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Thanks for the quick response.  I'm CC'ing the FSL list because it looks like bedpostx is not executing properly.

The nodif_brain_mask looks good (I've attached a representative screenshot).

However, the bedpostx output is not the right size and does not seem to be reconstructing the whole brain.  The input image (data.nii.gz) is 112 x 112 x 80, but the merged images are not.  For instance, merged_f1samples.nii.gz is only 112 x 112 x 48.  When viewing the volumes, most of the inferior slices are simply not there. The attached f1_missing_slices.png shows one of these images.

Also strange, the bedpostX directory still has the diff_slices folder, but the folder only has data_slice_0016 through data_slice_0028.

-Keith
--
Keith Yoder
PhD Candidate, Integrative Neuroscience
Social Cognitive Neuroscience Laboratory
The University of Chicago
5846 S. University Avenue, Kelly 312
Chicago, IL 60637
Phone: 574-215-9678
[log in to unmask]



On Thu, Jul 26, 2012 at 3:53 PM, Anastasia Yendiki <[log in to unmask]> wrote:

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
[log in to unmask]




On Fri, Oct 7, 2011 at 10:04 AM, Anastasia Yendiki
<[log in to unmask]> 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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