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 > > ------------------------------------------------------------------------ > *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 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > 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. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//
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