### COMMON OPTIONS AND THEIR MEANINGS ###
# -it       Get an interactive terminal #
# --rm      Clean up container on exit  #
# -v /A:/B  Mount /A inside image as /B #
#########################################

# Open an Ubuntu 18.04 Docker image with a BASH terminal
# and have your home folder available inside as /myhome
docker run -it --rm \
           -v ${HOME}:/myhome \
           ubuntu:18.04 /bin/bash

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "Prisma",
    "DeviceSerialNumber": "anon8928",
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "SoftwareVersions": "syngo_MR_E11",
    "MRAcquisitionType": "3D",
    "SeriesDescription": "ABCD-T1-NORM_SIEMENS_original_(baseline_year_1_arm_1)",
    "ProtocolName": "ABCD_T1w_MPR_vNav",
    "ScanningSequence": "GR_IR",
    "SequenceVariant": "SK_SP_MP",
    "ScanOptions": "IR_WE",
    "SequenceName": "tfl3d1_16ns",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND",
        "NORM"
    ],
    "SeriesNumber": 5,

{
    "descriptions": [
        {
            "dataType": "anat",
            "modalityLabel": "T1w",
            "criteria": {
                "SeriesDescription": "ABCD-T1_SIEMENS_original_(baseline_year_1_arm_1)"
            }
        },
        {
            "dataType": "func",
            "modalityLabel": "bold",
            "customLabels": "task-rest",
            "criteria": {
                "SeriesDescription": "ABCD-rsfMRI_SIEMENS_mosaic_original_(baseline_year_1_arm_1)"
            }
        }
    ]
}

# FIRST STEPS DIRECTLY FROM DCM2BIDS REPOSITORY
# 1. cd <YOUR_FUTURE_BIDS_FOLDER>
# 2. dcm2bids_scaffold
# 3. dcm2bids_helper -d <FOLDER_WITH_DICOMS_OF_A_TYPICAL_SESSION>
# 4. Build your configuration file with the help of the content
#    of tmp_dcm2bids/helper


# For the dcm2bids command itself:
#   DICOM_DIR is a directory of DICOMs
#   PARTICIPANT_ID and SESSION_ID are IDs picked by you
#   These IDs MUST be only alphanumeric with no symbols
#   CONFIG_FILE is a Dcm2Bids configuration JSON file
#   Read here for more on CONFIG_FILE:
#     https://cbedetti.github.io/Dcm2Bids/config/

dcm2bids -d DICOM_DIR -p PARTICIPANT_ID -s SESSION_ID -c CONFIG_FILE

usage: run.py [-h]
	              [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
	              bids_dir output_dir {participant,group}

	Example BIDS App entry point script.

	positional arguments:
	  bids_dir              The directory with the input dataset formatted
	                        according to the BIDS standard.
	  output_dir            The directory where the output files should be stored.
	                        If you are running a group level analysis, this folder
	                        should be prepopulated with the results of
	                        the participant level analysis.
	  {participant,group}   Level of the analysis that will be performed. Multiple
	                        participant level analyses can be run independently
	                        (in parallel).

	optional arguments:
	  -h, --help            show this help message and exit
	  --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
	                        The label(s) of the participant(s) that should be
	                        analyzed. The label corresponds to
	                        sub-<participant_label> from the BIDS spec (so it does
	                        not include "sub-"). If this parameter is not provided
	                        all subjects will be analyzed. Multiple participants
	                        can be specified with a space separated list.

# Run the abcd-hcp-pipeline on all subjects
# within the local /path/to/bids_dataset
# mounted "read-only" (ro) as /input
# and /path/to/outputs as /output
# and /path/to/freesurfer/license
# as /license

docker run -it --rm \
    -v /path/to/bids_dataset:/input:ro \
    -v /path/to/outputs:/output \
    -v /path/to/freesurfer/license:/license \
    dcanlabs/abcd-hcp-pipeline /input /output \
        --freesurfer-license=/license [OPTIONS]