Hi,
Can you show me the exact commands you used to
copy and run first_utils? Also, tell me what directory
each was run from. I suspect it is just a question of
the file not being in the right directory.
All the best,
Mark
On 17 Nov 2010, at 17:50, LEYRE ZUBIAURRE ELORZA wrote:
> Thanks so much Mark,
>
> I have copied the file R_Caud.bmv and the same problem is still there!
> Any idea??
>
> Thanks again,
>
> Leire
> > Date: Wed, 17 Nov 2010 17:31:25 +0000
> > From: [log in to unmask]
> > Subject: Re: [FSL] Vertex: bvars error?
> > To: [log in to unmask]
> >
> > Hi,
> >
> > OK, the problem is that the bvars file is missing the path
> > to the appropriate model file. I don't know why. Was it
> > created with an old version of FSL?
> >
> > Anyway, you can get around this problem by just copying
> > the file $FSLDIR/data/first/models_336_bin/intref_thal/R_Caud.bmv
> > to the directory where you are running first_utils. This will
> > then let you do the analysis without problems - at least it
> > fixed it at my end. For other structures you'd have to
> > copy (or link - which would be even better as it wouldn't
> > waste space) the relevant file from the $FSLDIR/data/first/...
> >
> > All the best,
> > Mark
> >
> >
> >
> > On 17 Nov 2010, at 13:51, Mark Jenkinson wrote:
> >
> > > Hi,
> > >
> > > Can you upload your bval and mat file to:
> > > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> > > and send us the reference number.
> > >
> > > This should allow us to figure out the problem.
> > >
> > > All the best,
> > > Mark
> > >
> > > On 17 Nov 2010, at 12:55, Leire Zubiaurre-Elorza wrote:
> > >
> > >> Hi fslexperts,
> > >>
> > >> I have a problem with vertex analyses. When I run this command I get the following error :
> > >>
> > >> first_utils --vertexAnalysis --usebvars -i PLRtoPVLAll.bvars -d CAUDATE.mat -o LeireRCAUDATE --useReconNative --useRigidAlign -v
> > >> read model
> > >> Cannot open file.
> > >> Cannot open file.
> > >>
> > >> I guess I have a problem with bvars files but when I read them they are allright!!!
> > >>
> > >> Could anyone help me?
> > >>
> > >> Many thanks,
> > >> Leire
> > >>
> > >
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