Mitchell Horn
Research Computing Service, Boston University
Spring 2023

These are instruction notes for the fMRIPrep Tutorial. This is to be followed in correspondance to the fMRIPrep slides also found in this directory. For questions about using fMRIPrep on the SCC please contact us at help@scc.bu.edu. 


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 new directory:
  []$ cd /projectnb/YOUR_PROJECT/
  []$ cp /project/scv/examples/imaging/tut_fmriprep_scc/fmriprep_tutorial.zip .
  []$ unzip fmqc_tutorial.zip
  []$ cd fmqc_tutorial


2. Change into an example BIDS directory.
  []$ cd /BIDS
  []$ ls -lF


3. Check that there are infact DICOMS in your new subject directory:
  []$ less 220801_Rise_demo_01/RAW

  ctrl+z

4. Remove the DICOMS we downloaded (we won't need them for the tutorial):
  []$ rm -rf 220801_Rise_demo_01

5. Create configuration file for YAXIL to convert DICOMS --> BIDS:
  a. Load a text editor and make the file:
  []$ sublime test.yaml

  b. Copy the below text between the # exactly as is:

####################################################

func:
  bold:
   - scan: 16
     task: rest
     run: 1

anat:
  T1w:
   - scan: 7
     run: 1

#####################################################

6. Download the study again using YAXIL, but this time use the .yaml file to convert directly into BIDS:
  []$ ArcGet.py -a xnat -l 220801_Rise_demo_01 -p Workshop -f bids -c test.yaml -o . 

7. Check that there are infact BIDS data in your new subject directory:
  []$ ls -l sub-220801Risedemo01/ses-220801Risedemo01/anat/
  []$ ls -l sub-220801Risedemo01/ses-220801Risedemo01/func/

8. Review the simplified single subject submission file to see the requirements:
  []$ cd qsub
  []$ sublime fmriprep_single.qsub

9. Make the changes required for submission:
  a. Open the qsub file:
  []$ sublime fmriprep_single.qsub

  b. Add your project to lines #4:
    4. #$ -P YOUR_PROJECT_CODE

  c. (optional) Add the output directory to store the submission files. Currently stores in same folder 'qsub':
    19. #$ -o /my/directory

  d. (optional) Add the path to your input BIDS and output directories. Currently pulls from 1-level up and saves to 1-level up derivatives:
    29. fmriprep input output

10. Submit the job
  []$ qsub fmriprep_single.qsub

11. Check that your submission starts (can take a few minutes):
  []$ watch qstat -u YOUR_USERNAME

  ctrl+z
  
12. NOTE: there is a more advance submission script for submitting multiple subjects. Let review the submission file:
  []$ sublime fmriprep_MULTI.qsub

13. While that job process (should take about 2 hours), lets review an existing output:
  []$ cd ../derivatives
  []$ firefox sub-tutorial.html