def hrfplot2(in_file, maxT):
import numpy as np
import matplotlib.pyplot as plt
from pylab import figure, axes, pie, title, show
from nipy.modalities.fmri import hrf
from nipy.modalities.fmri.utils import T, lambdify_t
import csv
with open(in_file) as f:
reader = csv.reader(f, delimiter=str("\t"))
d = list(reader)
mat = np.array(d)
onsets = mat[:, 0]
int_lst_onsets = [int(float(x)) for x in onsets]
int_lst_onsets.sort()
glover = hrf.glover(T)
tb = int_lst_onsets
bb = 1
nb = bb * sum([glover.subs(T, T - t) for t in tb])
nbv = lambdify_t(nb)
t = np.linspace(0, float(maxT), 10000)
plt.plot(t, nbv(t), c='b', label=in_file)
for t in tb:
plt.plot([t, t], [0, bb * 0.1], c='r')
plt.legend()
plt.show()
def convolve_regressors(paradigm, hrf_model, end_time, fir_delays=[0],
fir_duration=1.):
""" Creation of a formula that represents
the convolution of the conditions onset with a certain hrf model
Parameters
----------
paradigm: paradigm instance
hrf_model: string that can be 'Canonical',
'Canonical With Derivative' or 'FIR'
that specifies the hemodynamic reponse function
end_time: float,
end time of the paradigm (needed only for block designs)
fir_delays=[0], optional, array of shape(nb_onsets) or list
in case of FIR design, yields the array of delays
used in the FIR model
fir_duration=1., float, duration of the FIR block
in general it should eb equal to the tr
Returns
-------
f: formula instance,
contains the convolved regressors as functions of time
names: list of strings,
the condition names, that depend on the hrf model used
if 'Canonical' then this is identical to the input names
if 'Canonical With Derivative', then two names are produced for
input name 'name': 'name' and 'name_derivative'
fixme
-----
normalization of the columns of the design matrix ?
"""
listc = []
hnames = []
typep = paradigm.type
for nc in np.unique(paradigm.con_id):
onsets = paradigm.onset[paradigm.con_id == nc]
nos = np.size(onsets)
if paradigm.amplitude is not None:
values = paradigm.amplitude[paradigm.con_id == nc]
else:
values = np.ones(nos)
if nos < 1:
continue
if typep == 'event':
if hrf_model == "Canonical":
c = utils.define(
nc, utils.events(onsets, values, f=hrf.glover))
listc.append(c)
hnames.append(nc)
elif hrf_model == "Canonical With Derivative":
c1 = utils.define(
nc, utils.events(onsets, values, f=hrf.glover))
c2 = utils.define(nc + "_derivative",
utils.events(onsets, values, f=hrf.dglover))
listc.append(c1)
listc.append(c2)
hnames.append(nc)
hnames.append(nc + "_derivative")
elif hrf_model == "FIR":
for i, ft in enumerate(fir_delays):
lnames = nc + "_delay_%d" % i
changes = np.hstack((onsets + ft,
onsets + ft + fir_duration))
ochanges = np.argsort(changes)
lvalues = np.hstack((values, np.zeros(nos)))
changes = changes[ochanges]
lvalues = lvalues[ochanges]
c = utils.define(lnames,
utils.step_function(changes, lvalues))
listc.append(c)
hnames.append(lnames)
else:
raise NotImplementedError('unknown hrf model')
elif typep == 'block':
offsets = onsets + paradigm.duration[paradigm.con_id == nc]
intervals = [[on, off] for (on, off) in zip(onsets, offsets)]
blks = utils.blocks(intervals, values)
changes = np.hstack((onsets, offsets))
cvalues = np.hstack((values, - values))
if hrf_model == "Canonical":
c = utils.convolve_functions(blks, hrf.glover(hrf.T),
[0, end_time], 0.001)
listc.append(c)
hnames.append(nc)
elif hrf_model == "Canonical With Derivative":
c1 = utils.convolve_functions(blks, hrf.glover(hrf.T),
[0, end_time], 0.001)
c2 = utils.events(changes, cvalues, f=hrf.glover)
listc.append(c1)
listc.append(c2)
hnames.append(nc)
hnames.append(nc + "_derivative")
elif hrf_model == "FIR":
raise NotImplementedError(
'block design are not compatible with FIR')
else:
raise NotImplementedError('unknown hrf model')
# create the formula
p = formula.Formula(listc)
return p, hnames
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Plot of the canonical Glover HRF
"""
import numpy as np
from nipy.modalities.fmri import hrf, utils
import matplotlib.pyplot as plt
# hrf.glover is a symbolic function; get a function of time to work on arrays
hrf_func = utils.lambdify_t(hrf.glover(utils.T))
t = np.linspace(0,25,200)
plt.plot(t, hrf_func(t))
a=plt.gca()
a.set_xlabel(r'$t$')
a.set_ylabel(r'$h_{can}(t)$')
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Plot of the canonical Glover HRF
"""
import numpy as np
from nipy.modalities.fmri import hrf, utils
import matplotlib.pyplot as plt
# hrf.glover is a symbolic function; get a function of time to work on arrays
hrf_func = utils.lambdify_t(hrf.glover(utils.T))
