Dear CoNN experts,

I have a CONN batch script (attached) that successfully processes my rs-fMRI files  from a simple folder structure (subjectXXX/anat/mprage.nii and subjectXXX/func/lfo.nii). The script uses the standard conn pipeline in volumetric MNI space.

Additionally, I have run recon-all in FreeSurfer in the T1-MRI image from the same subjects. Now I would like to run the CoNN pipeline but only considering within-cortex connectivity measures, i.e. a vertexwise surface CONN analysis. Having the standard freesurfer folder structure (e.g. subjectXXX/mri/, subjectXXX/surf, etc), how should I change the batch script to perform an intracortical surface-based analysis?

As far as I understand, CoNN will project the volumetric functional data within the anatomical cortical surface (mri_vol2surf –projfrac 0.5?) and then perform the connectivity computations only in the intracortical vertices. This allows a surface-based smoothing that is no longer isotropic and therefore can be higher (i.e. 10mm or 15mm). Could you also please guide me on how to introduce this surface based smoothing in the batch_script?

I have read similar posts in the forum regarding this topic, but my particular unsolved issue is regarding the batch script and required directory structure for it to work.

Thanks a lot in advance!!