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 > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, April 01, 2014 7:16 PM > To: 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 >> 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 > > > 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 > > -- 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