t = np.linspace(0, 25, 200)
plt.plot(t, hrf_func(t))
a = plt.gca()
a.set_xlabel(r'$t$')
a.set_ylabel(r'$h_{can}(t)$')
"""
Plot of the canonical Glover HRF
"""
import numpy as np
from nipy.modalities.fmri import hrf
import pylab
from matplotlib import rc
rc('text', usetex=True)
t = np.linspace(0,25,200)
pylab.plot(t, hrf.glover(t))
a=pylab.gca()
a.set_xlabel(r'$t$')
a.set_ylabel(r'$h_{can}(t)$')
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """ This example uses a different HRF for different event types """ import numpy as np import matplotlib.pyplot as plt from nipy.modalities.fmri import hrf from nipy.modalities.fmri.utils import T, lambdify_t # HRFs as functions of (symbolic) time glover = hrf.glover(T) afni = hrf.afni(T) ta = [0,4,8,12,16]; tb = [2,6,10,14,18] ba = 1; bb = -2 na = ba * sum([glover.subs(T, T - t) for t in ta]) nb = bb * sum([afni.subs(T, T - t) for t in tb]) nav = lambdify_t(na) nbv = lambdify_t(nb) t = np.linspace(0,30,200) plt.plot(t, nav(t), c='r', label='Face') plt.plot(t, nbv(t), c='b', label='Object') plt.plot(t, nbv(t)+nav(t), c='g', label='Combined')
def make_bold(fname, stim_onset=None):
"""
Convert raw model output to BOLD signal
Parameters
----------
fname : str
File-name (including path if not in working directory) of HDF5 container that was generated
by `run_model`.
stim_onset : float
Time (in seconds) of stimulus onset. By default, onset/offset timings of
stimuli are stored in the HDF5 container generated by `run_model`. Only override
this setting, if you know what you are doing.
Returns
-------
Nothing : None
The computed BOLD signal is stored as dataset `BOLD` at the top level of the HDF5 container
specified by `fname`.
Notes
-----
Regional neural voltages are converted to BOLD time-series using the linear hemodynamic response
function proposed by Glover [1]_. For details consult the supporting information of our
paper [2]_.
References
----------
.. [1] Glover G. Deconvolution of Impulse Response in Event-Related BOLD FMRI.
NeuroImage 9: 416-429, 1999.
.. [2] S. Fuertinger, J. C. Zinn, and K. Simonyan. A Neural Population Model Incorporating
Dopaminergic Neurotransmission during Complex Voluntary Behaviors. PLoS Computational Biology,
10(11), 2014.
"""
# Make sure container exists and is valid
f = checkhdf(fname, peek=True)
try:
V = f['V'].value
except:
f.close()
raise ValueError("HDF5 file " + fname +
" does not have the required fields!")
# Compute cycle length based on the sampling rate used to generate the file
N = f['params']['names'].size
s_rate = f['params']['s_rate'].value
n_cycles = f['params']['n_cycles'].value
len_cycle = f['params']['len_cycle'].value
cycle_idx = int(np.round(s_rate * len_cycle))
# Make sure `stim_onset` makes sense
if stim_onset != None:
scalarcheck(stim_onset, 'stim_onset', bounds=[0, len_cycle])
# Get task from file to start sub-sampling procedure
task = f['params']['task'].value
# Compute cycle length based on the sampling rate used to generate the file
N = f['params']['names'].size
n_cycles = f['params']['n_cycles'].value
len_cycle = f['params']['len_cycle'].value
cycle_idx = int(np.round(s_rate * len_cycle))
# Compute step size and (if not provided by the user) compute stimulus onset time
dt = 1 / s_rate
if stim_onset == None:
stim_onset = f['params']['stimulus'].value
# Use Glover's Hemodynamic response function as convolution kernel (with default length 32)
hrft = utils.lambdify_t(hrf.glover(utils.T))
hrf_kernel = np.hstack((np.zeros(
(int(s_rate * stim_onset), )), hrft(np.arange(0, 32, dt))))
# Convolve the de-meaned model time-series with the kernel
convV = ndimage.filters.convolve1d((V.T - V.mean(axis=1)).T,
hrf_kernel,
mode='constant')
# Allocate space for BOLD signal
BOLD = np.zeros((N, n_cycles))
# Sub-sample convoluted data depending on task to get BOLD signal
if task == 'speech':
# Get interval to be considered for boldification
start = int(np.round(f['params']['speechoff'].value * s_rate))
stop = start + int(np.round(f['params']['acquisition'].value * s_rate))
elif task == 'rest':
# Get interval to be considered for boldification
start = 0
stop = int(np.round(f['params']['stimulus'].value * s_rate))
else:
raise ValueError("Don't know what to do for task " + task)
# Compute BOLD signal for all time points
for j in xrange(n_cycles):
BOLD[:, j] = convV[:, start:stop].mean(axis=1)
start += cycle_idx
stop += cycle_idx
# Re-scale the the signal
BOLD = BOLD * 0.02
# Save it to the file
try:
f.create_dataset('BOLD', data=BOLD)
except:
f['BOLD'].write_direct(BOLD)
f.close()
