Hi - please see the FAQ on RAM issues:
http://www.fmrib.ox.ac.uk/fslfaq/#general_ram
In particular, with very large numbers of subjects, it may not so much
be the RAM that is limiting things but the fact that you are using 32-
bit rather than 64-bit. If you switched to 64-bit Linux then hopefully
(e.g.) 4GB ram and 20GB swap would be sufficient for this kind of
dataset.
Cheers.
On 30 May 2008, at 19:22, Russell Chu wrote:
> Hi,
> I'm running FSL 4 on a 32-bit WinXP machine w/ 4GB RAM and 5GB of
> paging
> file (2.8GB user memory and 1.9GB used swap allocated to the virtual
> machine). The fractional anisotropy maps are 128 x 128 x 28 with
> 1.72mm x
> 1.72mm x 4mm resolution. I'm getting the error message below when
> running
> 'tbss_3_postreg -S' on 60 subjects. Is this an out of memory error?
> About
> how much RAM do you use to process your own datasets with 64-bit Linux
> machines? Thank you very much for your time and attention.
>
> cheers
> Russell
>
>
> [fsl@localhost toProcess]$ tbss_3_postreg -S
> using pre-chosen target for registration
> transforming all FA images into MNI152 space
> M023-DTI_FA_FAi
> M025-DTI_FA_FAi
> M026-DTI_FA_FAi
> .
> .
> .
> M124-DTI_FA_FAi
> M125-DTI_FA_FAi
> M126-DTI_FA_FAi
> merging all upsampled FA images into single 4D image
> creating valid mask and mean FA
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): St9bad_alloc
> /usr/local/fsl/bin/tbss_3_postreg: line 177: 7390 Aborted
> $FSLDIR/bin/fslmaths all_FA -max 0 -Tmin -bin mean_FA_mask -odt char
> ** ERROR (nifti_image_read): failed to find header file for
> 'mean_FA_mask'
> ** ERROR: nifti_image_open(mean_FA_mask): bad header info
> Error: failed to open file mean_FA_mask
> ERROR: Could not open image mean_FA_mask
> Image Exception : #22 :: Failed to read volume mean_FA_mask
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/tbss_3_postreg: line 178: 7405 Aborted
> $FSLDIR/bin/fslmaths all_FA -mas mean_FA_mask all_FA
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): St9bad_alloc
> /usr/local/fsl/bin/tbss_3_postreg: line 179: 7412 Aborted
> $FSLDIR/bin/fslmaths all_FA -Tmean mean_FA
> skeletonising mean FA
> ** ERROR (nifti_image_read): failed to find header file for 'mean_FA'
> ** ERROR: nifti_image_open(mean_FA): bad header info
> Error: failed to open file mean_FA
> ERROR: Could not open image mean_FA
> Image Exception : #22 :: Failed to read volume mean_FA
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> /usr/local/fsl/bin/tbss_3_postreg: line 190: 7415 Aborted
> $FSLDIR/bin/tbss_skeleton -i mean_FA -o mean_FA_skeleton
> now view mean_FA_skeleton to check whether the default threshold of
> 2000
> needs changing, when running:
> tbss_4_prestats [threshold]
> [fsl@localhost toProcess]$
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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