Hi Keith - This seems to be a different problem here, since all the bedpostx outputs are there and are loaded in without a problem. The error occurs after that. What's the size of your images? Does the mask file look normal?
Thanks, a.y
On Thu, 26 Jul 2012, Keith Yoder wrote:
Hi,
Was there any resolution to this issue? I'm having a similar problem running trac-all on a Linux cluster.
I think bedpostx works if I call it directly from the command line twice. The first time, bedpostx_postproc.sh doesn't seem to work and the *samples.nii.gz files are only created if I rerun bedpostx. However, trac-all...-path fails. I've attached the trac-all-path output and pasted the relevant section below:
Creating output directory/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dpath/lh.cst_AS_av g33_mni_flt Loading DWIs from /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/dwi.nii.gz Loading mask from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/diff/aparc+ aseg_mask.flt.nii.gz Loading BEDPOST parameter samples from /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri.bedpostX Loading segmentation map from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/mni/aparc+a seg.nii.gz Loading b-values from /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvals Loading gradients from /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvecs Segmentation fault (core dumped)
Here are the contents of the subjects bedpostX directory:
bvals bvecs commands.txt diff_slices dyads1_dispersion.nii.gz dyads1.nii.gz dyads2_dispersion.nii.gz dyads2.nii.gz logs mean_dsamples.nii.gz mean_f1samples.nii.gz mean_f2samples.nii.gz mean_ph1samples.nii.gz mean_ph2samples.nii.gz mean_S0samples.nii.gz mean_th1samples.nii.gz mean_th2samples.nii.gz merged_f1samples.nii.gz merged_f2samples.nii.gz merged_ph1samples.nii.gz merged_ph2samples.nii.gz merged_th1samples.nii.gz merged_th2samples.nii.gz monitor nodif_brain_mask.nii.gz xfms
Also, I'm attaching the bvals, bvecs, dmrirc.local, trac-all.error, and trac-all.log for the subject. Let me know if there is any other information you need.
Thanks in advance, Keith -- Keith YoderPhD Candidate, Integrative Neuroscience Social Cognitive Neuroscience Laboratory The University of Chicago 5846 S. University Avenue, Kelly 312 Chicago, IL 60637 Phone: 574-215-9678 kjyoder@uchicago.edu
On Fri, Oct 7, 2011 at 10:04 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Judit, 1. If you can run bedpostx directly then you should do: bedpostx /usr/local/freesurfer/subjects/C001/dmri Note that this dmri directory and the one you tried to run bedpostx_single_slice.sh on are different, so I'm not sure which location is the right one where your data is, but in any case you don't need to run bedpostx_single_slice.sh. 2. The error seems to occur either when it's reading the bvecs file, or right after that when it's accessing the bedpostx outputs. So I'd try to look those for that subject and see if everything is ok. Hope this helps, a.y On Fri, 7 Oct 2011, Judit Haasz wrote: Hi, I ran into 2 problems related to tracula. 1. trac-all -bedp command exits with following message. WARN: Running FSL's bedbost locally - this might take a while >> > WARN: It is recommended to run this step on a cluster >> > bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri >> > subjectdir is /usr/local/freesurfer/subjects/C001/dmri >> > Making bedpostx directory structure >> > Queuing preprocessing stages >> > [: 223: NONE: unexpected operator >> > [: 314: NONE: unexpected operator >> > [: 327: xbedpostx_pre: unexpected operator >> > [: 486: x: unexpected operator >> > [: 486: -le: argument expected >> > Queuing parallel processing stage >> > [: 223: NONE: unexpected operator >> > [: 327: xbedpostx: unexpected operator >> > [: 486: x53: unexpected operator >> > 0 slices processed >> > Queuing post processing stage >> > [: 223: NONE: unexpected operator >> > [: 314: NONE: unexpected operator >> > [: 327: xbedpostx_post: unexpected operator >> > [: 486: x: unexpected operator >> > [: 486: -le: argument expected >> > This problem has been posted in May and June. bedpostx from command line runs perfectly and that is how I have been running it so far. One of u suggested to try the following:/usr/local/fsl/bin/bedpostx_single_slice.sh/disks/open/judit/subjects/diffu sion_tutorial/dtisubjects2005/subj_523/dmri 2 1 1000 1250 25 1 0
then I got: ** ERROR (nifti_image_read): failed to find header filefor'/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/ dmr i/data_slice_0000' **ERROR:nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisub jects2 005/subj_523/dmri/data_slice_0000): bad header info ERROR: failed to openfile/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/ dmri /data_slice_0000 ERROR: Could not openimage/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523 /dmri /data_slice_0000 Image Exception : #22 :: Failed to readvolume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_52 3/dmri /data_slice_0000 An exception has been thrown Failed to readvolume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_52 3/dmri /data_slice_0000Trace: read_volume4DROI. Done Can u suggest a reason behind all this? This happens on Linux machine (2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM Version: Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode). On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz 6-core Intel Xeon processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp runs well. My other question is: trac-all -path exists with error (in case of a single subject): Loading DWIsfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ dmri /dwi.nii.gz Loading maskfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ dlab el/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samplesfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ dmri .bedpostX Loading segmentation mapfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ dlab el/mni/aparc+aseg.nii.gz Loading b-valuesfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ dmri /bvals Loading gradientsfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ dmri /bvecs Segmentation fault Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Oct 7 10:21:20 CEST 2011 thanks for help. Judit
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