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 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: 7. Present a brain anatomical atlas and its template. 8. Present the tools needed for non-linear registration. 9. Show the result of an atlas-based segmentation result. 10. Use nilearn to calculate the resting-state functional connectivity matrix of the subject. 11. Plot it with Bokeh.