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
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