Hi Ansgar - Most likely everything is fine. Sometimes the script that's
built into bedpost to monitor its progress gives this error but in fact
everything has ran fine. You should check that all the outputs are there
in the dmri.bedpostX directory. See for list of bedpost output files:
http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html
a.y
On Wed, 28 Sep 2011, Ansgar Furst wrote:
> Hi Anastasia,
> Thanks so much for your message. You were right about the recon directory, the
> contents had been accidentally moved elsewhere (sorry!) and once I moved them
> back and reran the script everything worked like a charm without any errors.
> However, it looks like I'm now stuck at the next processing stage (fsl's
> bedpostX). I pasted the output with the error message below. FYI: I'm
> unfortunately forced to run the bedpostX on a single Linux box (64-bit dual
> core
> with 8GB of RAM) which I hope is OK?
> Thanks so much for all your help,
>
> Ansgar
>
> ==================================================
> trac-all -bedp -c scripts/dmrirc_single_subject_1only
> INFO: SUBJECTS_DIR is /home/ajfurst/Data/WRIISC
> INFO: Diffusion root is /home/ajfurst/Data/WRIISC/TRACULA
> Actual FREESURFER_HOME /usr/local/freesurfer
> ln -sf
> /home/ajfurst/Data/WRIISC/TRACULA/015/dlabel/diff/anat_brain_mask.bbr.nii.gz
> /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/nodif_brain_mask.nii.gz
> ln -sf /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/dwi.nii.gz
> /home/ajfurst/Data/WRIISC/TRACULA/015/dmri/data.nii.gz
> WARN: Running FSL's bedbost locally - this might take a while
> WARN: It is recommended to run this step on a cluster
> bedpostx_seychelles /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
> subjectdir is /home/ajfurst/Data/WRIISC/TRACULA/015/dmri
> Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
> 0 slices processed
> 5 slices processed
> 6 slices processed
> 7 slices processed
> 8 slices processed
> 9 slices processed
> 9 slices processed
> 10 slices processed
> 11 slices processed
> 11 slices processed
> 12 slices processed
> 12 slices processed
> 13 slices processed
> 14 slices processed
> 14 slices processed
> 14 slices processed
> 15 slices processed
> 15 slices processed
> 16 slices processed
> 16 slices processed
> 16 slices processed
> 17 slices processed
> 17 slices processed
> 17 slices processed
> 18 slices processed
> 18 slices processed
> 18 slices processed
> 18 slices processed
> 19 slices processed
> 19 slices processed
> 19 slices processed
> 19 slices processed
> 20 slices processed
> 20 slices processed
> 20 slices processed
> 20 slices processed
> 21 slices processed
> 21 slices processed
> 21 slices processed
> 21 slices processed
> 21 slices processed
> 22 slices processed
> 22 slices processed
> 22 slices processed
> 22 slices processed
> 23 slices processed
> 23 slices processed
> 23 slices processed
> 23 slices processed
> 23 slices processed
> 24 slices processed
> 24 slices processed
> 24 slices processed
> 24 slices processed
> 24 slices processed
> 24 slices processed
> 25 slices processed
> 25 slices processed
> 25 slices processed
> 25 slices processed
> 25 slices processed
> 26 slices processed
> 26 slices processed
> 26 slices processed
> 26 slices processed
> 26 slices processed
> 26 slices processed
> 27 slices processed
> 27 slices processed
> 27 slices processed
> 27 slices processed
> 27 slices processed
> 28 slices processed
> 28 slices processed
> 28 slices processed
> 28 slices processed
> 28 slices processed
> 28 slices processed
> 29 slices processed
> 29 slices processed
> 29 slices processed
> 29 slices processed
> 29 slices processed
> 29 slices processed
> 30 slices processed
> 30 slices processed
> 30 slices processed
> 30 slices processed
> 30 slices processed
> 30 slices processed
> 31 slices processed
> 31 slices processed
> 31 slices processed
> 31 slices processed
> 31 slices processed
> 32 slices processed
> 32 slices processed
> 32 slices processed
> 32 slices processed
> 32 slices processed
> 32 slices processed
> 33 slices processed
> 33 slices processed
> 33 slices processed
> 33 slices processed
> 33 slices processed
> 33 slices processed
> 34 slices processed
> 34 slices processed
> 34 slices processed
> 34 slices processed
> 34 slices processed
> 35 slices processed
> 35 slices processed
> 35 slices processed
> 35 slices processed
> 35 slices processed
> 35 slices processed
> 36 slices processed
> 36 slices processed
> 36 slices processed
> 36 slices processed
> 36 slices processed
> 37 slices processed
> 37 slices processed
> 37 slices processed
> 37 slices processed
> 37 slices processed
> 38 slices processed
> 38 slices processed
> 38 slices processed
> 38 slices processed
> 38 slices processed
> 39 slices processed
> 39 slices processed
> 39 slices processed
> 39 slices processed
> 39 slices processed
> 40 slices processed
> 40 slices processed
> 40 slices processed
> 40 slices processed
> 41 slices processed
> 41 slices processed
> 41 slices processed
> 41 slices processed
> 41 slices processed
> 42 slices processed
> 42 slices processed
> 42 slices processed
> 42 slices processed
> 43 slices processed
> 43 slices processed
> 43 slices processed
> 43 slices processed
> 44 slices processed
> 44 slices processed
> 44 slices processed
> 44 slices processed
> 45 slices processed
> 45 slices processed
> 45 slices processed
> 46 slices processed
> 46 slices processed
> 46 slices processed
> 46 slices processed
> 47 slices processed
> 47 slices processed
> 47 slices processed
> 48 slices processed
> 48 slices processed
> 49 slices processed
> 49 slices processed
> 49 slices processed
> 50 slices processed
> 50 slices processed
> 51 slices processed
> 51 slices processed
> 52 slices processed
> 53 slices processed
> Queuing post processing stage
> 58 slices processed
> For some reason the bedpostX process DOES NOT appear
> to have successfully completed. Please examine your
> results carefully.
> /usr/local/freesurfer/bin/bedpostx_seychelles: line 281: kill: (12792) - No
> such
> process
> ===================================================
>
> On Thu, Sep 22, 2011 at 5:17 AM, Anastasia Yendiki
> <ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Ansgar - Currently there's no way to specify multiple scans for
> the same subject as dicom files, sorry. You can concatenate the DWIs
> from the 2 scans in one nifti file, and also concatenate the
> bvecs/bvals from the two scans, and pass the concatenation to
> dmrirc.
>
> As for your error, it looks like maybe the freesurfer recon wasn't
> found, so it skipped some steps (diffusion-to-anatomical
> registration and mask creation). Does the freesurfer recon dir
> /home/ajfurst/Data/WRIISC/014/ exist?
>
> a.y
>
>
>
>
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