Dear Doug,

I have Bold fMRI data (6 minutes of acquisition which is equal to 180 volume for every run). The total number for images is 140 (50 controls and 90 patients). I plan to use FSFAST (FS V6.0) to study:

1. The difference between the groups in global functional connectivity

2. Seed-based functional connectivity analysis depending on an ROI  for a difference in a voxel-wise analysis between PET images for the same subjects.

My questions are:

1. In this data set I have only one run for every subject. I am wondering if FSFAST  can analyze fMRI data (one run per subject). 

2. FSFAST depends on  the recons, meaning it depends on the ROIs in wmparc, aseg and apare+aseg atlases. Can FSFAST accept an external ROI for seed based functional connectivity analysis?

I highly appreciate your advice

John