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 <ayend...@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 <ayend...@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 <ayend...@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 <ayend...@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 <ayend...@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 <ayend...@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.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
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > > The information in this e-mail is intended only for the person to
> > > > > > whom
> > > > it
> > > > > is
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> > > > > > the
> > > > > > e-mail
> > > > > > contains patient information, please contact the Partners Compliance
> > > > > > HelpLine at
> > > > > > http://www.partners.org/complianceline . If the e-mail was sent to
> > > > > > you
> > > > in
> > > > > > error
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> > > > > >
> > > > > >
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