Dear Stefano,
> I believe so. This was the first question I asked myself when I got the error message. To verify that I was using the most recent version of FSL, I deleted my old FSL, downloaded the most recent version, and performed a full install of the software. I then went to the website and downloaded/installed the most recent patch - fsl-centos5_64-patch-5.0.2.1_from_5.0.1.tar.gz. I verified that when I call FSL, this is the directory that's used with the "which fsl" command. The license files, etc, say I have FSL 4.1. Do you know what else I can do to check that I'm using the correct software?
it sounds like you have done what you can to ensure you have the latest version. Can I please ask you to re-run it with the --very_verbose switch so we can get a better idea when in the process the crash occurs?
Jesper
>
>
> Stefano Marenco, MD
> NIMH/CBDB
> 10 Center Drive, Bldg 10 room 3C103
> Bethesda MD 20892
> Tel 301 435-8964
> Fax 301 480-7795
> Email: [log in to unmask]
>
>
> -----Original Message-----
> From: Jesper Andersson [mailto:[log in to unmask]]
> Sent: Wednesday, February 13, 2013 3:40 AM
> To: [log in to unmask]
> Subject: Re: [FSL] eddy crash: NEWMAT::IndexException
>
> Hi Stefano,
>
>> I tried running eddy in the latest FSL version with this command line:
>>
>> eddy --imain=allRawData.nii.gz --mask=nodif_brain_mask.nii --acqp=my_acq_param_allData.txt --index=allData_index.txt --bvecs=bvecs_allData --bvals=bvals_allData --topup=my_topup_results --out=eddy_wTopup_out
>>
>> and got this error message.
>>
>> terminate called after throwing an instance of 'NEWMAT::IndexException'
>> Abort
>>
>> I was able to use all these same files to run eddy and then applytopup consecutively. So, I think the files are fine.
>
> can you please let me know which version you are running? This sounds like a problem that we had for the first release of eddy, but which has since been fixed.
>
> Jesper
>
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