Conducting resting state fMRI with subject-specific downsampled cortex

Dear NeuroStars community,

I am hoping to conduct an EEG source localization and resting state fMRI data analysis in the same space, thus assuming I would use the same subject specific cortex.

The problem I am running into is that the Brainstorm software, which I am using for my source localization, imports a subject’s Freesurfer folder and than produces a 15002 vertices downsampled cortex, which is what I would like to do my fMRI analysis with.

When Brainstorm imports the Freesurfer folder, it produces both the downsampled cortex and white matter which can then be exported as .gii files.

This is what I have done so far, mind you I am trying to do the resting state analysis with the CONN toolbox since ideally I would keep all my data in the Matlab environment.

  1. I use Freesurfer’s mri_convert to change the .gii files into .white and .pial files.
  2. To import this into CONN, I replace the original .white .pial files with the ones I’ve made from the downsampled Brainstorm files.
  3. At this point, I run into errors in CONN which I’ve appropriately posted on their board.

I’m not super familiar with f/MRI analyses, so I was hoping for any thoughts or comments as to what may be a simple way to somehow conduct an fMRI analysis on this downsampled cortex I get from Brainstorm.

Thank you very much,