Neuroimaging Analysis at Scale  (Jul. 2020) (Old site; new site is at https://scinet.courses)

Assignment

We’ve downloaded a few DICOM datasets to SciNet’s teach cluster.

They are located in /scinet/course/ss2020/5_neuroimaging/data/

You can symlink the DICOM data to your own folder using:

ln -s /path/to/original /path/to/link

eg. ln -s /scinet/course/ss2020/5_neuroimaging/data/ixi ~/data/ixi

If you need to access dcm2niix, it’s available on SciNet using module load dcm2niix/1.0.20200331

The assignment is to convert one of these datasets to be BIDS-compatible. Please save your work in a text file or script for submission.

Once you have completed the conversion, you can check whether it’s correct by heading to the BIDS Validator in the browser or running the following command line script:

./scinet/course/ss2020/5_neuroimaging/run_bids_validator.sh <BIDS_FOLDER>

Keep in mind, your BIDS conversion doesn’t have to be completely accurate. We’ll be taking a look at the submissions and guide everyone on any common missteps on Thursday.

Bonus Section - use pybids and nibabel to understand more about the data

1. Use pybids to see if the dataset is complete. How many subjects do you have? How many sessions? Are there fMRI task? Have all participants completed the whole neuroimaging run (or are some expected scans missing?).

2. Use pybids to print the filepath of one the first subjects anatomical nifti file.

3. Use nibabel to get the voxel size of this file from question 2.