Also - did you look into the 2GB process limit - is that applying on your
linux machine? XP is almost certainly worse....
Cheers.
On Fri, 15 Oct 2004, Christian F. Beckmann wrote:
> Hi
>
> there is no limitation build into FSL - are you sure that you don't
> have NANs or something similar stored in the file?
> Can you please send us the output from fslerrorreport (a new script
> which compiles plenty of information about the machine and your setup).
> Also, if you send us a link for downloading an example file we can have
> a look at it in detail.
> cheers
> christian
>
>
>
> On 15 Oct 2004, at 00:08, Axel Thielscher wrote:
>
> > Hi,
> >
> > thanks a lot for the information concerning the swap space.
> >
> > However, after increasing swap space to 10GB and trying out several
> > variants (including update to FSL version 3.2, as well as a try using
> > Windows XP with 4GB swap), FSL still doesn't process the EPI-File.
> > FSLview
> > accepts it, but film_gls still doesn't read the file.
> >
> > So my question is:
> > Does anyone have experience with FSL and EPI-files around the size I
> > try to
> > use (630MB, 1280 volumes)? Does it work at all, or does FSL have some
> > kind
> > of internal limitation? Thanks for the help!
> >
> > Bye,
> > Axel
> >
> >
> >
> >
> >
> > On Mon, 11 Oct 2004 13:55:16 +0200, Cornelius Werner <co.werner@FZ-
> > JUELICH.DE> wrote:
> >
> >> OK, here some refinements for systems running a kernel 2.6:
> >>
> >> - swap files should have the same speed as swap partitions
> >> - you can have up to 32 swap files/partitions
> >> - with a current mkswap (in util-linux), each file/partition can have
> >> up
> >> to 64GB. Without that, it's 2GB.
> >>
> >> - with kernel 2.6, processes can grow up to any size (physical ram +
> >> swap
> >> is the limit)
> >> - file sizes on block-oriented devices can be in the terabyte range
> >> (32bit)
> >>
> >> Hope that helps,
> >> Cornelius
> >>
> >>
> >>
> >>
> >> On Mon, 11 Oct 2004 13:37:06 +0200, Cornelius Werner
> >> <[log in to unmask]> wrote:
> >>
> >>> Besides, swap FILES are extremely slow as opposed to true swap
> >>> PARTITIONS.
> >>> And multiple swap partitions will be reasonably fast only if placed
> >>> on
> >>> different (physical) hard drives (like in a RAID system). Remember to
> >>> give
> >>> each swap partition entry in your /etc/fstab the same pri=xx
> >>> statement.
> >>>
> >>> Best regards,
> >>> Cornelius
> >>>
> >>>
> >>> On Mon, 11 Oct 2004 11:26:30 +0100, Stephen Smith
> >>> <[log in to unmask]>
> >>> wrote:
> >>>
> >>>> Sure - that all makes sense, thanks. Though note - I was referring
> >>>> not
> >>>> to
> >>>> maximum swap size, but there's a separate point, which is that I
> >>>> think
> >>>> that on some OS's there is a limit to the max size that a single
> >>>> process
> >>>> can have, which I think may be 2GB on linux - I think there's ways
> >>>> to
> >>>> change that.
> >>>>
> >>>> Cheers.
> >>>>
> >>>>
> >>>>
> >>>> On Mon, 11 Oct 2004, Denis Brown wrote:
> >>>>
> >>>>> For what it's worth...
> >>>>>
> >>>>> Bear in mind that you can set up multiple swap partitions or swap
> >>>>> files
> >>>>> (each 2GB in size) and use them. If I recall reading correctly,
> >>>>> up to
> >>>>> eight partitions/files can be used to give the equivalent of 16GB
> >>>>> under
> >>>>> a
> >>>>> 2.4 series kernel. The 2.6 kernel may have expanded that. I
> >>>>> have
> >>>>> never
> >>>>> had to set up systems that support more than a single swap
> >>>>> partition so
> >>>>> I
> >>>>> cannot speak from experience.
