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Subject:

AW: [FSL] FEEDS w/ WinXP

From:

Andreas Bartsch <[log in to unmask]>

Reply-To:

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

Date:

Thu, 4 Nov 2004 11:38:40 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1 lines)

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



	-----Urspr√ľngliche 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

	>

	>

	>         -----Urspr√ľngliche 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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