Mitchell Horn
Research Computing Service, Boston University
Summer 2024

Please contact us at help@scc.bu.edu. 

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BIDS

1. Copy the tutorial data to your local project space. 
  a. To see the SCC projects you're a part of:
  []$ groups

  b. Copy the tutorial .zip file to your project directory:
  []$ cd /projectnb/YOUR_PROJECT/
  []$ cp /project/scv/examples/imaging/data.zip .
  []$ unzip data.zip

  c. Explore the data (DICOMS):
  []$ ls data/demo/RAW

2. Convert DICOMS to NIFTI 
  []$ module load dcm2niix
  []$ mkdir data/demo/NIFTI
  []$ dcm2niix -o data/demo/NIFTI/ data/demo/RAW/*

3. Explore the converted data (NIFTI):
  []$ ls data/demo/NIFTI

  a. explore the header information
  []$ module load sublime
  []$ sublime data/demo/NIFTI/RAW_T1*.json

  b. explore the imaging data
  []$ module load freesurfer
  []$ freeview data/demo/NIFTI/RAW_T1*.nii.gz

4. Explore BIDS datastructure (this was done for you!)
  a. look at the YAML file to see what was sorted
  []$ sublime data/yaxil/test.yaml

  b. look at the dataset descriptopn
  []$ sublime data/yaxil/dataset_description.json

  c. look at the output format (also refer to slides)
  []$ tree data/yaxil/sub*

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