Dear Anastasia, Re-running bedpostX just did it and I didn't encounter the problem on any subjects after that. Everything is running great now. I just had 2 more follow-up questions: what's the best way to concatenate the 2 repeat DICOM DWI series into 1 NIFTI file (you mentioned that below)? How do I extract average FA values constrained by the extracted fiber tracts? Thanks so much for all your help, Ansgar
On Wed, Sep 28, 2011 at 5:07 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
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.htmlhttp://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 ayendiki@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.yThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.