Hello again,

Somehow I figured out the error I had related to *.config. Now I am able to run successfully all the 8 steps for 1 subject. I can see all the files generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz, sig.nii.gz etc.

But when I try to display any of these files using FreeView (after overlaying over inflated surface), it doesn't display anything and gives me error "freadFloat: fread failed".

I would really appreciate any suggestions how can I display functional connectivity maps?

Thanks,

On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja <mj70481@gmail.com> wrote:

Hello everyone,

I am following this page to process fMRI data:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

I am able to run until step-3 but at step 4, I am not sure what should be directory to run this command. If I run the command in SUBJECTS_DIR directory, it runs for a second and creates a mean*.config file. But next step 5 requires *.config file to run, not the mean*.config

Just a quick background:
I preprocessed all subjects structural data using recon-all and the processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder after preprocessing functional data (after running step-3) is also in SUBJECTS_DIR path.

Any help would be greatly appreciated.

MJ