Hi Doug, I changed the file permissions to be executable and it passed this stage. It then gets stuck when looking for bet.fsl:
# ---------- Using FSL's BET to Extract Brain------------------ # /applications/freesurfer/BSMT_project/bsmt103/bold bet.fsl /tmp/mkbrainmask_76128/in.nii /tmp/mkbrainmask_76128/brain -m -f 0.1 bet.fsl: Command not found. ERROR: bet failed Was there something wrong in the insatallation that it is missing those files? Thanks! Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question a couple of thiings to check: make sure it is exectuable and make sure that you rehash your path. Make sure that if you type fslmaths.fsl that it runs something On 04/02/2014 03:23 AM, Eiran Harel wrote: > Thanks Doug, i downloaded it and now the file exists: > > $FREESURFER_HOME/bin/fslmaths.fsl > > Unfortuantely it is still not running and gives the same error when running > preproc-sess: > > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 > -nerode 0 > ERROR: cannot find either fslmaths for avwmaths > > How can i proceed? > Thanks, > Eiran > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, April 02, 2014 12:41 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] preprocessing question > > thanks, it must be something in our distribution script affecting mac > > On 04/01/2014 05:13 PM, Markus Gschwind wrote: >> Thanks Doug, >> >> I notice that on my Mac >> build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 >> >> ...I don't have fslmaths.fsl neither. There are only >> >> $ which $FREESURFER_HOME/bin/fsl* >> /Applications/freesurfer/bin/fsl_label2voxel >> /Applications/freesurfer/bin/fsl_rigid_register >> /Applications/freesurfer/bin/fsl_sub_mgh >> /Applications/freesurfer/bin/fslregister >> >> $ which $FREESURFER_HOME/bin/*.fsl >> /Applications/freesurfer/bin/epidewarp.fsl >> /Applications/freesurfer/bin/fscalc.fsl >> /Applications/freesurfer/bin/mri_motion_correct.fsl >> >> (I never executed the above mentioned process of Eiran thoug...) >> >> Best, >> Markus >> >> >> >> >> >> 2014-04-01 18:36 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>: >> >> That is weird. You can get a copy from here >> >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac >> >> copy it to >> >> $FREESURFER_HOME/bin/fslmaths.fsl >> >> >> On 04/01/2014 12:25 PM, Eiran Harel wrote: >> > Hi Doug, >> > No, it does not exist. >> > What should i do? >> > Thanks, >> > Eiran >> > ________________________________________ >> > From: freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> [freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of >> Douglas N Greve [gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>] >> > Sent: Tuesday, April 01, 2014 7:16 PM >> > To: freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> > Subject: Re: [Freesurfer] preprocessing question >> > >> > does $FREESURFER_HOME/bin/fslmaths.fsl exist? >> > >> > On 04/01/2014 03:59 AM, Eiran Harel wrote: >> >> Dear freesurfers, >> >> I have installed freesurfer and fsl on my Mac: >> >> * >> >> * >> >> *-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 >> --------* >> >> *Setting up environment for FreeSurfer/FS-FAST (and FSL)* >> >> *FREESURFER_HOME /Applications/freesurfer* >> >> *FSFAST_HOME /Applications/freesurfer/fsfast* >> >> *FSF_OUTPUT_FORMAT nii.gz* >> >> *SUBJECTS_DIR /Applications/freesurfer/subjects* >> >> *MNI_DIR /Applications/freesurfer/mni* >> >> *FSL_DIR /usr/local/fsl* >> >> >> >> I am trying to run Preproc-sess command: >> >> >> >> *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm >> 5 -fsd >> >> bold -stc odd -per-run -force* >> >> >> >> and get this error: >> >> >> >> *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 >> >> -ndil 1 -nerode 0* >> >> *ERROR: cannot find either fslmaths for avwmaths* >> >> * >> >> * >> >> Any suggestions? >> >> Thanks! >> >> Eiran >> >> >> >> >> >> >> >> >> >> <http://www.tasmc.org.il/be-well/Pages/default.aspx> >> >> <https://www.facebook.com/ichilov.medical> >> >> <http://twitter.com/tasmc1> <http://www.youtube.com/tasmc1> >> >> <http://www.tasmc.org.il/sites/en/Pages/default.aspx> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 <tel:617-724-2358> >> > Fax: 617-726-7422 <tel:617-726-7422> >> > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://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 >> <mailto: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. >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://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 <mailto: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 > -- > 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 > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
