You might want to make sure you are not running out of memory. When ran on
a group of 90 subjects the swap_subjectwise process would die with less
than about 40GB memory available (RAM+swap), and the subsequent steps
would fail.
Cheers
Inge
On Tue, June 29, 2010 17:31, Matt Glasser wrote:
> Perhaps you are exceeding the maximum allowable time on that queue.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Liz Selgrade
> Sent: Tuesday, June 29, 2010 10:04 AM
> To: [log in to unmask]
> Subject: [FSL] tbss_x error during subjectwise reassignment
>
> Hi Saad and Group,
>
> I'm trying to run tbss_x on a group of 72 subjects and am having problems.
> I previously ran it successfully on a group with 44 subjects.
>
> Everything seems to run fine until subjectwise reassignment. These are
> the
> error messages I'm getting from that point on:
>
> /home/ess25/tbss_x: line 213: 7338 Killed
> $FSLDIR/bin/swap_subjectwise -m mean_FA_skeleton_mask -r .veclist.txt -f
> .scalist.txt -b subjectwise_realigned -v
> merging final results
> F1
> ** ERROR (nifti_image_read): failed to find header file for
> 'subjectwise_realigned_voxelwise_realigned_????_scalars1.*'
> ** ERROR:
> nifti_image_open(subjectwise_realigned_voxelwise_realigned_????_scalars1.*):
> bad header info
> Error: failed to open file
> subjectwise_realigned_voxelwise_realigned_????_scalars1.*
> Cannot open volume
> subjectwise_realigned_voxelwise_realigned_????_scalars1.*
> for reading!
> F2
> ** ERROR (nifti_image_read): failed to find header file for
> 'subjectwise_realigned_voxelwise_realigned_????_scalars2.*'
> ** ERROR:
> nifti_image_open(subjectwise_realigned_voxelwise_realigned_????_scalars2.*):
> bad header info
> Error: failed to open file
> subjectwise_realigned_voxelwise_realigned_????_scalars2.*
> Cannot open volume
> subjectwise_realigned_voxelwise_realigned_????_scalars2.*
> for reading
>
> I thought that it might be a problem with memory, but I get the same
> errors
> when trying it with two different SGEs. (When it fails on the second SGE,
> I
> get "31283 Killed" instead of "7338 Killed.") It also seems unlikely to
> me
> that it's a problem with the inputs, as I've checked them individually.
> Any
> thoughts of what might be going on?
>
> Thanks!
> Liz Selgrade
>
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