Hi, I seem to have even less files: Eran-Harels-MacBook-Pro:/applications/freesurfer] eiran% which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl [Eran-Harels-MacBook-Pro:/applications/freesurfer] eiran% which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel
Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Thursday, April 03, 2014 3:43 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi Eiran and Doug, I do not have bet.fsl neither (c.f. previous mail with the list of what I had). It seems that there is quite some more missing in the mac build... This is what I find on my ubuntu installation freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 $ ls $FREESURFER_HOME/bin/*.fsl /usr/local/freesurfer/bin/bet.fsl /usr/local/freesurfer/bin/epidewarp.fsl /usr/local/freesurfer/bin/flirt.fsl /usr/local/freesurfer/bin/fscalc.fsl /usr/local/freesurfer/bin/fslmaths.fsl /usr/local/freesurfer/bin/fslorient.fsl /usr/local/freesurfer/bin/fslswapdim.fsl /usr/local/freesurfer/bin/mri_motion_correct.fsl /usr/local/freesurfer/bin/slicetimer.fsl $ ls $FREESURFER_HOME/bin/fsl* /usr/local/freesurfer/bin/fsl_label2voxel /usr/local/freesurfer/bin/fslmaths.fsl /usr/local/freesurfer/bin/fslorient.fsl /usr/local/freesurfer/bin/fslregister /usr/local/freesurfer/bin/fsl_rigid_register /usr/local/freesurfer/bin/fsl_sub_mgh /usr/local/freesurfer/bin/fslswapdim.fsl And this is what I have on my Mac OSX installation (freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0) $ 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 Best, Markus 2014-04-03 13:35 GMT+02:00 Eiran Harel <eir...@tlvmc.gov.il<mailto:eir...@tlvmc.gov.il>>: 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<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: Wednesday, April 02, 2014 5:21 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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<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: Wednesday, April 02, 2014 12:41 AM > To: freesurfer@nmr.mgh.harvard.edu<mailto: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> >> <mailto: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> >> >> <mailto: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> >> >> <mailto: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> >> <mailto: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> >> >> <mailto: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> >> >> <mailto: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> >> <mailto:gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> >> > Phone Number: 617-724-2358<tel:617-724-2358> >> <tel:617-724-2358<tel:617-724-2358>> >> > Fax: 617-726-7422<tel:617-726-7422> >> <tel:617-726-7422<tel:617-726-7422>> >> > >> > Bugs: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://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> >> <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> >> >> <mailto: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> >> >> <mailto: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> >> <mailto:gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358<tel:617-724-2358> >> <tel:617-724-2358<tel:617-724-2358>> >> Fax: 617-726-7422<tel:617-726-7422> <tel:617-726-7422<tel:617-726-7422>> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://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> >> <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> >> <mailto: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<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<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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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