[Freesurfer] Error in qdec: load data file

Hi FreeSurfers, I have trouble loading the .dat file into qdec, receiving the following error message: Verifying subject data.sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject 'DEM001.freesurfer' > in > SUBJECTS_DIR My SUBJECTS_DIR is set correctly a

[Freesurfer] group difference thickness map

Dear freesurfers, I am trying to create a map that shows the vertex-wise magnitude of thinning (f.e.) between two groups, similar to Fig5 in Dickerson et al., 2009. I know how to extract the group-average thickness map from the beta.mg (mri_convert beta.mgh group1.mgh --frame 0 etc.), assuming tha

[Freesurfer] intersection between ROI masks

Dear freesurfers, how can I compute the intersection between binarized masks? Thank you for your support, Miranka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information i

[Freesurfer] generate binary mask from GLM output

Dear Freesurfers, I would to like to generate a binary surface-based mask from the GLM output file (e.g., sig.mgh) the way that vertices above a certain p threshold are set to 1 and below this threshold to 0. I believe I can use this mask in the mri_glmfit procedure? Thank you for helpful inform