Tutorials for manipulating neuroimaging data in Python (nibabel)

[effigies]

Tutorials for manipulating neuroimaging data in Python

Project Description

A large number of file formats used in neuromaging analysis have Python support (many of them in nibabel, although a number of one-off packages exist). However, documentation may be missing or difficult to find. A useful resource would be a consolidated set of tutorials that walk through loading, modifying, creating, saving and visualizing files.

If you have experience with a file format you'd like to share, cool. If you have a file format you want to learn to work with, we can explore them in Jupyter notebooks, and turn those explorations into tutorials.

Skills required to participate

At least one of these would be good to have:

1) Python (especially Python 3) and numpy experience. 2) Experience working with at least one neuroimaging data format.

But neither is necessary.

Preparation material

Some official (or semi-official), non-Python, documentation for existing formats (in no principled order):

• NIfTI-1
• NIfTI-2
• GIFTI
• CIFTI-2
• MINC1
• MINC2
• BRIK/HEAD
• MGH, DICOM
• TrackVis .trk
• MRtrix .tck

Some existing tutorials/resources:

• NiBabel 101 (notebook) covers NIfTI-1 images
• From the 2017 Nipype workshop:
  • Using Python for neuroimaging](https://github.com/nipy/workshops/blob/master/170327-nipype/notebooks/nibabel_nilearn/nibabel_nilearn.ipynb)
  • Surface plotting example

Non-nibabel software:

• pdb_files
• pydicom

I'll add any suggestions others have. Especially if they use non-NIfTI-1 formats.

Provide links to preparation material / online tutorials. You can, for example, have a look at our list of online tutorials.

[josepman]

Hi effigies, what is your name in Mattermost (or any other way to discuss it with you)?

[effigies]

@ markiewicz