Hi,
This is likely either a big-RAM problem (in which case see the FSL
FAQ) or a previous large-image FSL bug. I think the very latest
version of FSL (4.1.2) may have fixed the latter (Matthew can comment
further on this maybe) so you may be ok if you just install the latest
version and try again?
Cheers.
On 14 Jan 2009, at 08:00, Lars Tjelta Westlye wrote:
> Hi,
>
> I'm running TBSS (FSL 4.1.1-centos5_64) on a dataset comprising 433 FA
> volumes. Everything runs fine up to tbss_3_postreg -S subsequent to
> the
> fslmerge command at line 164 in the tbss_3_postreg script where it
> errors
> attempting to compute the mask and mean FA. That is, all_FA.nii.gz is
> generated (2.5 GB), but FSL can't seem to read the file:
>
> ****
> [larstw@psyk077 stats]$ fslhd all_FA.nii.gz
> ** ERROR: nifti_image_open(all_FA): bad header info
> Error: failed to open file all_FA
> ERROR: Could not open file
> ****
>
> The same error appears when trying to open the 4D volume in Fslview.
> However, Freesurfer's mri_info yields the following info, which
> seems fine
> to me:
>
> ****
> [larstw@psyk077 stats]$ mri_info all_FA.nii.gz
> Volume information for all_FA.nii.gz
> type: nii
> dimensions: 182 x 218 x 182 x 433
> voxel sizes: 1.0000, 1.0000, 1.0000
> type: FLOAT (3)
> fov: 182.000
> dof: 0
> xstart: -91.0, xend: 91.0
> ystart: -109.0, yend: 109.0
> zstart: -91.0, zend: 91.0
> TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
> 0.00 degrees
> nframes: 433
> ras xform present
> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
> -1.0000
> : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a =
> -17.0000
> : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s =
> 19.0000
> Orientation : LAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
> -1.0000 0.0000 0.0000 90.0000
> 0.0000 1.0000 0.0000 -126.0000
> 0.0000 0.0000 1.0000 -72.0000
> 0.0000 0.0000 0.0000 1.0000
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
> -1.0000 0.0000 0.0000 90.0000
> -0.0000 1.0000 -0.0000 126.0000
> -0.0000 -0.0000 1.0000 72.0000
> 0.0000 0.0000 0.0000 1.0000
> ****
>
> I have approx 1TB available disk space. This is the output of free -
> m (16
> GB RAM, 18 GB swap):
>
> ***
> [larstw@psyk077 stats]$ free -m
> total used free shared buffers
> cached
> Mem: 16053 4316 11736 0 475
> 1748
> -/+ buffers/cache: 2092 13960
> Swap: 18433 4781 13652
> ***
>
> ***
> [larstw@psyk077 stats]$ uname -a
> Linux psyk077.uio.no 2.6.18-92.1.22.el5 #1 SMP Fri Dec 5 09:28:22
> EST 2008
> x86_64 GNU/Linux
> ***
>
> Is this expected behavior on datasets of this size? Could the
> problem be
> due to insufficient memory on my system, and do you have any
> suggestions
> on how to solve this? It should be noted that everything works
> nicely with
> smaller datasets, although I would like to include everything in one
> run.
>
> Thank you very much,
> Lars
>
---------------------------------------------------------------------------
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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