I'll defer to Doug/Zeke/Nick on this one Bruce On Tue, 1 Apr 2014, Eiran Harel wrote:
Thanks Markus. Doug, Bruce, any 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 4:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question
Well, Eiran, That seems all fine. Maybe Bruce or Doug can jump in and help? Sorry! Markus
2014-04-01 15:25 GMT+02:00 Eiran Harel eiranh@tlvmc.gov.il: Hi Markus, [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% more $FSL_DIR/etc/fslversion 5.0.6 [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% echo $FSLDIR /usr/local/fsl
Thanks! 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 2:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question
Hi, Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that can be used in FSL, I think it is not necessary to have matlab working for FSL to work.
There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab).
The error message tells you that freesurfer doesn't find fslmaths in the fsl directory...
Can you post here the exact result of
more $FSL_DIR/etc/fslversion
and
echo $FSLDIR #(without the _ between FSL and DIR!)
Best, Markus
2014-04-01 12:13 GMT+02:00 Eiran Harel eiranh@tlvmc.gov.il: Hi Markus, Thanks, it's is in FSL_DIR /usr/local/fsl. Is MATLAB necessary to run FSL? 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 12:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question
Hi, what does it say when you type which fsl which fslmath ?
It mud be the same thing as FSL_DIR /usr/local/fsl It is possible that the FSL_DIR specified in the freesurfersetup is not the good one…
Best, Markus
2014-04-01 10:25 GMT+02:00 Eiran Harel eiranh@tlvmc.gov.il: Hi Markus, 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
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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