Yep, Steve is right: although I got it to run with just 1GB physical RAM there may be various issues. The machine I was able to get bet2 within feeds to finish was with cygwin on a separate partition, with separate virtual memory assigned to it. I am also not sure whether the HDD (8MB cache) would be expected to make a difference to windoze.
Cheers-
Andreas
-----Ursprüngliche Nachricht-----
Von: Stephen Smith [mailto:[log in to unmask]]
Gesendet: Do 04.11.2004 09:49
An: [log in to unmask]
Cc:
Betreff: Re: [FSL] FEEDS w/ WinXP
Well, I probably woudn't worry about this unless you need to use BET2
under Cygwin - I'm really not sure how well Windows/Cygwin can be expected
to run such a huge process.
Cheers.
On Wed, 3 Nov 2004, Bennett Landman wrote:
> First, thanks for getting back to me.
>
> I upgraded the machine to 1 GB of physical RAM and 1.5 GB of swap space
> (with an additional 3 GB of free space left on the drive). I reran the FEEDS
> test suite and am still getting the same error (see below). Is there a way
> to show that this is a memory problem? (I do not see any errors saying that
> I am running low on virtual memory.)
>
> I appreciate your help,
> Bennett Landman
> [log in to unmask]
>
>
> bennett@M205 /usr/local/feeds
> $ ./RUN bet2
>
> FSL Evaluation and Example Data Suite v3.2
>
> start time = Wed Nov 3 17:04:14 EST 2004
> hostname = M205
> os = CYGWIN_NT-5.1 M205 1.5.11(0.116/4/2) 2004-09-04 23:17 i686 unknown
> unknow
> n Cygwin
>
>
> /bin/rm -rf /usr/local/feeds/results ; mkdir /usr/local/feeds/results
>
>
> Starting BET2 at Wed Nov 3 17:04:15 EST 2004
> checking error on T1 brain extraction:
> % error = 0.0
> checking error on skull and scalp surfaces:
> No output image created
> Warning - test failed!
> No output image created
> Warning - test failed!
> No output image created
> Warning - test failed!
>
> Warning - not all tests passed
>
> end time = Wed Nov 3 17:30:21 EST 2004
>
>
> -----Original Message-----
> From: Andreas Bartsch [mailto:[log in to unmask]]
> Sent: Monday, November 01, 2004 10:29 AM
> Subject: AW: [FSL] FEEDS w/ WinXP
>
> Hi Bennett-
>
> this is related to deficient memory preventing the generation of skull +
> scalp surface images.
> Increase virtual memory of let the system administer its size. That should
> do it - at least if you have a minimum of 1GB physical RAM.
> Best regards-
> Andreas
>
>
> -----Ursprüngliche Nachricht-----
> Von: Bennett Landman [mailto:[log in to unmask]]
> Gesendet: Mo 01.11.2004 13:18
> An: [log in to unmask]
> Cc:
> Betreff: [FSL] FEEDS w/ WinXP
>
>
>
> Good morning,
>
> My FEEDS validation suite is failing for the BET2 surfaces under
> winXP.
> (Full feeds output included below.) I also installed the complete
> cygwin
> kit (as per the last message on this topic), but the problem
> persists. I'd
> very much appreciate any help setting up FSL under winXP.
>
> Thanks,
> Bennett Landman
> [log in to unmask]
>
> bennett@M205/usr/local/feeds
> $ time ./RUN all
>
> FSL Evaluation and Example Data Suite v3.2
>
> start time = Sun Oct 31 22:42:49 EST 2004
> hostname = M205
> os = CYGWIN_NT-5.1 M205 1.5.11(0.116/4/2) 2004-09-04 23:17 i686
> unknown
> unknow
> n Cygwin
>
>
> /bin/rm -rf /usr/local/feeds/results ; mkdir
> /usr/local/feeds/results
>
>
> Starting PRELUDE & FUGUE at Sun Oct 31 22:42:53 EST 2004
> % error = 0.0
> % error = 0.0
>
> Starting SUSAN at Sun Oct 31 22:43:02 EST 2004
> % error = 0.0
>
> Starting SIENAX (including testing BET and FLIRT and FAST) at Sun
> Oct 31
> 22:46:1
> 8 EST 2004
> checking error on BET:
> % error = 0.0
> checking error on FLIRT:
> % error = 0.33
> checking error on FAST:
> checking error on single-image binary segmentation:
> % error = 0.4
> checking error on partial volume images:
> % error = 0.38
> % error = 0.26
> % error = 0.24
> checking error on SIENAX volume outputs:
> % error = 0.09
> % error = 0.0
> % error = 0.05
> % error = 0.05
> % error = 0.1
>
> Starting BET2 at Sun Oct 31 23:05:04 EST 2004
> checking error on T1 brain extraction:
> % error = 0.0
> checking error on skull and scalp surfaces:
> No output image created
> Warning - test failed!
> No output image created
> Warning - test failed!
> No output image created
> Warning - test failed!
>
> Starting FEAT at Sun Oct 31 23:39:32 EST 2004
> checking error on filtered functional data:
> % error = 0.21
> checking error on raw Z stat images:
> % error = 0.26
> % error = 0.22
> % error = 0.28
> checking error on thresholded Z stat images:
> % error = 0.21
> % error = 0.27
> % error = 0.33
> checking error on position of largest cluster of Talairached
> zfstat1:
> % error = 0.01
> % error = 0.02
> % error = 0.08
> % error = 0.01
> % error = 0.0
> % error = 0.04
>
> Starting MELODIC at Mon Nov 1 00:00:58 EST 2004
> % error = 0.0
>
> Starting FDT (bedpost) at Mon Nov 1 00:21:50 EST 2004
> checking error on bedpost output:
> % error = 0.25
> % error = 0.01
> % error = 0.07
> % error = 0.07
> % error = 0.1
> % error = 0.22
> % error = 0.22
>
> Warning - not all tests passed
>
> end time = Mon Nov 1 01:07:15 EST 2004
>
>
> real 144m32.312s
> user 0m0.180s
> sys 0m0.980s
>
>
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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