Hi Peter,
Normally this is fixed by re-running concat_bvars, and I am surprised that this has not fixed your problem. However, as you've done that and it is still failing then I can see two options:
(i) edit the bvars files to change the line at the top to fix the FSL path
(ii) re-run FIRST, concat_bvars and first_utils all on the same machine
All the best,
Mark
On 28 Aug 2014, at 15:59, Peter van Ruitenbeek <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I seemed to have encountered a known problem, but which I can't overcome nonetheless.
>
> The problem is that when I run first_utils as such:
>
> first_utils --vertexAnalysis --usebvars -i con_L_Accu.bvars -d Design.mat -o Left_Accumbens/age_left_accumbens_MNI --useReconMNI --useRigidAlign -v >& Left_Accumbens/age_Left_Accumbens_MNI.txt
>
> I get the error message;
>
> Warning: does not exist. Attempting to switch to: /apps/leuven/thinking/2014a/software/FSL/5.0.4-intel-2014a/fsl
>
> read model
> Not a vtk file (error in line 1).
> Not a vtk file (error in line 1).
>
> If I understand previous posts about this problem correctly, this occurs when the concat_bvars and first_utils commands are not performed on the same system. In my case this is (partly) correct.
>
> First, I did performed all processes on the same high peformance cluster, but this produced the above error.
> Second, I tried tho perform concat_bvars and first_utils on my desktop pc; same error.
> I next changed the path to the FSL directory mentioned in the second line of the .bvars file to '/usr/share/fsl/5.0/data/first/models_336_bin/L_Accu_bin.bmv' (which is stated in the rror) and used concat_bvars, and subsequently first_utils; same error.
> Finally, tried changing the path to '/usr/share/fsl/5.0', concat_bvars, first_utils; same thing again.
>
> I have now run out of ideas. Does anyone have a possible solution?
>
> Thanks in advance!
>
> Best regards,
>
> Peter
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