Convert DICOM data to BIDS

[alexfoias]

Assuming that the PATH_INPUT_DATASET is organized like:

|-- data
    |-- 5416
    |   |-- 5416_T1
    |   |   |-- IM-0001-0001.dcm
    |   |   |-- IM-0001-0002.dcm
    |   |   |-- IM-0001-0003.dcm
    |   |   |-- IM-0001-0004.dcm
    |   |   |-- IM-0001-0005.dcm
    |   |   |-- IM-0001-0006.dcm
    |   |   |-- IM-0001-0007.dcm
    |   |   |-- IM-0001-0008.dcm
    |   |   |-- IM-0001-0009.dcm
    |   |   |-- IM-0001-0010.dcm
    |   |   |-- IM-0001-0011.dcm
    |   |   |-- IM-0001-0012.dcm
    |   |-- 5416_T2
    |       |-- IM-0001-0001.dcm
    |       |-- IM-0001-0002.dcm
    |       |-- IM-0001-0003.dcm
    |       |-- IM-0001-0004.dcm
    |       |-- IM-0001-0005.dcm
    |       |-- IM-0001-0006.dcm
    |       |-- IM-0001-0007.dcm
    |       |-- IM-0001-0008.dcm
    |       |-- IM-0001-0009.dcm
    |       |-- IM-0001-0010.dcm
    |       |-- IM-0001-0011.dcm
    |       |-- IM-0001-0012.dcm
    |-- 5493
        |-- 5493_T1
        |   |-- IM-0001-0001.dcm
        |   |-- IM-0001-0002.dcm
        |   |-- IM-0001-0003.dcm
        |   |-- IM-0001-0004.dcm
        |   |-- IM-0001-0005.dcm
        |   |-- IM-0001-0006.dcm
        |   |-- IM-0001-0007.dcm
        |   |-- IM-0001-0008.dcm
        |   |-- IM-0001-0009.dcm
        |   |-- IM-0001-0010.dcm
        |   |-- IM-0001-0011.dcm
        |   |-- IM-0001-0012.dcm
        |   |-- IM-0001-0013.dcm
        |-- 5493_T2
            |-- IM-0001-0001.dcm
            |-- IM-0001-0002.dcm
            |-- IM-0001-0003.dcm
            |-- IM-0001-0004.dcm
            |-- IM-0001-0005.dcm
            |-- IM-0001-0006.dcm
            |-- IM-0001-0007.dcm
            |-- IM-0001-0008.dcm
            |-- IM-0001-0009.dcm
            |-- IM-0001-0010.dcm
            |-- IM-0001-0011.dcm
            |-- IM-0001-0012.dcm
            |-- IM-0001-0013.dcm

Fixes #3

[alexfoias]

@andrewsm8 I have an initial version of the script if you want to give it a try. thanks.

[alexfoias]

1. Create temporary folder:

mkdir convert_sci
cd convert_sci

2. Download and add dcm2niix to the path:

curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_mac.zip
unzip dcm2niix_mac.zip
export PATH=$PWD:$PATH

3. Create a new file environment.yml
   touch environment.yml
   Using your favorite text editor add this content:

name: convert_sci
channels:
    - conda-forge
dependencies:
    - dcm2bids
    - pip

4. Finally, create a new conda environment to install dcm2bids:

conda env create -f environment.yml
source activate convert_sci

5. Run script
   python curate_bids_ucd.py -i PATH_TO_DATASET_TO_CONVERT -o OUTPUT_PATH -c PATH_TO_CONFIG_FILE

Note:
What I did to have a stable config for dcm2niix was to add the following line in .zshrc:
export PATH=PathToDCM2niix:$PATH
This way you don't have to do step 2 (export command) every time when you want to run dcm2bids

[naga-karthik]

Closing as all data we currently have are in BIDS format.