Hi all,
sorry for reviving this super old thread, but it came up here as well
with Freesurfer 6.0.0.
> 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
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
Hi Anastasia,
I checked the dmri.bedpostx directory.
Unless nodif_brain, all files are there.
Sincerely,
Florian
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
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
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
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
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
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.
Hi Florian - Do these files exist?
/data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.mghdti.bvecs
/data/physics/florian/nii/102485074_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 may have to transpose the bval and bvec files.
On 07/29/2013 11:17 AM, 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.
Hello,
Thank you for your quick answer.
I already run tracula with the transposed bvec and bval files but i keep
getting the same kind of error.
With kind regards,
Florian Borsodi
Chris Watson 29.07.13 19.12 Uhr
You may have to transpose the bval and bvec
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