Hi Emmanuelle,
If for some reason a bvars file is missing the path data, you can modify it with a _plain_ text editor - the second line contains the path to the bmv file used. Note that it's important to only edit the second line - most of the file is binary data and should not be modified in any way. An example of the first 3 lines is given below:
****START******
this is a bvars file
/usr/local/fsl/data/first/models_317_bin/L_Hipp_bin.bmv
NumberOfSubjects 1
****END******
Kind Regards
Matthew
> Hi,
>
> I have a problem that has already been discussed in many threads, but most of the time, the final solution is not listed. When running first_utils, I get the following error:
>
> Warning: does not exist. Attempting to switch to: /usr/share/fsl/5.0
> read model
> Not a vtk file (error in line 1).
> Not a vtk file (error in line 1).
>
> - I am running un Ubuntu with the automatic download in /usr/share/fsl/5.0 instead of in /usr/local/, but FSLDIR is correctly set as such.
>
> - My bvars files (ex, Subject01/*.bvars) are also correctly pointing to /usr/share/fsl/5.0/data/first/models_336_bin/, which does contain many bmv files and three subdirectories. However I can't open the concatenated all.bvars because it is too big. The result of head -n3 all.bvars is:
> This is a bvars file
>
> NumberOfSubjects 2 (I know, 2 is not many, I was only testing, here).
>
>
> - I re-ran First recently, I haven't changed the files since, I haven't changed FSL version since.
>
> - Running with the fewest options possible produces no output: fsl5.0-first_utils -i all.bvars -o shape_analysis/test -v
> Running with bvars produces the error: fsl5.0-first_utils -i all.bvars -o shape_analysis/test -v --usebvars
>
> - I have fsl-first-data: using apt-get install fsl-first-data, the output is:
> fsl-first-data is already the newest version.
>
>
>
> What else is there to try?
>
>
> Thank you very much,
>
>
> Emmanuelle
>
>
>
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