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>: > 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 >
_______________________________________________ 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.
