With the latest docker image, run gets completed with no errors. But no output dwi directory gets created and hence no output.
And two text files are generated and stored at input data dwi folder.
Only anat, fmap and figures are in dmriprep output directory.
Command used:
sudo docker run -ti --rm -v /home/n/BIDS/05225665_01/:/inputs -v /home/n/dmriprep/05225665_01/:/outputs -v /home/v/freesurfer:/freesurfer -v /home/n/dmriprep/work/:/work nipreps/dmriprep:latest /inputs /outputs participant -w /work --participant-label 0522566501 --fs-license-file /freesurfer/license.txt --ignore fieldmaps --fs-no-reconall --output-spaces MNI152NLin6Asym:res-2
Hello @nabaruns,
I hope all is well. Were you able to figure this issue with dmriprep? I am currently facing the same thing while using dmriprep 0.4.0. I stopped using dmriprep 0.5.0 version for now as it was giving me lots of error with use-syn-sdc flag and output-spaces type. As you described, I am also not getting any error towards the end however it just creates anat folder w/o dwi folder. The command that I have used is as follow:
docker run -ti -v /home/ubuntu/tracktbi:/inputs -v /home/ubuntu/tracktbi/derivatives:/outputs -v ${fslicense}:/opt/freesurfer/license.txt:ro nipreps/dmriprep:0.4.0 /inputs /outputs participant --participant-label 011011 -v --ignore fieldmaps --use-syn-sdc --output-spaces MNI152NLin6Asym --low-mem --fs-subjects-dir /outputs/freesurfer --fs-no-reconall --notrack
Based on a suggestion here, I also tried to create a new output directory inside my bids derivative folder which is tracktbi/derivatives in my case as follow, but still I do not get an output dwi folder, not sure if I am doing anything wrong. May you please suggest if you got it working and how?
docker run -ti -v /home/ubuntu/tracktbi:/inputs -v /home/ubuntu/tracktbi/derivatives/dmriprep:/outputs -v /home/ubuntu/tracktbi/derivatives:/fs_outputs -v ${fslicense}:/opt/freesurfer/license.txt:ro nipreps/dmriprep:0.4.0 /inputs /outputs participant --participant-label 011011 -v --ignore fieldmaps --use-syn-sdc --output-spaces MNI152NLin6Asym --low-mem --fs-subjects-dir /fs_outputs/freesurfer --fs-no-reconall --notrack
Thank you,
Sneha
I am having the same problem with dmriprep 0.5.0.
Preprocessing of dwi seems to be completed without errors but no output dwi folder is created.
Any suggestions on that?
No solution yet, not sure what is going on. It is weird that it creates all other folder except dwi. Hoping someone can help figure it out.