Hi,
Are you running this command on the same machine as you ran the FIRST segmentations on?
It is complaining that it cannot find the appropriate model files, which is normally due to running parts on different machines where FSLDIR is set differently. Note that you need to run the first segmentations (i.e. run_first_all) as well as concat_bvars and first_utils on the same machine (or anything with the same FSLDIR setting). If you haven't then you can edit the bvars file with a text editor and change the appropriate line (should be the second line) to change the path for your new FSLDIR location.
All the best,
Mark
On 28 Aug 2013, at 03:58, Evan Lutkenhoff <[log in to unmask]> wrote:
> Hi, I'm getting an error when trying to run a vertex analysis (first_utils --vertexAnalysis) following the tutorial for guidance. My command is:
>
> first_utils --vertexAnalysis --usebvars -i ${struct}_all.bvars -d design_matrix.mat -o shape_analysis/name_${struct} --useReconNative --useRigidAlign --debug -v
>
> The error is:
> Warning: does not exist. Attempting to switch to: /space/raid/fmri/fsl-5.0.4-centos6_64
> read model
> Not a vtk file (error in line 1).
> Not a vtk file (error in line 1).
>
> There is no output generated from the command, just the error message. Before concatenating all my bvar files, I double-checked that they were all created using the same version of FSL (as suggested by another post) and that each structure used the same model, and received no errors. I also receive the same error when using the --useReconMNI flag instead of --useReconNative. I created the design matrix using FSL's GLM gui and received no errors. In addition, all other FSL functions/commands seem to be working (it is installed on a shared OpenSuse linux cluster).
>
> Any help with this error would be greatly appreciated.
> Thanks,
> Evan Lutkenhoff
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