Table Of Contents

Previous topic

neurospin.neuro.fmri.realign4d

Next topic

neurospin.neuro.linear_model

This Page

neurospin.neuro.image_classes

Module: neurospin.neuro.image_classes

Inheritance diagram for nipy.neurospin.neuro.image_classes:

Input/output functions. This ‘high-level’ module is not meant to stay permanently in fff, but is supplied to fff users so that they can process data for real until fff is properly integrated into nipy.

Classes

fmri_image

class nipy.neurospin.neuro.image_classes.fmri_image(img, tr=1.0, tr_slices=None, start=0.0, slice_axis=2, slice_order='ascending', interleaved=False)

Bases: nipy.neurospin.neuro.image_classes.image

__init__(img, tr=1.0, tr_slices=None, start=0.0, slice_axis=2, slice_order='ascending', interleaved=False)
inverse_time_transform(z, tt)
time_transform(z, t)
z_to_slice(z)
Account for the fact that slices may be stored in reverse order wrt the scanner coordinate system convention (slice 0 == bottom of the head)

image

class nipy.neurospin.neuro.image_classes.image(obj=None, transform=None, voxsize=None, iolib='pynifti')
__init__(obj=None, transform=None, voxsize=None, iolib='pynifti')

Basic image class.

transform: 4x4 transformation matrix from array to scanner coordinate system.

IMPORTANT NOTE: the image class assumes that the scanner coordinate system is ALWAYS right-handed and such that x increases from left to right, y increases from posterior to anterior, and z increases in the inferior to superior direction. This transformation is thus exactly what the nifti norm calls the ‘qform’.

save(filename)
Save an image as described by a dictionary with keys ‘array’ and voxsize’.
set_array(array)