Usage

dicom_to_dpacc_bids.py

To process all dicom files under a dicom directory, and compare them to another BIDS directory for any protocol differences, use the command below.

dicom_to_dpacc_bids.py \
    --input_dir ROOT/OF/DICOM_DIR \
    --subject_name SubjectName \    # without 'sub-'
    --session_name SessionName \    # without 'ses-'
    --output_dir OUTPUT/DIR/ROOT \
    --standard_dir BIDS/SESSION/OF/STANDARD/DATA

This wll save the outputs under MRI_ROOT.

1. --input_dir can virtually take any form of structure as long as there are dicom files under the directory.

   • eg) PHOENIX/PROTECTED/PronetLA/raw/BW00001/mri/BW00001_MR_2021_07_22_1

2. For --subject_name, use the subject ID. sub- prefix will be attached in front of the given subject name.

   • eg) --subject_name BW00001

3. For --session_name, use the date and unique label number without any spaces, -, or _.

   • eg) --session_name 202107221

4. --output_dir is the root directory of the output. This path is where sourcedata, rawdata and derivatives directories will be created.

   • eg) -output_dir MRI_ROOT

5. --standard_dir is the root of BIDS session that you would like to compare the protocols of the --input_dir.

   • eg) rawdata/sub-ProNETUCLA/ses-phantom

Available options

1. Run extra QC to make comparison to different standard BIDS directory.

--qc_subdir QC_SUBDIR, -qs QC_SUBDIR
                      ExtraQC output directory name.

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 \
    --qc_subdir comparison_to_phantom \
    --output_dir MRI_ROOT \
    --standard_dir rawdata/sub-ProNETUCLA/ses-phantom \

Output structure

MRI_ROOT/
├── sourcedata
│   └── BW00001
│       └── ses-202107221
│           ├── 01_Localizer
│           ├── ...
│           └── 30_rfMRI_REST_PA
├── rawdata
│   └── sub-BW00001
│       └── ses-202107221
│           ├── anat
│           │   ├── sub-BW00001_ses-202107221_rec-nonnorm_run-1_T1w.json
│           │   └── ...
│           ├── dwi
│           │   ├── sub-BW00001_ses-202107221_acq-176_dir-PA_run-1_dwi.bval
│           │   └── ...
│           ├── fmap
│           │   ├── sub-BW00001_ses-202107221_acq-13_dir-AP_run-3_epi.json
│           │   └── ...
│           ├── func
│           │   ├── sub-BW00001_ses-202107221_task-rest_dir-AP_run-1_bold.json
│           │   └── ...
│           ├── ignore
│           │   ├── sub-BW00001_ses-202107221_ignore-bids_num-1_localizer1.json
│           │   └── ...
│           └── sub-BW00001_ses-202107221_scans.tsv
└── derivatives
    ├── dwipreproc
    │   └── sub-BW00001
    │       └── ses-202107221
    ├── fmriprep
    ├── mriqc
    │   ├── sub-BW00001
    │   │   └── ses-202107221
    │   │       ├── anat
    │   │       └── func
    │   ├── sub-BW00001_ses-202107221_rec-nonnorm_run-1_T1w.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
                ├── summary_b0.png
                ├── summary_dwi.png
                ├── summary_fmri.png
                ├── volume_slice_number_comparison_log.csv
                ├── within_phantom_qc.txt
                ├── sub-BW00001_ses-202107221_acq-176_dir-PA_run-1_dwi.png
                └── ...