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
