Hi Tim
Can you zip the "logs" directory (inside the bedpostx output directory) and send it to us?
Saad
On 31 Jan 2012, at 17:22, Tim van Hartevelt wrote:
> Dear FSL,
>
> We appear to experience some difficulties with running bedpostX on our DTI data.
> We have acquired our data on a clinical Philips Achieva 1.5 Tesla Magnet in Oxford. Diffusion MRI was acquired by using a single-shot echo planar imaging-based sequence with coverage of the whole brain; repetition time (TR), 9390ms; echo time (TE), 65ms. DTI images utilised 32 optimal nonlinear diffusion weighting directions (b = 1200 s/mm2) and 2 non-diffusion weighted volumes; reconstructed matrix=128x128x45; reconstructed voxel size 2.0mm x 2.0mm x 2.0mm.
> After a processing stage that takes up to a few days, we receive the following message (also see Processing stage of bedpostX below): For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully.
> After careful examination we find that the dyads<i> files are missing as well as the mean_th, mean_ph and mean_f files. However, when running datacheck everything seems to be alright. We also find no problems with our dtifit. And to make matters more complicated, this problem does not occur with all of our datasets.
> Please find below the files after completing bedpostX, the output of datacheck, and the process log (that runs for several days instead of approx 20 hours).
>
> I hope you’ll be able to help us. Many thanks in advance.
>
> All very best,
> Tim
>
>
> Files present after bedpostX is done
> bvals
> bvecs
> commands.txt
> logs
> mean_dsamples.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
>
> Processing stage of bedpostX
> Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
> 0 slices processed
> 2 slices processed
> 3 slices processed
> 4 slices processed
> 4 slices processed
> 4 slices processed
> 5 slices processed
> 5 slices processed
> 5 slices processed
> 5 slices processed
> 6 slices processed
> 6 slices processed
> 6 slices processed
> …
> 45 slices processed
> 46 slices processed
> 46 slices processed
> 47 slices processed
> Queuing post processing stage
> 48 slices processed
> For some reason the bedpostX process DOES NOT appear
> to have successfully completed. Please examine your
> results carefully.
> Done!
>
> Data check
> bedpostx_datacheck forbedpost
> forbedpost/data
> data_type INT16
> dim1 480
> dim2 480
> dim3 48
> dim4 34
> datatype 4
> pixdim1 0.5208333135
> pixdim2 0.5208333135
> pixdim3 3.2567176819
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
> forbedpost/nodif_brain_mask
> data_type FLOAT32
> dim1 480
> dim2 480
> dim3 48
> dim4 1
> datatype 16
> pixdim1 0.5208333135
> pixdim2 0.5208333135
> pixdim3 3.2567176819
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
> num lines in forbedpost/bvals
> 1
> num words in forbedpost/bvals
> 34
> num lines in forbedpost/bvecs
> 3
> num words in forbedpost/bvecs
> 102
>
>
> --
> Tim van Hartevelt
>
> Department of Psychiatry
> Oxford University
> Warneford Hospital
> Oxford
> OX3 7JX
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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