You should also look at the FSFAST tutorial on our wiki. What version are you using? Version 6 should not need bet.fsl. Just in case you can use this version
https://gate.nmr.mgh.harvard.edu/safelinks/greve/bet.fsl
On 05/11/2017 12:50 PM, Brad Matushewski wrote:
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?
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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
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