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nipy / dmriprep

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dMRIprep 0.5.0: No folder output dir of dwi created #115

Open nabaruns opened 3 years ago

nabaruns commented 3 years ago

Description

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.

What I Did

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

Meryam1985 commented 3 years ago

Hello create a new folder in your BIDS location, then give its path as output. I tried a command line similar to yours. and everything goes without error ... except that in the output folder I had only: figures, log, anat I didn't have DWI.

pandyasneha commented 3 years ago

Hello @nabaruns and @Meryam1985 ,

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 @Meryam1985 suggestion, 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

Meryam1985 commented 3 years ago

Hello Unfortunately, I did not find a solution for this problem. Cordially.

nabaruns commented 3 years ago

Hi everyone, kindly check the following thread of reply from the team: dmriprep reply.

We are currently using QSIprep instead.

pandyasneha commented 3 years ago

Thank you @nabaruns for your response. Let me follow up with the team in the response link you have references above.