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
The information in this e-mail is intended only for the person to whom
it
is
addressed. If you believe this e-mail was sent to you in error and 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 but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.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
addressed. If you believe this e-mail was sent to you in error and 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 but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 $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.
I believe this is only half the truth. Sure, changing the interpreter to /bin/bash fixes the issue, but underlying assumption is wrong and should be addressed with a future release of Freesurfer I think.
Using bash-syntax in a /bin/sh (posix shell) interpreted script is simply an error and should be fixed by either removing the bashism[1] (arrays in this case) or by explicitly switching to /bin/bash.
[1] http://mywiki.wooledge.org/Bashism
best regards Michael Krause
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Borsodi Florian -
Michael Krause