Thanks Doug,
I notice that on my Mac build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
...I don't have fslmaths.fsl neither. There are only
$ which $FREESURFER_HOME/bin/fsl*
/Applications/freesurfer/bin/fsl_label2voxel /Applications/freesurfer/bin/fsl_rigid_register /Applications/freesurfer/bin/fsl_sub_mgh /Applications/freesurfer/bin/fslregister
$ which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl /Applications/freesurfer/bin/fscalc.fsl /Applications/freesurfer/bin/mri_motion_correct.fsl
(I never executed the above mentioned process of Eiran thoug...)
Best, Markus
2014-04-01 18:36 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
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-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ greve@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
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