bc-jupyterNotebook

This repo contains Brain common Jupyter notebooks, corresponding library wth functions that support the Jupyter notebooks

ENIGMA_Cortical_Thickness run through steps of ENIGMA Cortical Thickness pipeline:

1. MRI image preprocessing using FreeSurfer
2. Extract thickness and area values for cortical subfields from FreeSurfer result
3. Quality contral visualization
4. Group comparison based on different measures of cortical subfields between mental disease cohorts and health contral.

ENIGMA_subcortical_volume

1. MRI image preprocessing using FreeSurfer
2. Extract volume sizes of subcortical subfields from FreeSurfer result
3. Outlier detection
4. Quality contral visualization

ENIGMA_Hippocampal_Subfield

1. MRI image preprocessing and hippocampal subfield segmentation using seFreeSurfer
2. Extract volume sizes of hippocampal subfields from FreeSurfer result
3. Outlier detection
4. Quality contral visualization
5. Scatter plots on 12 subfields (left vs right)
6. Analysis on individual subfield

MJFF

1. Basic statistics on PPMI data
2. Analysis across projects
3. Statistical analysis on asseessments
4. Group comparison between cohorts with different mutations and heath control
5. Statistical analysis between cohorts with and without LRRK2 mutation.