Re: [Freesurfer] [tracula] error running trac-all -prep
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 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. 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 "AA". 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 ___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] [tracula] error running trac-all -prep
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/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'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 > "AA". > > 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 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] Antw: Re: [tracula] error running trac-all -prep
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/102485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/102485074_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/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'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 > > "AA". > > > > 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 pu02neu003:/data/physics/florian/nii> flip4fsl /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 10.5469 fslswapdim /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig.nii.gz x -y z /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /data/physics/florian/nii/102485074_20080319/dmri/dwi_orig_flip.nii.gz pu02neu003:/data/physics/florian/nii> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Antw: Re: [tracula] error running trac-all -prep
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/102485074_20080319/dmri/dwi_orig.nii.gz > > /data/physics/florian/nii/102485074_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/102485074_20080319/dmri/dwi_orig.mghdti.bvec > s > > > > > > >>/data/physics/florian/nii/102485074_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. > > > >
Re: [Freesurfer] [tracula] error running trac-all -prep
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/102485074_20080319/dmri/dwi_orig.nii.gz
> > > /data/physics/florian/nii/102485074_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/102485074_20080319/dmri/dwi_orig.mghdti.bvec
> > s
> > >
> > > >
> > >>/data/physics/florian/nii/102485074_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 ab
Re: [Freesurfer] [tracula] error running trac-all -prep
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/102485074_20080319/dmri/dwi_orig.nii.gz
> > > > /data/physics/florian/nii/102485074_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.
Re: [Freesurfer] [tracula] error running trac-all -prep
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 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 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 err
Re: [Freesurfer] [tracula] error running trac-all -prep
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 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 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 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 l
