Dr. Kyle Kurkela
Research Computing Service, Boston University
Spring 2025

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

====================================================================================
BIDS

1. Copy the tutorial data to your local project space. 
  a. Copy the tutorial .zip file to the directory you wish to work in:
  []$ cd /projectnb/YOUR_PROJECT/some_directory
  []$ cp /project/scv/examples/imaging/tut_dataprep_scc/* .
  []$ unzip dicom.zip
  * Note: you can also use the 00_getdata.sh bash script to copy the data:
  []$ 00_getdata.sh

  b. Explore the data (DICOMS):
     view the dicom directory
  []$ ls dicom/
     explore the header of one of the dicom files
  []$ module load afni
  []$ dicom_hdr dicom/1.3.12.2.1107.5.2.43.166024.30000022072919140806900000007-16-120-1ytpsbb.dcm

2. Convert DICOMS to NIFTI 
  []$ module load dcm2niix
  []$ mkdir nifti
  []$ dcm2niix -o nifti/ dicom/*

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

  a. explore the header information
  []$ module load sublime
  []$ sublime nifti/dicom_T1_MEMPRAGE_1.0mm_p3_20220801133223_7.json

  b. explore the imaging data
  []$ module load freesurfer
  []$ freeview nifti/dicom_T1_MEMPRAGE_1.0mm_p3_20220801133223_7.nii

4. Convert the DICOMs to BIDS
  
  a. load the dcm2bids module
  []$ module load dcm2bids

  b. create a new directory where you want to store your BIDS formated data
  []$ mkdir bids

  c. create a bids 'scaffold' -- a directory with all the BIDS files and folders
  []$ dcm2bids_scaffold -o bids

  d. create a config.json file using your preferred text editor
  []$ module load sublime
  []$ sublime config.json

  e. bids-ify your DICOM files!!
  []$ dcm2bids -d dicom -p 001 -c config.json -o bids

  f. remove the temporary bids directory
  []$ rm -rf bids/tmp_dcm2bids

  g. test the dataset using the bids valdiator
  []$ firefox --new-window https://bids-standard.github.io/bids-validator/ &

  h. add some text to the README file
  []$ module load sublime
  []$ sublime bids/README

  i. remove the two subjects from the participants.tsv file
  []$ module load sublime
  []$ sublime bids/participants.tsv

  j. test the dataset again
  []$ firefox --new-window https://bids-standard.github.io/bids-validator/ &

5. Explore BIDS datastructure

  a. look at the dataset descripton, README, participants.tsv
  []$ sublime bids/dataset_description.json
  []$ sublime bids/README
  []$ sublime bids/participants.tsv

  b. look at the output format
  []$ tree bids/

====================================================================================
MRIQC
  
  a. open the mriqc.qsub file and edit the file paths to suit your needs:
  []$ module load sublime
  []$ sublime 02_mriqc.qsub 

  b. submit the job to the queue to run. It should take less than 20 minutes to run
  []$ qsub 02_mriqc.qsub

  c. Once the job has finished running, inspect the html reports using a web browser:
  []$ firefox --new-window bids/derivatives/mriqc/sub001_task-checkerboard_bold.html &

====================================================================================
FMRIPREP

  a. open the mriqc.qsub file and edit the file paths to suit your needs:
  []$ module load sublime
  []$ sublime 03_fmriprep.qsub

  b. submit the job to the queue to run. It should take less than 2 hours to run
  []$ qsub 03_fmriprep.qsub

  c. Once the job has finished running, inspect the html reports using a web browser:
  []$ firefox --new-window bids/derivatives/fmriprep/sub-001.html &