Dear Eelke,
Thank you for your response. We have indeed moved our FSL installation, and FIRST had run before that move.
Unfortunately we have not been able to solve the problem. I'm working with a very large dataset located on a server managed by others, hence I can't create links in /opt/. Rerunning everything won't be feasible in the short term either. We've also tried changing $FSLDIR to /opt/fsl/5.0.9/data/, which did result in FIRST_UTILS finding the .bmv files (in the fall-back loop), but then it could not locate the standard brain anymore (ERROR: Could not open image /opt/fsl/5.0.9/data//data/standard/MNI152_T1_1mm).
Do you have any other ideas? Thanks again Eelke, your help is very much appreciated!
All my best,
Lizanne
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Eelke Visser [[log in to unmask]]
Sent: Monday, March 07, 2016 5:21 AM
To: [log in to unmask]
Subject: Re: [FSL] first_utils code error
Hi Lizanne,
Normally first_utils tries to load the model file from the location where it was when you ran first. Have you reinstalled FSL or moved to a different machine in between those steps?
The ‘Attempting to switch’ message means that it couldn’t find the file and is having another go at finding it using a fallback mechanism (which isn’t very reliable). The easiest fix is probably to rerun first, or if this is your own machine, to create a link at /opt/fsl to /opt/fsl/5.0.9.
Hope that helps,
Eelke
> On 7 Mar 2016, at 12:30, Schweren, Lizanne <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> I'm experiencing a problem with first_utils. It seems to me that there may be an erroneous reference in the fsl code:
>
> > first_utils --vertexAnalysis --usebvars -i $hemi.$roi.bvars -d design.mat -o $hemi.$roi --useReconNative --useRigidAlign --useScale
>
>
>
> Warning: /opt/fsl/data/first/models_336_bin/intref_thal/L_Caud.bmv does not exist. Attempting to switch to: /opt/fsl/5.0.9first/models_336_bin/intref_thal/L_Caud.bmv
>
> Cannot open file.
>
> Cannot open file.
>
> Warning: /opt/fsl/data/first/models_336_bin/intref_thal/R_Caud.bmv does not exist. Attempting to switch to: /opt/fsl/5.0.9first/models_336_bin/intref_thal/R_Caud.bmv
>
> Cannot open file.
>
> Cannot open file.
>
>
>
> The .bmv files do exist in my FSL folder (version 5.0.9) folder, but the word '/data/' is missing in the path first_utils is trying to use. The .bmv files are in /opt/fsl/5.0.9/data/first/models_336_bin/intref_thal/R_Caud.bmv].
>
>
>
> I hope you can help me. Thank you very much again!
>
> All my best,
> Lizanne
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