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Subject:

Re: Flirt problem

From:

"Christian F. Beckmann" <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 28 May 2004 18:17:53 +0100

Content-Type:

text/plain

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text/plain (110 lines)

On 28 May 2004, at 17:55, Himachandra Chebrolu wrote:

> Thats a problem with your libraries.Try to get one of those binary
> files online.They have nothing to do with FSL.
> Thanks,
> Himachandra
>


NO! DON'T DO THIS UNDER ANY CIRCUMSTANCES

flirt_noopt is ONLY for RH8/9  (please read the FAQ ! ) and  you should
not be surprised that it does not run on your RH 7.3 system! Please
don't try to make it run by replacing  libstdc++ as this is very
dangerous and might make your entire machine unuseable.

As Mark has said earlier - with 867 volumes in standard space you are
likely to be out of memory: if you do everything at once you will need
6GB of memory (91x109x109x32x867x2 bytes) - that's why splitting it in
3 chuncks worked - it got you under your process size limit...

cheers
christian

> Wei Qiu <[log in to unmask]> wrote:
> Dear Mark,
>
> I am using RH7.3. Loading flirt_noopt in my machine, here is the error
> mesage.
>
> flirt: error while loading shared libraries: libstdc++.so.5: cannot
> open
> shared object file: No such file or directory
>
> Meanwhile, the total time point is 867 and Tr=2.5
>
> Thanks!
>
> wei
>
>
>
> On Mon, 24 May 2004, Mark Jenkinson wrote:
>
> > Hi,
> >
> > Have you looked at:
> > http://www.fmrib.ox.ac.uk/fslfaq/#flirt_crash
> > ?
> >
> > There are some problems on RH9 which can be fixed by using
> > the non-optimised version. Otherwise, converting to standard
> > space does take up a lot of memory and disk. How many time
> > points are you trying?
> >
> > All the best,
> > Mark
> >
> >
> >
> > On Monday, May 24, 2004, at 02:57 pm, Wei Qiu wrote:
> >
> > > Dear all,>  >
> > > I am getting into trouble for registering a
> > > functional data (45 minutes, 142049280b) into MNI tal space.
> > >
> > > Here is what I did.
> > >
> > > 1) get the example_func2standard.mat (functional--> ana-->
> standard)
> > > 2) then flirt the functional into MNI space
> > > flirt -in f_brain -ref standard -out f_brain2stand -init
> > > example_func2standard.mat -applyxfm
> > >
> > > while i ran it, the program aborted. I guess the problem is our
> data
> > > is too big.
> > >
> > > 3) Then I splited the data into 3 pieces in time domain and then
> used
> > > the
> > > flirt command as above. It worked well for each piece. Now I have
> to
> > > concatenate it back.
> > >
> > > avwmerge -t outfile a b c
> > >
> > > As always "The segmentation fault" error message came out.
> > > Our computer is in huge RAM (4! GBRAM, 8GB swap space and 3TB).
> > >
> > > Did I make mistake somewhere. Any suggestion will be greatly
> > > appreciated!
> > >
> > > Thanks again!
> > >
> > > Wei
> >
>
>
>
> Do you Yahoo!?
> Friends. Fun. Try the all-new Yahoo! Messenger
--
  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

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