Dear FSL experts,
I can confirm that we have encountered similar error (SIGSEGV
segmentation violation) after upgrading from Debian 8.0 to Debian 9.0
on multiple mashines. Both PC's are high-end Intel mashines, one with
32 GB memory and the other one with 64 GB memory, so I seriously doubt
it is a low memory. We have tested a dataset which worked with
previous Debian version.
Previous version of FSL (fsl package): 5.0.9-4~nd80+1
Current version of FSL: 5.0.9-4-nd90+1
Any suggestions?
Thanks
Pavel
On 5 January 2018 at 12:52, Helen Beaumont
<[log in to unmask]> wrote:
> How much memory do you have? I got a segmentation error with eddy_openmp on
> some images, and traced it down to out-of-memory.
>
>
> On 05/01/18 11:06, Jesper Andersson wrote:
>
> Dear Veronica,
>
> I am afraid that I only confirmed your suspicion that it was a problem with
> your distribution/installation. I ran your exact commands on both the data
> sets you sent me, and the results look good (and no crashes). I am afraid it
> is little else I can do right now since I don’t have a Ubuntu system myself.
>
> Has anyone else seen the problems that Veronica describes on a Ubuntu
> installation? And more importantly has anyone found a solution?
>
> Jesper
>
>
> On 4 Jan 2018, at 17:20, VERONICA MUNOZ RAMIREZ
> <[log in to unmask]> wrote:
>
> Dear Jesper,
>
> Thank you for your reponse. The command I use for my data is the following :
>
> status=system([FSLcommand 'topup --imain=b0_PA.nii --datain=acqparams.txt
> --config=/media/veronica/DATAPART1/Donnees/DTIPark/b02b0.cnf
> --out=topup_results']);
>
> I call it from matlab; b0_PA is the result of the fslmerge of "b0_P"
> (nodif_PA) and "rb0_A" (coregistered nodif_AP). I use coregistration because
> I only have a few transverse slices.
>
> But the command doesn' work for the provided FSL test data either. For this
> I use the exact command as on the tutorial :
>
> topup --imain=AP_PA_b0 --datain=acqparams.txt --config=b02b0.cnf
> --out=topup_AP_PA_b0 --iout=topup_AP_PA_b0_iout --fout=topup_AP_PA_b0_fout
>
> I uploaded the both sets of data and commands onto the tarball.
>
> Thanks again and best regards for you too,
>
> Veronica
> ________________________________
> De: "Jesper Andersson" <[log in to unmask]>
> À: "FSL" <[log in to unmask]>
> Envoyé: Jeudi 4 Janvier 2018 17:17:58
> Objet: Re: [FSL] Topup systematic segmentation error
>
> Dear Veronica,
>
> I am afraid that I don’t have access to an Ubuntu version, so I cannot check
> that specifically for you. But if you send me your data along with the exact
> topup call that give you this problem I can check if I get the same problem
> with my version.
>
> If so, stick all the files referred to on the topup command line into a
> tar-ball and upload it to
>
> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5F
>
> Best regards Jesper
>
>
> On 4 Jan 2018, at 09:48, VERONICA MUNOZ RAMIREZ
> <[log in to unmask]> wrote:
>
> Dear FSL users,
>
> I have been having problems with "topup", I thought that the problem was
> coming from my data but when using the FDT sample data I have the same error
> : Segmentation fault (core dumped).
> I guess there's something wrong with my installation, I'm running FSL on
> Ubuntu 17.10 (artful) and I have read that other users have had problems
> with this version as well.
> Any advice would be greatly appreciated.
>
> Sincerely,
>
> --
> Verónica Muñoz Ramírez
> PhD student - Université Grenoble Alpes
> Grenoble Institute of Neuroscience
> +33 (0) 6 48 46 76 33
>
>
>
>
> --
> Verónica Muñoz Ramírez
> PhD student - Université Grenoble Alpes
> Grenoble Institute of Neuroscience
> +33 (0) 6 48 46 76 33
>
>
>
--
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-- MUDr. Pavel Hok
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-- Laboratoř funkční magnetické rezonance
-- Neurologická klinika
-- Lékařská fakulta
-- Univerzita Palackého v Olomouci
-- Fakultní nemocnice Olomouc
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-- Laboratory of functional magnetic resonance imaging
-- Department of Neurology
-- Faculty of Medicine and Dentistry
-- Palacky University Olomouc
-- University Hospital Olomouc
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