> >>>>>
> >>>>> Best regards,
> >>>>> Denis
> >>>>>
> >>>>>
> >>>>> On Mon, 11 Oct 2004, Stephen Smith wrote:
> >>>>>
> >>>>>> Hi. This is a very large dataset - you'll need quite a lot more
> >>>>>> swap
> >>>>>> probably - try 4GB (though you may have a problem with the 2GB
> >>>>> process
> >>>>>> limit on linux if you need more than that - though I think you can
> >>>>>> change the kernel params to increase that?).
> >>>>>>
> >>>>>> Cheers.
> >>>>>>
> >>>>>>
> >>>>>> On Fri, 8 Oct 2004, Axel Thielscher wrote:
> >>>>>>
> >>>>>>> Hi - I try to analyze an EP image series created with AFNI using
> >>>>> the
> >>>>>>> GLM-module of FSL. I used 3dAFNItoANALYZE provided by AFNI to
> >>>>> transform the
> >>>>>>> EP BRIK to an 4D-Analyze-File. The size of this file is either
> >>>>> around 630 MB
> >>>>>>> (voxel values stored as integer) or 1.3GB (voxel values stored as
> >>>>> floating
> >>>>>>> point) and it contains 1280 volumes of one session.
> >>>>>>>
> >>>>>>> The analysis with FEAT doesn't work with either of the two files.
> >>>>> More
> >>>>>>> specifically, the command
> >>>>>>> /usr/local/fsl/bin/film_gls -rn stats -noest filtered_func_data
> >>>>> design.mat
> >>>>>>> 11.12 3201
> >>>>>>> fails and is apparently unable to read to file.
> >>>>>>>
> >>>>>>> My computer: Red Hat Linux 9, Intel P-4, 1GB RAM, 2GB swap space
> >>>>>>>
> >>>>>>> Does this problem stem from insufficient swap space? The analysis
> >>>>> with AFNI
> >>>>>>> works fine, but I would be happy to use the more advanced
> >>>>>>> features
> >>>>> such as
> >>>>>>> prewhitening etc. provided by FSL. How much memory do you
> >>>>>>> recommend
> >>>>> for
> >>>>>>> input file sizes as quoted above? Can this failure be caused by
> >>>>>>> a
> >>>>> different
> >>>>>>> problem?
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>> Axel
> >>>>>>>
> >>>>>>
> >>>>>> Stephen M. Smith DPhil
> >>>>>> Associate Director, FMRIB and Analysis Research Coordinator
> >>>>>>
> >>>>>> Oxford University Centre for Functional MRI of the Brain
> >>>>>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> >>>>>> +44 (0) 1865 222726 (fax 222717)
> >>>>>>
> >>>>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >>>>>>
> >>>>>
> >>>>
> >>>> --
> >>>> Stephen M. Smith DPhil
> >>>> Associate Director, FMRIB and Analysis Research Coordinator
> >>>>
> >>>> Oxford University Centre for Functional MRI of the Brain
> >>>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> >>>> +44 (0) 1865 222726 (fax 222717)
> >>>>
> >>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Cornelius Werner, AiP
> >>> Institut fuer Medizin (IME)
> >>> AG Kognitive Neurologie
> >>> Forschungszentrum Juelich
> >>> 52425 Juelich
> >>> Germany
> >>>
> >>> Tel. +49-(0)2461-61-8609
> >>>
> >>
> >>
> >>
> >> --
> >> Cornelius Werner
> >> Institut fuer Medizin (IME)
> >> AG Kognitive Neurologie
> >> Forschungszentrum Juelich
> >> 52425 Juelich
> >> Germany
> >>
> >> Tel. +49-(0)2461-61-8609
> >
> >
> --
> Christian F. Beckmann
> Oxford University Centre for Functional
> Magnetic Resonance Imaging of the Brain,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
> Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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