Hi Anastasia,

Yes, i am running this on ubuntu 12.04.

Sincerely,
Florian

>>> Anastasia Yendiki  20.08.13 17.38 Uhr >>>

Hi Florian - Are you running this on an ubuntu system by any chance?

a.y

On Tue, 20 Aug 2013, Borsodi Florian wrote:

> Hi Anastasia,
> 
> Thank you for your help.
> I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the 
> command "xfmrot" changed the dots back to
> commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 
> and reran trac-all. After changing the
> system language everything was genereted correctly and trac-all -prep ran 
> without any errors.
> I'm so glad. 
> 
> Then, I started the next step "trac-all -bedp" and got a syntax error 
> "/usr/local/freesurfer/bin/bedpostx_mgh: 131:
> /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I 
> also attached the the logfile. I was reading
> about this error in the mail archive. Would I have to run "bedpostx" outside 
> of tracula ?
> 
> Sincerely,
> Florian
> 
> >>> Anastasia Yendiki  19.08.13 17.54 Uhr >>>
> 
> Hi Florian - Can you please change the decimal commas to points and try
> again?
> 
> a.y
> 
> On Mon, 19 Aug 2013, Borsodi Florian wrote:
> 
> > Hi Anastasia,
> >
> > Here are the bvec and bval files you asked me about.
> >
> > Sincerely,
> > Florian
> >
> > >>> Anastasia Yendiki  18.08.13 22.52 Uhr >>>
> >
> > Hi Florian - Can you please also attach the bvecs/bvals files from the
> > dmri directory?
> >
> > Thanks,
> > a.y
> >
> > On Sun, 18 Aug 2013, Borsodi Florian wrote:
> >
> > > 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  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  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  02.08.13 0.41 Uhr
> > > >>>
> > > > >
> > > > > Hi Florian - Do these files exist?
> > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec
> > > s
> > > >
> > > > >
> > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval
> > > s
> > > >
> > > > >
> > > > >
> > > > > 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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> > >
> > >
> >
> >
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