[STORY] Deploy diffusion MRI preprocessing BIDS app (qsiprep) in XNAT container service

[tclose]

Description

As a researcher, I want to be able to run a diffusion preprocessing BIDS app (e.g. dmriprep or qsiprep) using the XNAT container service, so that I can conveniently run it over all the sessions in my project. I would like to input all relevant scan types

• T1-weighted
• diffusion-weighted MRI

Acceptance Criteria

• [x] diffusion preprocessing BIDS app (qsiprep) image builds and launches successfully on a number of different XNAT projects/acquisition protocols
• [x] tests for qsiprep are added to repo

[Mahdieh-dst]

---Debugging---

Current Issue: ValueError: File not found: '/.../single_subject_DEFAULT_wf/dwi_preproc_wf/pre_hmc_wf/merge_minus/dwi_denoise_dir_LR_dwi_wf/denoiser/sub-DEFAULT_dir-LR_dwi_denoised.nii.gz'

Note: The sub-DEFAULT_dir-LR_dwi_denoised.nii.gz file does exist in /work/bids-dataset/sub-DEFAULT/dwi though.

Current Actions: (1) I ran the command in the command.txt file and got this error: dwidenoise: [ERROR] cannot access file "/work/bids-dataset/sub-DEFAULT/dwi/sub-DEFAULT_dir-LR_dwi.nii.gz": No such file or directory dwidenoise: [ERROR] error opening image "/work/bids-dataset/sub-DEFAULT/dwi/sub-DEFAULT_dir-LR_dwi.nii.gz"

**However, The sub-DEFAULT_dir-LR_dwi_denoised.nii.gz file does exist in /work/bids-dataset/sub-DEFAULT/dwi.

(2) To troubleshoot item (1), we installed MRTrix on the local machine and could open that file in mrview with no problem. So, no problem with that file! I am not sure, why the file cannot be found when running qsiprep???