Ariel Rokem, University of Washington eScience Institute
Follow along at
Brain connections change with development
Individual differences account for differences in behaviour
Adapt with learning
This has clinical significance
Neural activity: functional MRI
Anatomy: structural MRI
...
Brain connectivity: diffusion MRI
Started in 2009 by Eleftherios Garyfallidis
Contributors from at least six different countries and many different labs
gtab = gradient_table(...)
model = ReconstModel(gtab, ...)
fit = model.fit(data, ...) # => ReconstFit
prediction = fit.predict(gtab, ...)
For example
model = dti.TensorModel(gtab)
fit = model.fit(data1)
prediction = fit.predict(gtab)
RMSE = np.sqrt(\
np.mean((prediction - data2) ** 2), -1))
rRMSE = RMSE / np.sqrt(\
np.mean((data1 - data2) ** 2), -1))
Rokem et al. (2015)
Corpus callosum
Corticospinal tract
Superior
longitudinal fasciculus
DTI
Crossing fiber model
Rokem et al. (2015)
When you've only measured once
k-fold cross-validation
# Use a k of 2
dti_pred = kfold_xval(dti_model, data, 2)
csd_pred = kfold_xval(csd_model, data, 2)
Algorithm 1
Algorithm 2
LiFE: Linear Fascicle Evaluation
Forward model from the tracks to the measured signal
Pestilli et al. (2014)
From diffusion to tracks
From tracks to diffusion
...
=
Pestilli et al. (2014)
Solve for
>>> X.shape
(10e8, 10e6)
Pestilli et al. (2014)
fiber_model = life.FiberModel(gtab)
fit = fiber_model.fit(data, tracks)
prediction = fit.predict(gtab)
optimized_tracks = tracks[fit.beta>0]
The verical occipital fasciculus - a century old controversy
Yeatman et al. (2014)
The verical occipital fasciculus - a century old controversy
Yeatman et al. (2014)
Resolved through computational neuroanatomy!
Yeatman et al. (2014)
The VOF is strategically located
Takemura et al. (2014)
To transmit information between dorsal and ventral visual areas
Takemura et al. (2014)
Collaborators
Dipy:
Eleftherios
Garyfallidis
Stefan
Van der Walt
Bago
Amirbekian
Collaborators
Stanford VISTA lab:
Brian
Wandell
Franco
Pestilli
Jason
Yeatman
(now at UW ILABS!)
Hiromasa
Takemura
http://arokem.org
arokem@gmail.com
@arokem
github.com/arokem