Quick Quality Check (QQC)

QQC is a Python library for checking protocol deviations in the U24 MRI dicoms.

Check out our full documentation

Note: The project is under the active development.

Simple example

• To process dicom files under PHOENIX/PROTECTED/PronetLA/raw/BW00001/mri/BW00001_MR_2021_07_22_1,
• compare them to a BIDS session rawdata/sub-ProNETUCLA/ses-humanpilot,
• and save the outputs under MRI_ROOT, use the command below

$ dicom_to_dpacc_bids.py \
   --input_dir PHOENIX/PROTECTED/PronetLA/raw/BW00001/mri/BW00001_MR_2021_07_22_1 \
   --subject_name BW00001 \
   --session_name 202107221 \
   --output_dir MRI_ROOT \
   --standard_dir rawdata/sub-ProNETUCLA/ses-humanpilot \

Command above creates structure below

MRI_ROOT/
├── sourcedata                               
│   └── BW00001
│       └── ses-202107221                     # cleaned up dicoms
│           ├── 01_Localizer
│           ├── ...
│           └── 30_rfMRI_REST_PA
├── rawdata
│   └── sub-BW00001
│       └── ses-202107221                     # BIDS nifti files
│           ├── anat
│           │   ├── sub-BW00001_ses-202107221_rec-nonnorm_run-1_T1w.json
│           │   ├── ...
│           │   └── sub-BW00001_ses-202107221_rec-norm_run-1_T2w.nii.gz
│           ├── dwi
│           │   ├── sub-BW00001_ses-202107221_acq-176_dir-PA_run-1_dwi.bval
│           │   ├── ...
│           │   └── sub-BW00001_ses-202107221_acq-b0_dir-AP_run-2_sbref.nii.gz
│           ├── fmap
│           │   ├── sub-BW00001_ses-202107221_acq-13_dir-AP_run-3_epi.json
│           │   ├── ...
│           │   └── sub-BW00001_ses-202107221_acq-8_dir-PA_run-2_epi.nii.gz
│           ├── func
│           │   ├── sub-BW00001_ses-202107221_task-rest_dir-AP_run-1_bold.json
│           │   ├── ...
│           │   └── sub-BW00001_ses-202107221_task-rest_dir-PA_run-2_sbref.nii.gz
│           ├── ignore
│           │   ├── sub-BW00001_ses-202107221_ignore-bids_num-1_localizer1.json
│           │   ├── ...
│           │   └── sub-BW00001_ses-202107221_ignore-bids_num-6_localizer_aligned3.nii.gz
│           └── sub-BW00001_ses-202107221_scans.tsv
└── derivatives
   ├── dwipreproc
   │   └── sub-BW00001
   │       └── ses-202107221
   ├── mriqc
   │   ├── sub-BW00001
   │   │   └── ses-202107221
   │   │       ├── anat
   │   │       │   ├── sub-BW00001_ses-202107221_rec-nonnorm_run-1_T1w.json
   │   │       │   ├── sub-BW00001_ses-202107221_rec-nonnorm_run-1_T2w.json
   │   │       │   ├── sub-BW00001_ses-202107221_rec-norm_run-1_T1w.json
   │   │       │   └── sub-BW00001_ses-202107221_rec-norm_run-1_T2w.json
   │   │       └── func
   │   │           ├── sub-BW00001_ses-202107221_task-rest_dir-AP_run-1_bold.json
   │   │           ├── sub-BW00001_ses-202107221_task-rest_dir-AP_run-2_bold.json
   │   │           ├── sub-BW00001_ses-202107221_task-rest_dir-PA_run-1_bold.json
   │   │           └── sub-BW00001_ses-202107221_task-rest_dir-PA_run-2_bold.json
   │   ├── sub-BW00001_ses-202107221_rec-nonnorm_run-1_T1w.html
   │   ├── sub-BW00001_ses-202107221_rec-nonnorm_run-1_T2w.html
   │   ├── sub-BW00001_ses-202107221_rec-norm_run-1_T1w.html
   │   ├── sub-BW00001_ses-202107221_rec-norm_run-1_T2w.html
   │   ├── sub-BW00001_ses-202107221_task-rest_dir-AP_run-1_bold.html
   │   ├── sub-BW00001_ses-202107221_task-rest_dir-AP_run-2_bold.html
   │   ├── sub-BW00001_ses-202107221_task-rest_dir-PA_run-1_bold.html
   │   └── sub-BW00001_ses-202107221_task-rest_dir-PA_run-2_bold.html
   └── quick_qc
       └── sub-BW00001
           └── ses-202107221
               ├── bval_comparison_log.txt
               ├── csa_headers.csv
               ├── json_check_image_orientation_in_anat.csv
               ├── json_check_image_orientation_in_dMRI_fMRI_and_distortionMaps.csv
               ├── json_check_shim_settings.csv
               ├── json_comparison_log.txt
               ├── scan_order.csv
               ├── series_count.csv
               ├── sub-BW00001_ses-202107221_acq-176_dir-PA_run-1_dwi.png
               ├── sub-BW00001_ses-202107221_acq-176_dir-PA_run-1_sbref.png
               ├── sub-BW00001_ses-202107221_acq-b0_dir-AP_run-1_dwi.png
               ├── sub-BW00001_ses-202107221_acq-b0_dir-AP_run-1_sbref.png
               ├── sub-BW00001_ses-202107221_acq-b0_dir-AP_run-2_dwi.png
               ├── sub-BW00001_ses-202107221_acq-b0_dir-AP_run-2_sbref.png
               ├── sub-BW00001_ses-202107221_rec-nonnorm_run-1_T1w.png
               ├── sub-BW00001_ses-202107221_rec-nonnorm_run-1_T2w.png
               ├── sub-BW00001_ses-202107221_rec-norm_run-1_T1w.png
               ├── sub-BW00001_ses-202107221_rec-norm_run-1_T2w.png
               ├── summary_b0.png
               ├── summary_dwi.png
               ├── summary_fmri.png
               ├── volume_slice_number_comparison_log.csv
               └── within_phantom_qc.txt