I imagine this issue has been solved by now but just for the record I ran into a similar issue. In my case the problem turned out to be that FSL installs by default in /usr/local/fsl/bin but FSFAST was looking for it in /bin

This was on OS X 10.8.2 with FSL Installer - Version 2.0.10 and Freesurfer 5.2.0.

Is there some way to set up Freesurfer so it'll look in the correct directory? For now I'm copying the critical files to /bin but am hoping there is a better solution.

Thanks!

Joe

It could be. It uses fsl only to create a mask of the brain, so it probably does not need a full fsl install, but it might need more than you have. doug

On 3/25/12 7:05 AM, Kiley Seymour wrote: Hi again, Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed?

Thanks

K

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*From:* Kiley Seymour kiley_seym...@yahoo.com.au *To:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, 23 March 2012 3:04 PM *Subject:* mkbrainmask-sess

Dear Freesurfers,

I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). I was unable to run this command as freesurfer could not find/media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). Any help with this would be much appreciated.

Thanks

Kiley

FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d~/data1/RETINOTOPY

/media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o/tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostname FreeSurfer machine i686 user virtualuser

input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0

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