Hello Anastasia,
I have been trying to run through the tutorial with one of the subjects from the tutorial(elmo.2008) to familiarize myself with Tracula. The preprocessing step seems to have been completed without any errors (Log file attached).However, when I proceed with the ball and stick model fit step, I get the following error
bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu 12.04 with FSL 5.0.9.
In an earlier post where the same error was encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html) you recommended running bedpostx directly.
Would this impact the results or run time in any way? and is there something I can do to fix this error if it is likely to take much longer?
Thanks!
-Prad
Hi Prad - What will affect the speed is whether you run it locally on your computer (in which case it'll process one slice after the other) or on a cluster (in which case all the slices will be processed in parallel on different nodes of the cluster). This is the case regardless of the version that you use.
Best,
a.y
On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
Hello Anastasia,
I have been trying to run through the tutorial with one of the subjects from the tutorial(elmo.2008) to familiarize myself with Tracula. The preprocessing step seems to have been completed without any errors (Log file attached).However, when I proceed with the ball and stick model fit step, I get the following error
bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu 12.04 with FSL 5.0.9.
In an earlier post where the same error was encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html) you recommended running bedpostx directly.
Would this impact the results or run time in any way? and is there something I can do to fix this error if it is likely to take much longer?
Thanks!
-Prad
Hi Anastasia,
Thank you for clarifying that. I have a follow up question.
To avoid this error while running the ball and stick model fit( Syntax error: "(" unexpected), I ran it locally using "bedpostx $path_to_dmri".
The results of the overall path statistics differ from those in the tutorial. I've attached my results for the left ILF (pathstats.overall_redone.txt) and the tutorial results (pathstats.overall_original.txt)
Is this difference due to running them on different machines or is because I had to run the bedpostx command directly ?
Thanks! -Prad _______________________________
_________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Monday, March 7, 2016 10:19 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula bedpostx error
Hi Prad - What will affect the speed is whether you run it locally on your computer (in which case it'll process one slice after the other) or on a cluster (in which case all the slices will be processed in parallel on different nodes of the cluster). This is the case regardless of the version that you use.
Best,
a.y
On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
Hello Anastasia,
I have been trying to run through the tutorial with one of the subjects from the tutorial(elmo.2008) to familiarize myself with Tracula. The preprocessing step seems to have been completed without any errors (Log file attached).However, when I proceed with the ball and stick model fit step, I get the following error
bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu 12.04 with FSL 5.0.9.
In an earlier post where the same error was encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html) you recommended running bedpostx directly.
Would this impact the results or run time in any way? and is there something I can do to fix this error if it is likely to take much longer?
Thanks!
-Prad
Hi Prad - I'm guessing the tutorial was generated with an earlier version of bedpostx, tracula, or a combination of both. So I wouldn't expect to find the exact same values. As long as things run and the files are generated, it looks like you're fine.
Best,
a.y
On Mon, 7 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
Hi Anastasia,
Thank you for clarifying that. I have a follow up question.
To avoid this error while running the ball and stick model fit( Syntax error: "(" unexpected), I ran it locally using "bedpostx $path_to_dmri".
The results of the overall path statistics differ from those in the tutorial. I've attached my results for the left ILF (pathstats.overall_redone.txt) and the tutorial results (pathstats.overall_original.txt)
Is this difference due to running them on different machines or is because I had to run the bedpostx command directly ?
Thanks! -Prad _______________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Sent: Monday, March 7, 2016 10:19 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula bedpostx error
Hi Prad - What will affect the speed is whether you run it locally on your computer (in which case it'll process one slice after the other) or on a cluster (in which case all the slices will be processed in parallel on different nodes of the cluster). This is the case regardless of the version that you use.
Best,
a.y
On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote:
Hello Anastasia,
I have been trying to run through the tutorial with one of the subjects from the tutorial(elmo.2008) to familiarize myself with Tracula. The preprocessing step seems to have been completed without any errors (Log file attached).However, when I proceed with the ball and stick model fit step, I get the following error
bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu 12.04 with FSL 5.0.9.
In an earlier post where the same error was encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html) you recommended running bedpostx directly.
Would this impact the results or run time in any way? and is there something I can do to fix this error if it is likely to take much longer?
Thanks!
-Prad
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Bharadwaj, Pradyumna - (prad)