Generating simulated activation maps

The module nipy.labs.utils.simul_multisubject_fmri_dataset contains a various functions to create simulated activation maps in two, three and four dimensions. A 2D example is surrogate_2d_dataset(). The functions can position various activations and add noise, both as background noise and jitter in the activation positions and amplitude.

These functions can be useful to test methods.

Example

# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np

import pylab as pl

from nipy.labs.utils.simul_multisubject_fmri_dataset import \
     surrogate_2d_dataset

pos = np.array([[10, 10],
                [14, 20],
                [23, 18]])
ampli = np.array([4, 5, 2])

# First generate some noiseless data
noiseless_data = surrogate_2d_dataset(n_subj=1, noise_level=0, spatial_jitter=0,
                                      signal_jitter=0, pos=pos, ampli=ampli)

pl.figure(figsize=(10, 3))
pl.subplot(1, 4, 1)
pl.imshow(noiseless_data[0])
pl.title('Noise-less data')

# Second, generate some group data, with default noise parameters
group_data = surrogate_2d_dataset(n_subj=3, pos=pos, ampli=ampli)

pl.subplot(1, 4, 2)
pl.imshow(group_data[0])
pl.title('Subject 1')
pl.subplot(1, 4, 3)
pl.title('Subject 2')
pl.imshow(group_data[1])
pl.subplot(1, 4, 4)
pl.title('Subject 3')
pl.imshow(group_data[2])

(Source code, png, hires.png, pdf)

../_images/surrogate_array.png

Function documentation

nipy.labs.utils.simul_multisubject_fmri_dataset.surrogate_2d_dataset(n_subj=10, shape=(30, 30), sk=1.0, noise_level=1.0, pos=array([[ 6, 7], [10, 10], [15, 10]]), ampli=array([3, 4, 4]), spatial_jitter=1.0, signal_jitter=1.0, width=5.0, width_jitter=0, out_text_file=None, out_image_file=None, seed=False)

Create surrogate (simulated) 2D activation data with spatial noise

Parameters:

n_subj: integer, optionnal

The number of subjects, ie the number of different maps generated.

shape=(30,30): tuple of integers,

the shape of each image

sk: float, optionnal

Amount of spatial noise smoothness.

noise_level: float, optionnal

Amplitude of the spatial noise. amplitude=noise_level)

pos: 2D ndarray of integers, optionnal

x, y positions of the various simulated activations.

ampli: 1D ndarray of floats, optionnal

Respective amplitude of each activation

spatial_jitter: float, optionnal

Random spatial jitter added to the position of each activation, in pixel.

signal_jitter: float, optionnal

Random amplitude fluctuation for each activation, added to the amplitude specified by ampli

width: float or ndarray, optionnal

Width of the activations

width_jitter: float

Relative width jitter of the blobs

out_text_file: string or None, optionnal

If not None, the resulting array is saved as a text file with the given file name

out_image_file: string or None, optionnal

If not None, the resulting is saved as a nifti file with the given file name.

seed=False: int, optionnal

If seed is not False, the random number generator is initialized at a certain value

Returns:

dataset: 3D ndarray

The surrogate activation map, with dimensions (n_subj,) + shape

nipy.labs.utils.simul_multisubject_fmri_dataset.surrogate_3d_dataset(n_subj=1, shape=(20, 20, 20), mask=None, sk=1.0, noise_level=1.0, pos=None, ampli=None, spatial_jitter=1.0, signal_jitter=1.0, width=5.0, out_text_file=None, out_image_file=None, seed=False)

Create surrogate (simulated) 3D activation data with spatial noise.

Parameters:

n_subj: integer, optionnal

The number of subjects, ie the number of different maps generated.

shape=(20,20,20): tuple of 3 integers,

the shape of each image

mask=None: Nifti1Image instance,

referential- and mask- defining image (overrides shape)

sk: float, optionnal

Amount of spatial noise smoothness.

noise_level: float, optionnal

Amplitude of the spatial noise. amplitude=noise_level)

pos: 2D ndarray of integers, optionnal

x, y positions of the various simulated activations.

ampli: 1D ndarray of floats, optionnal

Respective amplitude of each activation

spatial_jitter: float, optionnal

Random spatial jitter added to the position of each activation, in pixel.

signal_jitter: float, optionnal

Random amplitude fluctuation for each activation, added to the amplitude specified by ampli

width: float or ndarray, optionnal

Width of the activations

out_text_file: string or None, optionnal

If not None, the resulting array is saved as a text file with the given file name

out_image_file: string or None, optionnal

If not None, the resulting is saved as a nifti file with the given file name.

seed=False: int, optionnal

If seed is not False, the random number generator is initialized at a certain value

Returns:

dataset: 3D ndarray

The surrogate activation map, with dimensions (n_subj,) + shape

nipy.labs.utils.simul_multisubject_fmri_dataset.surrogate_4d_dataset(shape=(20, 20, 20), mask=None, n_scans=1, n_sess=1, dmtx=None, sk=1.0, noise_level=1.0, signal_level=1.0, out_image_file=None, seed=False)

Create surrogate (simulated) 3D activation data with spatial noise.

Parameters:

shape = (20, 20, 20): tuple of integers,

the shape of each image

mask=None: brifti image instance,

referential- and mask- defining image (overrides shape)

n_scans: int, optional,

number of scans to be simlulated overrided by the design matrix

n_sess: int, optional,

the number of simulated sessions

dmtx: array of shape(n_scans, n_rows),

the design matrix

sk: float, optionnal

Amount of spatial noise smoothness.

noise_level: float, optionnal

Amplitude of the spatial noise. amplitude=noise_level)

signal_level: float, optional,

Amplitude of the signal

out_image_file: string or list of strings or None, optionnal

If not None, the resulting is saved as (set of) nifti file(s) with the given file path(s)

seed=False: int, optionnal

If seed is not False, the random number generator is initialized at a certain value

Returns:

dataset: a list of n_sess ndarray of shape

(shape[0], shape[1], shape[2], n_scans) The surrogate activation map