Perfect, thanks Doug!

2016-10-06 17:34 GMT+02:00 Douglas Greve greve@nmr.mgh.harvard.edu:

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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