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.
