Scripts for freesurfer group analysis

Reconstruction

before group analysis start you need to reconstruct all study subjects by running run_all.sh in subjects folder

Set up

before before group analysis start you need to supply .fsgd file (example) with your reconstructed subjects separated into two classes and two .mtx contrast files with "1 -1", "-1 1" in them (1, 2)

Run

bash command example:

bash run_all.sh ./msa-c_vs_gamers_control/subjects/ ./degradation_study.fsgd control_vs_msa-c.mtx msa-c_vs_control.mtx 

Remarks

• recon_all_in_folder.sh assumes that every subject has its own folder, in each subj folder there is a single MPRAGE file which freesurfer will user for reconstruction

• run_all.sh generates two analysis results, one for negative contrast, one for positive contrast. we need to visualize the one with correct clusters, for example:

good output:

with existing cluster info:

...
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ    CWP    CWPLow    CWPHi   NVtxs    WghtVtx   Annot
   1        4.4127  135350    446.85    -50.3  -54.3    5.3  0.00020  0.00000  0.00040    798     2679.53  bankssts
   2        5.1951   74452    257.17    -12.5  -90.7   25.6  0.00539  0.00400  0.00679    310     1037.82  superiorparietal
   3        4.8151   46866    204.00     -8.0  -65.7   55.5  0.01772  0.01534  0.02010    443     1593.59  superiorparietal

bad output:

with empty cluster info:

...
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ    CWP    CWPLow    CWPHi   NVtxs    WghtVtx   Annot