Hi, Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that can be used in FSL, I think it is not necessary to have matlab working for FSL to work.
There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab). The error message tells you that freesurfer doesn't find fslmaths in the fsl directory... Can you post here the exact result of more $FSL_DIR/etc/fslversion and echo $FSLDIR #(without the _ between FSL and DIR!) Best, Markus 2014-04-01 12:13 GMT+02:00 Eiran Harel <eir...@tlvmc.gov.il>: > Hi Markus, > Thanks, it's is in FSL_DIR /usr/local/fsl. > Is MATLAB necessary to run FSL? > EIran > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ > markus.gschw...@gmail.com] > *Sent:* Tuesday, April 01, 2014 12:55 PM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] preprocessing question > > Hi, > what does it say when you type > which fsl > which fslmath > ? > > It mud be the same thing as > FSL_DIR /usr/local/fsl > > It is possible that the FSL_DIR specified in the freesurfersetup is not > the good one... > > Best, > Markus > > > 2014-04-01 10:25 GMT+02:00 Eiran Harel <eir...@tlvmc.gov.il>: > >> Hi Markus, >> Thanks, i did install fsl and when i type fslmaths it gives me the help >> for that command. >> Any other suggestions? >> Eiran >> ------------------------------ >> >> >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ >> markus.gschw...@gmail.com] >> *Sent:* Tuesday, April 01, 2014 11:11 AM >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] preprocessing question >> >> Hi! >> >> Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) >> What happens if you type in your terminal >> fslmaths >> ? >> >> Best, >> Markus >> 2014-04-01 9:59 GMT+02:00 Eiran Harel <eir...@tlvmc.gov.il>: >> >>> 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 >>> 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 >> 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 > 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. > >
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