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.
- 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 \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