y lh.paired.05.mgh --fsgd diff.fsgd --osgm --surf fsaverage lh --cortex --glmdir lh.05_diff.glmdir
I found an area of difference in cortical thickness and I would like to know the thickness values of this area for all of the input in paired.fsgd, not just the differences I get from the y.ocn.dat file.
How do I extract thickness values from the lh.paired.00.mgh file using the label file of the significant cluster?
All the best, Anders
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