Thanks, i did install fsl and when i type fslmaths it gives me the help for that command.
Any other suggestions?
Eiran
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@gmail.com]
Sent: Tuesday, April 01, 2014 11:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] preprocessing question
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 <eiranh@tlvmc.gov.il>:
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Applications/freesurferFSFAST_HOME /Applications/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Applications/freesurfer/subjectsMNI_DIR /Applications/freesurfer/mniFSL_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 0ERROR: cannot find either fslmaths for avwmaths
Any suggestions?Thanks!Eiran
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