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Nipy on functional brain MRI

Translations: en

Description

Alexandre Savio - Nipy on functional brain MRI [EuroPython 2016] [22 July 2016] [Bilbao, Euskadi, Spain] (https://ep2016.europython.eu//conference/talks/nipy-on-functional-brain-mri)

This is an introductory talk to modern brain image analysis tools. I will show how to use nipy tools to process one resting-state fMRI subject, perform intra-subject registration, ICA analysis to extract and visualize resting-state networks. If the time allows me I will introduce an anatomical brain atlas and how to perform non-linear registration to do atlas-based segmentation.


This is an introductory talk to modern brain image analysis tools. I will show how to use nipy tools to process one resting-state fMRI subject, perform intra-subject registration, ICA analysis to extract and visualize resting-state networks. If the time allows me I will introduce how to perform non-linear registration to to atlas-based segmentation.

The outline of the talk:

  1. Present the COBRE dataset and show its characteristics.
  2. Use nibabel to open a NifTI file and see the matrix/volume parameters.
  3. Use nilearn.plotting to show the anatomical image.
  4. Use nipy to co-register the anatomical image to the fMRI image.
  5. Use nilearn to perform CanICA and plot ICA spatial segmentations.

If time allows:

  1. Present a brain anatomical atlas and its template.
  2. Present the tools needed for non-linear registration.
  3. Show the result of an atlas-based segmentation result.
  4. Use nilearn to calculate the resting-state functional connectivity matrix of the subject.
  5. Plot it with Bokeh.
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