Hi Markus,

Thanks, i did install fsl and when i type fslmaths it gives me the help for that command.

Any other suggestions?

Eiran

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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

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>:

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

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