Hello Freesurfer crowd.  I am working on try to get my first fMRI scan working.  I have come a long ways in terms of setting things up but have reached a road block that I have unable to get past.

I have been following along the slides from the power point presentation “FSFAST Part 2”.  I got as far as slide #32: Preprocessing Command”.  Specifically, I entered the following command:

preproc-sess

-sf sessids

-surface fsaverage lhrh

-mni305

-fwhm 5

-pre-run

Things started to happen but finished rather quickly.  I looked through the text output and it would appear that it cannot find the bet.fsl tools(?). 

I looked at the directory to where it was looking at it IS in there (i.e. /usr/local/freesurfer/bin/bet.fsl)

I also labelled things exactly as outlined: (i.e. /usr/local/freesurfer/subjects/handedness/project/Sess01)

I have attached a couple text files from the output logs.

What can I try next?

Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.

Laboratory for Brain & Heart Health
School of Kinesiology
Western University
Room 402, Arthur & Sonia Labatt Health Sciences Building
London, ON, Canada, N6A 5B9
Tel: (519) 661-2111 x 89066
Fax: (519) 850-2447