search

nipreps / dmriprep

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://www.nipreps.org/dmriprep
Apache License 2.0
65 stars 24 forks source link

No folder output directory of dwi created #165

Closed nabaruns closed 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. Only anat, fmap and figures are in dmriprep output directory.

And two text files are generated and stored at input data dwi folder.

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

josephmje commented 3 years ago

Thank you for raising this issue @nabaruns. dmriprep is still in an unstable state, so I would not recommend using it for analysis just yet. However, that doesn't mean that we can't write out the existing outputs to the dwi folder (see #161). I will get on that right away!

pandyasneha commented 3 years ago

Dear @oesteban has there been any update on the issue raised above? I tried running dmriprep with both 0.4.0 and 0.5.0 version, and am having similar problem, with no output dwi dir created.

oesteban commented 3 years ago

Hi @pandyasneha, unfortunatelly no news - but hopefully that may change soon as the new grant comes through.

pandyasneha commented 3 years ago

Thank you so much for the update. Looking forward to it.