Reconstruct with Generalized Q-Sampling Imaging

We show how to apply Generalized Q-Sampling Imaging [Yeh2010] to diffusion MRI datasets. You can think of GQI as an analytical version of DSI orientation distribution function (ODF) (Garyfallidis, PhD thesis, 2012).

First import the necessary modules:

import numpy as np
from dipy.data import fetch_taiwan_ntu_dsi, read_taiwan_ntu_dsi, get_sphere
from dipy.reconst.gqi import GeneralizedQSamplingModel
from dipy.direction import peaks_from_model

Download and read the data for this tutorial.

fetch_taiwan_ntu_dsi()
img, gtab = read_taiwan_ntu_dsi()

img contains a nibabel Nifti1Image object (data) and gtab contains a GradientTable object (gradient information e.g. b-values). For example to read the b-values it is possible to write:

print(gtab.bvals)

Load the raw diffusion data and the affine.

data = img.get_data()
print('data.shape (%d, %d, %d, %d)' % data.shape)

data.shape (96, 96, 60, 203)

This dataset has anisotropic voxel sizes, therefore reslicing is necessary.

affine = img.affine

Read the voxel size from the image header.

voxel_size = img.header.get_zooms()[:3]

Instantiate the model and apply it to the data.

gqmodel = GeneralizedQSamplingModel(gtab, sampling_length=3)

The parameter sampling_length is used here to

Lets just use one slice only from the data.

dataslice = data[:, :, data.shape[2] // 2]

mask = dataslice[..., 0] > 50

gqfit = gqmodel.fit(dataslice, mask=mask)

Load an ODF reconstruction sphere

sphere = get_sphere('repulsion724')

Calculate the ODFs with this specific sphere

ODF = gqfit.odf(sphere)

print('ODF.shape (%d, %d, %d)' % ODF.shape)

ODF.shape (96, 96, 724)

Using peaks_from_model we can find the main peaks of the ODFs and other properties.

gqpeaks = peaks_from_model(model=gqmodel,
                           data=dataslice,
                           sphere=sphere,
                           relative_peak_threshold=.5,
                           min_separation_angle=25,
                           mask=mask,
                           return_odf=False,
                           normalize_peaks=True)

gqpeak_values = gqpeaks.peak_values

gqpeak_indices show which sphere points have the maximum values.

gqpeak_indices = gqpeaks.peak_indices

It is also possible to calculate GFA.

GFA = gqpeaks.gfa

print('GFA.shape (%d, %d)' % GFA.shape)

With parameter return_odf=True we can obtain the ODF using gqpeaks.ODF

gqpeaks = peaks_from_model(model=gqmodel,
                           data=dataslice,
                           sphere=sphere,
                           relative_peak_threshold=.5,
                           min_separation_angle=25,
                           mask=mask,
                           return_odf=True,
                           normalize_peaks=True)

This ODF will be of course identical to the ODF calculated above as long as the same data and mask are used.

np.sum(gqpeaks.odf != ODF) == 0

True

The advantage of using peaks_from_model is that it calculates the ODF only once and saves it or deletes if it is not necessary to keep.

Yeh2010

Yeh, F-C et al., Generalized Q-sampling imaging, IEEE Transactions on Medical Imaging, vol 29, no 9, 2010.

Example source code

You can download the full source code of this example. This same script is also included in the dipy source distribution under the doc/examples/ directory.