Dependencies

DWIQC is built upon prequal, qsiprep, and FSL software packages. chromium is used for creating PNG files. The containers are based on Singularity.

Package	Version
prequal	1.1.0
qsiprep	0.18.0
FSL	6.0.7.16
chromium	102.0.5005.115

PreQual

DWIQC runs PreQual with the following command:

singularity run -e --env PYTHONUNBUFFERED=1 \
  --pwd /tmp \
  --contain \
  --nv \
  -B /path/to/inputs:/INPUTS/ \
  -B /path/to/outputs:/OUTPUTS \
  -B /tmp:/tmp \
  -B /path/to/freesurfer/license.txt:/APPS/freesurfer/license.txt \
  prequal_nrg.sif \
  --save_component_pngs \
  --subject <SUBJECT> \
  --project Proj \
  --session <SESSION> \
  --eddy_cuda 10.2 j \
  --num_threads 2 \
  --denoise on \
  --degibbs off \
  --rician off \
  --prenormalize on \
  --correct_bias on \
  --topup_first_b0s_only \
  --extra_eddy_args=--data_is_shelled+--ol_nstd=<STDEV>+--ol_type=gw+--repol+--estimate_move_by_susceptibility+--cnr_maps+--flm=quadratic+--interp=spline+--resamp=jac+--mporder=<MPORDER>+--niter=5+--nvoxhp=1000+--slspec=/INPUTS/<SPEC>+--slm=linear

QSIPrep

DWIQC runs QSIPrep with the following command:

singularity run --nv \
  qsiprep.sif \
  /path/to/bids \
  /path/to/outputs \
  participant \
  --output-resolution <RESOLUTION> \
  --eddy-config /path/to/bids/eddy_params_s2v_mbs.json \
  --fs-license-file /path/to/freesurfer/license.txt \
  -w /path/to/workdir \
  --pepolar-method TOPUP \
  --prefer_dedicated_fmaps \
  --b1-biascorrect-stage final \
  --separate-all-dwis \
  --notrack \
  --n_cpus 2 \
  --mem_mb 40000