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-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki
> <ayend...@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
>>
>>
>>
>>
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