Hi Lizanne,
Changing FSLDIR in that way was my first guess as well. I think you could take this one step further and make a directory in your home folder that contains the first models in first/ and the template in standard/. It’s not pretty, but if you then point FSLDIR to that directory, I think that should do the trick.
Best,
Eelke
> On 10 Mar 2016, at 06:47, Schweren, Lizanne <[log in to unmask]> wrote:
>
> 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
>
> ________________________________________
> 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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