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? > > Logo > > 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
