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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