Hi Paul,

Thanks for the sample data. I created a conversion function conn_cat2mgh (attached) that will convert your CAT12 output files to MGH/FREESURFER format. You may use that on your subject's CAT12 output files, e.g.:

   conn_cat2mgh /data/subject1/T1.nii

and that will create a few new files in MGH format (namely /data/subject1/surf/lh.pial, lh.white, lh.sphere.reg, rh.pial, rh.white, rh.sphere.reg, and /data/subject1/mri/T1.nii), which is all CONN will need to allow you to run surface-level analyses.

After this conversion, when you import your structural file into CONN (e.g. the original /data/subject1/T1.nii file), CONN will recognize these associated files and will allow you to run surface-based analyses in exactly the same way that you would do if you had preprocessed your anatomical data using FreeSurfer instead of CAT12. 

Please let me know if you run into any issues
Alfonso
Originally posted by Paul Dhami: