Hi Laura,
Yes please upload your data onto our server. It may help..
Also, I've just noticed that the last error you got from bedpostx
mentions line219 of the code. This suggests to me that you have been
using the released version of bedpostx, not the one I have sent you?
Can you please double-check that you've been using the version I sent
you?
Cheers,
Saad.
On 20 Aug 2009, at 18:20, Danielian, Laura (NIH/NINDS) [E] wrote:
> Hi Saad,
>
> Do you believe it's a problem with my system, or with the data?
> I've run bedpostx before (last year) on similar data sets without
> error, maybe on a previous version of FSL. Would it help if I
> shared a copy of the raw data with you? Do you think the results
> from running the script are valid (i.e. Can I trust the results even
> if it doesn't produce a clean output)? I'm not sure where to go
> from here.
>
> Thanks,
> Laura
>
>
> ---------------------------------
>
> Laura Danielian
> Biomedical Engineer
> National Institutes of Health
> Building 10 CRC Room 7-5753
> Bethesda, MD 20892
> 301-496-2168
>
>
> ________________________________
> From: Saad Jbabdi <[log in to unmask]>
> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
> Date: Thu, 20 Aug 2009 12:10:36 -0400
> To: <[log in to unmask]>
> Conversation: [FSL] bedpostx error
> Subject: Re: [FSL] bedpostx error
>
> Dear Laura,
> I'm glad it "sort of" worked.
>
> Unfortunately, the bedpostx script is not really designed to give
> useful error messages.. So it is hard for me to tell you what is
> happening, since I am unable to reproduce it over here.
> The only way I can figure out for sure what is happening is if I log
> into your system and run bedpostx myself :-)
>
> Sorry for this :-(
>
> Saad.
>
>
> On 20 Aug 2009, at 14:01, Danielian, Laura (NIH/NINDS) [E] wrote:
>
>> Saad,
>> The script ran with interesting results. The terminal output lists
>> "0 slices processed" a number of times and resulted in the following
>> error:
>> /usr/local/fsl-latest/bin/bedpostx: line 219: 10929 Terminated $
>> {subjdir}.bedpostX/monitor. Also, the data_slice and
>> nodif_brain_mask_slice files are still in the original bedpost
>> directory. However, the dyads seem correct and I was able to run
>> probtrackX on the data.
>>
>> Thanks,
>> Laura
>> ---------------------------------
>>
>> Laura Danielian
>> Biomedical Engineer
>> National Institutes of Health
>> Building 10 CRC Room 7-5753
>> Bethesda, MD 20892
>> 301-496-2168
>>
>>
>> ________________________________
>> From: Saad Jbabdi <[log in to unmask]>
>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>> Date: Wed, 19 Aug 2009 09:36:34 -0400
>> To: <[log in to unmask]>
>> Conversation: [FSL] bedpostx error
>> Subject: Re: [FSL] bedpostx error
>>
>> Hi Laura,
>>
>> Are you using parallel or serial processing? (i.e. is the SGE_ROOT
>> environment variable set?).
>>
>> Can you use this script instead (on clean subject directories) and
>> tell me what happens?
>>
>> Cheers,
>> Saad.
>>
>
> --
> Saad Jbabdi
> University of Oxford, FMRIB Centre
>
> JR Hospital, Headington, OX3 9DU, UK
> +44 (0) 1865 222523 (fax 717)
> www.fmrib.ox.ac.uk/~saad
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222523 (fax 717)
www.fmrib.ox.ac.uk/~saad
