Hi Anastasia,

I checked the dmri.bedpostx directory.
Unless "nodif_brain", all files are there.

Sincerely,
Florian

>>> Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> 22.08.13 15.06 Uhr >>>

Hi Florian - My guess is that everything ran fine and you don't need to
change anything else. Check that all the output files were created in the
dmri.bedpostX directory:
    http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html

a.y

On Thu, 22 Aug 2013, Borsodi Florian wrote:

> Hi Anastasia,
>
> This Ubuntu-related error is a tricky one.
> I changed the first line in those files you told me and reran trac-all. All
> three steps of trac-all ran without any errrors. I checked the FA maps and
> the MNI registration and everything looks fine.
>
> After running trac-all -bedp, the step stopped with the following line:
> "Queuing post processing stage
> /usr/local/freesurfer/bin/bedpostx_mgh: line 439: 9381 Terminated
> ${subjdir}.bedpostX/monitor."
> I think it's fine, because line 439 is the last line of the script, so it
> worked well.
> Maybe I have to change all ".sh" in the files to ".bash" to get all
> messages.
>
> Thank you so much for your big help.
> I hope I didn't cause you much trouble with my problems and questions.
>
> Sincerely,
> Florian
>
> >>> Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> 20.08.13 17.56 Uhr >>>
>
> This is an Ubuntu-related error that has surfaced recently because in
> Ubuntu /bin/sh is not a bash shell any more. To get around this, you can
> edit the first line of the scripts $FREESURFER_HOME/bin/bedpostx_mgh and
> $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace "/bin/sh" with
> "/bin/bash" on the first line of those two scripts.
>
> On Tue, 20 Aug 2013, Borsodi Florian wrote:
>
> > Hi Anastasia,
> >
> > Yes, i am running this on ubuntu 12.04.
> >
> > Sincerely,
> > Florian
> >
> > >>> Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> 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 <ayendiki@nmr.mgh.harvard.edu> 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 <ayendiki@nmr.mgh.harvard.edu> 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 <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.bve
> c
> > > > > s
> > > > > >
> > > > > > >
> > > > >>>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bva
> l
> > > > > 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
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > The information in this e-mail is intended only for the person
> to whom
> > > > > it
> > > > > > is
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> and the
> > > > > > > e-mail
> > > > > > > contains patient information, please contact the Partners
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> > > > > > >
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