Hi
I had the same problem earlier when running FDT, PROBTRACKX in a Linux virtual machine though the host machine was a 64 bit one. Turns out the machine came with "hardware virtualization" turned off as a factory default. I beleve this may be a usual case with most PCs. Due to this reason I was denied installing 64 bit Linux VM. So if your virtual machine is a 32 bit one and the host machine is 64 bit, go to your BIOS set up and enable the "hardware virtualization" then reinstall the 64 bit Linux VM and then reinstall 64 bit fsl and you will be fine. After doing these steps my problems were solved. I suspected that your machine is a 64 bit one as you have 3GB memory.
Best
Indika Walimuni
Research Associate
University of Texas Health Science Center
Houston, TX.
________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of David Flitney [[log in to unmask]]
Sent: Monday, June 01, 2009 7:23 AM
To: [log in to unmask]
Subject: Re: [FSL] Why probtrackx promts "Out of memory" ?
Hi,
Can you confirm that your computer is a 64bit machine. If not then, even though you have a lot of memory, probtrackx is still quite likely to be running out of virtual memory - perhaps you have access to a large memory profile 64bit machine for testing purposes?
On 1 Jun 2009, at 12:38, Nicozuo wrote:
Dear all,
I have downloaded some DTI data from https://www.mristudio.org/ .
I want to practice the FDT tool on the data above.
Unfortunately, after run "eddy_current" function and "bedpostx" function,
I tried to run "probtrackx" to track the fibers through one seed points as
the following command,
[code]
probtrackx -V 2 --mode=simple --
seedref=./bedpost.2fibers.bedpostX/nodif_brain_mask.nii.gz -
o ./dti_probtrack -x ./dti_probtrack/fdt_coordinates.txt -c 0.2 -S 2000 --
steplength=0.5 -P 5000 --forcedir --opd -
s ./bedpost.2fibers.bedpostX/merged -
m ./bedpost.2fibers.bedpostX/nodif_brain_mask.nii.gz --dir=./dti_probtrack
[/code]
and it promted the following errors,
[error]
basename ./bedpost.2fibers.bedpostX/merged
maskfile ./bedpost.2fibers.bedpostX/nodif_brain_mask.nii.gz
seeds ./dti_probtrack/fdt_coordinates.txt
output ./dti_probtrack
verbose 2
nparticles 5000
nsteps 2000
usef 0
rseed 12345
1_1
1_2
1_3
2_1
2_2
Image Exception : #99 :: Out of memory
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
[/error]
Since I just try to track the fibers going through one seed points storing in
the "fdt_coordinates.txt", why does it promt "Out of memory" ?? The version
of FDT toobox is 2.0, and the memory of the system is 3G. The tested DTI
data is 256*256*50*35, where 35 is the number of gradient direction (with 5
b=0 directions).
Thanks for any clues,
Nicozuo
--
Dave Flitney, IT Manager
Oxford Centre for Functional MRI of the Brain
E:[log in to unmask]<mailto:[log in to unmask]> W:+44-1865-222713 F:+44-1865-222717
URL: http://www.fmrib.ox.ac.uk/~flitney
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