you will have to create a binary mask from the sig map by thresholding at a given level, eg, mri_binarize --i sig.mgh --min 2 --o sig.bin2.mgh Then run mri_segstats --i y.mgh --seg sig.bin2.mgh --id 1 --avgwf y.bin2.dat where y.mgh is the --y input to mri_glmfit --id 1 means to take the forground of sig.bin2.mgh y.bin2.dat will be a text file with the mean of y for each subject in the binarized map
On 1/22/2020 9:32 AM, Amrita Bedi wrote:
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Hello Freesurfer developers,
I wanted to extract mean thickness values of all participants from the uncorrected significance maps obtained from mri glmfit for structural data instead of extracting it from the corrected maps from glmfit sim. Is there a way to do this?
Thank you.
Amrita
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