Dr. Kyle Kurkela
Research Computing Services, Boston University
Fall 2025

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

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

1. Copy the tutorial data 
  
  a. Navigate to the "tutorial" project directory
  []$ cd /projectnb/tutorial
  
  b. Create a new directory tuta#. Replace the "#" with your tutorial account number
  []$ mkdir tuta0
  
  c. Navigate to the your newly created "tuta#" directory
  []$ cd tuta0
  
  d. Copy zipped data your newly created "tuta#" directory 
  []$ cp /project/scv/examples/imaging/tut_dataprep_scc/* .
  
  e. Unzip the dicom data
  []$ unzip dicom.zip
  
  f. remove the compressed dicom archive
  []$ rm dicom.zip

2. Explore the DICOM files

  a. Navigate to the dicom directory
  []$ cd dicom

  b. Explore the files contained within the directory "dicom" using the file explorer. You can also inspect the data files using:
  []$ ls

  c. To see what a single DICOM file header looks like, you can use the AFNI's dicom_hdr tool:
  
  Load the SCC afni module to use afni commands:
  []$ module load afni/21.0.4

  To see the help information for this command:
  []$ dicom_hdr -help | less
    
  To inspect a DICOMs header information:
  []$ dicom_hdr 1.3.12.2.1107.5.2.43.166024.30000022072919140806900000007-9-99-nkpf0x.dcm | less

  Many software packages allow you to "see" dicom files. One example is the program mango.
  Once the UI is opened, navigate to a dicom file to "see" it:
  []$ module load mango/v4.1
  []$ mango

3. DICOMs -> NIFTIs

  a. load the SCC's dcm2niix module
  []$ module load dcm2niix/1.2024.02

  b. make a new directory called "nifti" to save the output
  []$ mkdir nifti

  c. take a quick look at the help for more options
  []$ dcm2niix -h | less

  d. convert from DICOM -> NIFTI! Will take a minute or two
  []$ dcm2niix -o nifti/ dicom/*

  e. Explore the files contained within the directory "nifti" using the file explorer. You can also inspect the data files using:
  []$ ls nifti

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

  g. explore the imaging data using freesurfer's freeview
  []$ module load freesurfer/7.4.1
  []$ freeview nifti/dicom_T1_MEMPRAGE_1.0mm_p3_20220801133223_7.nii

  h. explore the imaging data using mango.
     open up the file nifti/dicom_CheckerBoard_20220801133223_9.nii
  []$ module load mango/v4.1
  []$ mango

4. DICOMs -> NIFTIs -> BIDS

  a. load the dcm2bids module
  []$ module load dcm2bids/3.2.0

  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 meta data files and folders in place
  []$ dcm2bids_scaffold -o bids

  d. use the tree command to see how the directory is organized
  []$ tree bids/

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

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

  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/ &

====================================================================================
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 approximately 45 minutes to run
  []$ qsub 02_mriqc.qsub

  c. check on your job using the qstat command
  []$ qstat -u yourusername

  d. 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 approximately 1.5 hours to run
  []$ qsub 03_fmriprep.qsub

  c. check on your job using the qstat command
  []$ qstat -u yourusername

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