Hi Anastasia,

Thanks for your help. I renamed the directories and reran trac-all. It worked for the moment.
However, then I got another error: "bvecs and bvals don't have the same number of entries."
I don't know why, because they actually have the same number of entries.

I attached the logfile so that you may see what is going on. The error occours at line 1463.

Thank you in advance for your help.

Sincerely,
Florian


>>> Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> 15.08.13 18.01 Uhr >>>

Hi Florian - I see what's going on. Can you please rename the directory
/data/physics/florian/nii into something that doesn't include "nii", and
rerun? Because "nii" is a file extension, this confuses some of the
scripts.

Thanks,
a.y

On Thu, 15 Aug 2013, Borsodi Florian wrote:

> Hi Anastasia
>
> I ran the command you sent me and it runs without any errors.
> I also attached the command line for you.
>
> Furthermore i ran data with 12 diffusion directions and i keep getting the
> same kind of problems.
>
> sincerely
> Florian
>
> >>> Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> 02.08.13 19.59 Uhr >>>
>
> Hi Florian - Can you please run this command directly on the command line
> and see if there are any errors?
>
> flip4fsl
> /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz
> /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz
>
> Thanks,
> a.y
>
> On Fri, 2 Aug 2013, Borsodi Florian wrote:
>
> > Hi Anastasia
> >
> > Thank you for your answer.
> >
> > Yes, those files exist.
> > I also extracted the bvec an bval files with anotther software then
> dcm2nii
> > and i keep getting the same kind of error.
> > Also, about the 6 diffusion direction, those data i sent you, are just
> > testdata for running tracula.
> >
> > sincerely
> > Florian
> >
> > >>> Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> 02.08.13 0.41 Uhr >>>
> >
> > Hi Florian - Do these files exist?
> >/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvecs
>
> >
> >/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvals
>
> >
> >
> > The format of the bvecs and bvals that you sent seems fine, but (and this
> > has nothing to do with the error you're getting) I have to warn you that
> > you may not be able to get good results running probabilistic tractography
> > on this data. It looks like you're acquiring the same 6 diffusion
> > directions, repeated 8 times. Six directions is the absolute minimum for
> > reconstructing the tensor model, but will probably not be sufficient for
> > the crossing fiber model that bedpostx reconstructs (and is used by
> > tracula). Your scan time is better spent acquiring 48 different
> > directions, rather than the same 6 directions 8 times.
> >
> > a.y
> >
> > On Mon, 29 Jul 2013, Borsodi Florian wrote:
> >
> > > Hello,
> > >
> > > I have been trying to run tracula on my data and i keep getting the same
> > > kind of error repeatedly.
> > > For my imput I am using dicoms from a Siemens scanner with a stadard
> > > diffusion protocol. However, tracula cannot read the bvec and bval data
> > out
> > > of the dicom header. Therefore, I implemented bvec and bval files into
> the
> > > config file.
> > > After doing so, I got the error which says that tracula cannot find the
> > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files.
> > > I have tried many options, but still cannot find a solution.
> > > I am hoping to get some troubleshooting help.
> > >
> > > I have atteched my log- and config- files, as well as my bvec and bval
> > > files.
> > > To uphold patient confidentiality, I have encode the name patient's data
> > as
> > > "AAAAAA".
> > >
> > > I believe the problems are the bvec and bval files or their structures.
> > The
> > > log-file lete me assume this, especially the lines 202 - 205, 264 - 268
> > and
> > > 1480 - 1484.
> > >
> > > Thank you in advance for your help, and your speedy response.
> > >
> > > With kind regards,
> > >
> > > Florian Borsodi
> > > Department of Neurology
> > > Medical University of Graz
> > >
> > >
> >
> >
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