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HW2: BIDS
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README.md

README.md

HW2: BIDS Conversion

Due Feb 23.

Data Description

The raw DICOM data is located in /scratch/psyc5171/exercises/bidshw for a single subject, TD902TD (note you will need to copy and rename this folder).

The scans consist of:

  • Series 1-4: AutoAlign scout
  • Series 5: T1w MPRAGE
  • Series 6-7: One run of the 'music' fMRI task and corresponding singleband reference volume
  • Series 8: A physiological recording log. This should be ignored.
  • Series 9-10: First run of the 'prosody' fMRI task and corresponding singleband reference volume
  • Series 11: A physiological recording log. This should be ignored.
  • Series 12-13: Second run of the 'prosody' fMRI task and corresponding singleband reference volume
  • Series 14: A physiological recording log. This should be ignored.

Assignment

  1. Fork this repository
  2. Clone your fork to the cluster under your /scratch directory: git clone https://github.uconn.edu/$USER/hw2
  3. Convert the provided data to BIDS form using BIDS Coiner. Your resulting bids directory should be under the hw2 directory so that your changes can be commited using git.
  4. Add (git add -A) and commit (git commit) the resulting changes to your hw2 directory. MRI data will be automatically ignored when add files using git.
  5. Push changes to your remote (git push)
  6. Create a pull request to submit your assignment.

Important Changes

In class, the sbatch_step1.sh script renamed DICOM folders and created the bids/code/bidscoiner/samples directory. Since running the script twice creates nested DICOM directories which do not work with the conversion step, this has been split into two scripts:

  • sbatch_step1a.sh only creates bids/code/bidscoiner/samples
  • sbatch_step1b.sh only renames the DICOM folders. If you run step1b multiple times, you will get nested DICOM directories and the conversion will not work. Remember that DICOM files need to be in subject/series folder structure.

Somewhat Useful Tips

  • You will need to copy the provided TD902TD folder to your own directory and rename the folder to have the correct prefix. The subject folder should be placed under raw.
  • No major edits to the YAML file are required.
  • A partial bids directory tree has been created for you and the same scripts we used in class are under bids/code in this repository. You need to edit the scripts to use the appropriate paths, which depend on where you clone the repository to.
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