Hi Matthew,
Thanks for your reply. I started melodic again and will let it run.
Is it normal that no files are produced during this time? I was checking the output folder of melodic, but no files were added and nothing was added to the log file.
I will let you know what happened.
Thanks!
Heidi
================================================
Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
[log in to unmask]
www.maastrichtuniversity.nl
www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092
================================================
________________________________________
Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Matthew Webster [[log in to unmask]]
Verzonden: woensdag 20 februari 2013 17:03
Aan: [log in to unmask]
Onderwerp: Re: [FSL] Melodic crashes from gui and command line
Hello Heidi,
For a data set as large as yours a 35 hour+ runtime is not implausible - can you rerun the command line call that did _not_ use --report and leave it running? It might also be worth monitoring the jobs memory usage ( e.g. with top ) to make sure it does not exceed 12Gb.
Kind Regards
Matthew
> Dear Christian,
>
> Thanks for your feedback. I tried to run melodic from the command line as you suggested.
> As no report was generated by firefox, I ran it without the -report.
> I aborted the computer after 35 hours, as nothing was happening (even though the CPU was working for about 96%, seems like a crash). Melodic generated no file.
> To make sure it is not the code generating the figures, as you thought, I ran 4 subjects (2 by 2) and that was no problem. In less than 3 hours, Melodic finished successfully.
> I did analyses on 80 out of these 120 people, and that was neither a problem. Could it be that 120 people is too much for melodic?
> I don't think my computer is not powerful enough (intel i7, 3.8Ghz, 12GB memory, quad core) and I did run everything within Centos.
>
> Is it normal that it would take this long? Or is something else going on? I am desperate now, I have no idea what I could do?
> Any help or advice is welcome.
> Thanks!
> Heidi
> ________________________________________
> Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Christian F. Beckmann [[log in to unmask]]
> Verzonden: dinsdag 12 februari 2013 22:57
> Aan: [log in to unmask]
> Onderwerp: Re: [FSL] 120 subjects Melodic: only one component?
>
> Hi Heidi,
>
> I think you're reporting a whole set of unrelated things here. It looks like Melodic finishes and the mixture modelling does crash on your data. Can you do the following:
> (i) run melodic from the command line for the mixture modelling only:
>
> melodic -i bgimage --ICs=melodic_IC --mix=melodic_mix -v --report --Ostats
>
> and report on what you're getting.
>
> If that crashes then please run the same without the --report - if that works then the problem is in the code generating the figures, not anything to do with data size or number of subjects.
>
> hth
> Christian
>
>
>
>
>
>
> On 12 Feb 2013, at 22:46, "Jacobs H (NP)" <[log in to unmask]> wrote:
>
>> Hi all,
>>
>> I have been trying to run melodic on 120 subjects. However, melodic seems to stop after giving me one component in the firefox output (mixture modelling). The melodic_IC.nii.gz is complete, showing all 25 components. This was done on the latest version of FSL (5.2) on a Linux machine (Centos 6.3). FSL ran for about 16 hours and then stopped.
>> I thought I might have been the BBR registration (as I never used that before), but after a 7DOF registration, I got the same problem.
>>
>> So, then I tried to run the data on my Macbook pro with FSL version 4.1.9. FSL stopped during the PCA (total run time 25 hours).
>>
>> In earlier analyses, I was able to do the melodic on my Macbook pro (80 and 40 subjects) without problems.
>>
>> Could it be that 120 subjects it too much for melodic? Any help is appreciated as I have no idea what to do now.
>>
>> Any help is appreciated!
>> Best
>> Heidi
>>
>>
>>
>> ================================================
>> Dr. Heidi Jacobs
>> Postdoc researcher
>> Faculty of Health, Medicine and Life Sciences
>> School for Mental Health and Neurosciences
>> Division Cognitive Neuropsychiatry and Clinical Neurosciences
>> Alzheimer Center Limburg
>> [log in to unmask]
>> www.maastrichtuniversity.nl
>> www.heidijacobs.nl
>>
>> Dr. Tanslaan 12, 6229 ET Maastricht
>> P.O. Box 616, 6200 MD Maastricht, The Netherlands
>> T +31 43 38 84 090 F +31 43 38 84 092
>> ================================================
>
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