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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
This example routine simulates a number of pure Gaussian white noise
signals, then fits each one in terms of two regressors: a constant baseline,
and a linear function of time. The voxelwise t statistics associated
with the baseline coefficient are then computed.
"""
print __doc__
import numpy as np
from nipy.neurospin import glm
dimt = 100
dimx = 10
dimy = 11
dimz = 12
# axis defines the "time direction"
y = np.random.randn(dimt, dimx*dimy*dimz)
axis = 0
"""
y = random.randn(dimx, dimt, dimy, dimz)
axis = 1
"""
X = np.array([np.ones(dimt), range(dimt)])
X = X.transpose() ## the design matrix X must have dimt lines
#mod = glm.glm(y, X, axis=axis) ## default is spherical model using OLS
mod = glm.glm(y, X, axis=axis, model='ar1')
#mod = glm.glm(y, X, formula='y~x1+(x1|x2)', axis=axis, model='mfx')
##mod.save('toto')
##mod = glm.load('toto')
# Define a t contrast
tcon = mod.contrast([1,0])
# Compute the t-stat
t = tcon.stat()
## t = tcon.stat(baseline=1) to test effects > 1
# Compute the p-value
p = tcon.pvalue()
# Compute the z-score
z = tcon.zscore()
# Perform a F test without keeping the F stat
p = mod.contrast([[1,0],[1,-1]]).pvalue()
# Perform a conjunction test similarly
##p = mod.contrast([[1,0],[1,-1]], type='tmin').pvalue()
print np.shape(y)
print np.shape(X)
print np.shape(z)
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