dmripep dwi output space

[halilaziz]

Hello folks,
I am running dmriprep via docker.
It is finishing succesfully but when I check the output space, there are only anat, figures. and logs folders. There is no dwi folder. Is there any solution for it?
Thank you

You may find my docker command below:
docker run --rm -it -v /analysis/halilaziz/bids_raw:/data -v /analysis/halilaziz/dmriprep:/output -v /usr/local/local/opt/freesurfer6/license.txt:/usr/local/local/opt/freesurfer6/license.txt nipreps/dmriprep:latest /data /output/ participant --participant-label 12193 --nthreads 8 --omp-nthreads 8 --mem_mb 16000 --low-mem --notrack --fs-license-file /usr/local/local/opt/freesurfer6/license.txt --output-space dwi --skip-bids-validation

[maryjis]

Yes, I have the similar problem. With the latest docker image, run gets completed with no errors, but I have only two files in dwi output (brain mask and b0 ref), no one dwi derivitives

[halilaziz]

Hi Maria, I recommend you use just the FSL edyy_openmp command for the preprocessing. I think dmriprep is not so useful. Best Halil Aziz

…

-- *Halil Aziz VELIOGLU, PhD* *Postdoctoral Research Trainee* Feinstein Institute for Medical Research, Center for Psychiatric Neuroscience *Assistant Professor* Istanbul Medipol University, functional Imaging and Cognitive-Affective Neuroscience Lab (fINCAN) Maria Zubrikhina ***@***.***>, 7 Haz 2023 Çar, 10:26 tarihinde şunu yazdı:

Yes, I have the similar problem. With the latest docker image, run gets completed with no errors, but I have only two files in dwi output (brain mask and b0 ref), no one dwi derivitives — Reply to this email directly, view it on GitHub <#199 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALQXRDKVEGNJONH2DNBEJCLXKCFP5ANCNFSM6AAAAAAWVN2MXY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[arokem]

dmriprep is still pre-alpha software, so it still does not produce useful outputs. I think that's something we should add to the README and documentation of the software. I'll make a PR.