Re: [Freesurfer] [tracula] error running trac-all -prep - Freesurfer

22 Aug 2013


      Hi Anastasia,
I checked the dmri.bedpostx directory.
Unless "nodif_brain", all files are there.
Sincerely,
Florian
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Anastasia Yendiki  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:
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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
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Anastasia Yendiki  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:
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Hi Anastasia,
Yes, i am running this on ubuntu 12.04.
Sincerely,
Florian
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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:
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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
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commas. So, I changed our system language from de_AUT.UTF-8 to
en_US.UTF-8 and reran trac-all. After changing the
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system language everything was genereted correctly and trac-all -prep
ran without any errors.
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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:
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/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. "
I also attached the the logfile. I was
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reading
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about this error in the mail archive. Would I have to run "bedpostx"
outside of tracula ?
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Sincerely,
Florian
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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:
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Hi Anastasia,
Here are the bvec and bval files you asked me about.
Sincerely,
Florian
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> Anastasia Yendiki  18.08.13 22.52
Uhr >>>
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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:
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Hi Anastasia,
Thanks for your help. I renamed the directories and reran trac-all.
It
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worked for the moment.
However, then I got another error: "bvecs and bvals don't have the
same
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number of entries."
I don't know why, because they actually have the same number of
entries.
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I attached the logfile so that you may see what is going on. The
error
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occours at line 1463.
Thank you in advance for your help.
Sincerely,
Florian
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>> Anastasia Yendiki  15.08.13 18.01
Uhr >>>
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Hi Florian - I see what's going on. Can you please rename the
directory
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/data/physics/florian/nii into something that doesn't include "nii",
and
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rerun? Because "nii" is a file extension, this confuses some of the
scripts.
Thanks,
a.y
On Thu, 15 Aug 2013, Borsodi Florian wrote:
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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
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same kind of problems.
sincerely
Florian
>>> Anastasia Yendiki  02.08.13
19.59 Uhr
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Hi Florian - Can you please run this command directly on the
command line
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and see if there are any errors?
flip4fsl
/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz
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/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz
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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
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dcm2nii
> and i keep getting the same kind of error.
> Also, about the 6 diffusion direction, those data i sent you,
are just
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> testdata for running tracula.
>
> sincerely
> Florian
>
> >>> Anastasia Yendiki  02.08.13
0.41 Uhr
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>>
>
> Hi Florian - Do these files exist?
>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bve
c
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s
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>
>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bva
l
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s
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>
>
> The format of the bvecs and bvals that you sent seems fine, but
(and
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this
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> has nothing to do with the error you're getting) I have to warn
you that
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> you may not be able to get good results running probabilistic
tractography
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> on this data. It looks like you're acquiring the same 6
diffusion
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> directions, repeated 8 times. Six directions is the absolute
minimum for
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> reconstructing the tensor model, but will probably not be
sufficient for
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> the crossing fiber model that bedpostx reconstructs (and is used
by
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> 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
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same
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> > kind of error repeatedly.
> > For my imput I am using dicoms from a Siemens scanner with a
stadard
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> > diffusion protocol. However, tracula cannot read the bvec and
bval
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data
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> out
> > of the dicom header. Therefore, I implemented bvec and bval
files into
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the
> > config file.
> > After doing so, I got the error which says that tracula cannot
find
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the
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> > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals"
files.
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> > 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
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> > files.
> > To uphold patient confidentiality, I have encode the name
patient's
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data
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> as
> > "AAAAAA".
> >
> > I believe the problems are the bvec and bval files or their
structures.
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> The
> > log-file lete me assume this, especially the lines 202 - 205,
264 -
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268
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> 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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