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Hello Tim, It seems there is a problem in your dataset you give to BEDPOSTX and the dimensions you reconstruct to, after acquisition. According to what I understand, your image dimensions are 128*128*45 with 34 volumes..However, your datacheck shows 480*480*48 with 34 volumes. Hope this helps. Virendra ________________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Tim van Hartevelt [[log in to unmask]] Sent: Tuesday, January 31, 2012 11:22 AM To: [log in to unmask] Subject: [FSL] Problems running bedpostX 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 ________________________________ UT Southwestern Medical Center The future of medicine, today.