Garyfallidis

"""
==========================================
Motion correction of DWI data
==========================================
"""

import numpy as np
from dipy.viz import regtools
from dipy.data import fetch_stanford_hardi, read_stanford_hardi
from dipy.data.fetcher import fetch_syn_data, read_syn_data

Garyfallidis

dname = 'C:\\Users\\elef\\Data\\rodrigo\\'

fname1 = dname + 'ADRC_TMP_wholeBrain.trk.gz'

fname2 = dname + 'IIT2mean.trk'

from nibabel.streamlines import load

Garyfallidis

# -*- coding: utf-8 -*-

from __future__ import division

import numpy as np

from numpy.testing import (assert_, assert_equal, assert_array_equal,
                           assert_array_almost_equal, assert_almost_equal,
                           run_module_suite)

Garyfallidis

# -*- coding: utf-8 -*-
import numpy as np
from dipy.segment.clustering import QuickBundles
from dipy.segment.metric import IdentityFeature, Feature
from dipy.segment.metric import AveragePointwiseEuclideanMetric, EuclideanMetric, SumPointwiseEuclideanMetric

#data = np.random.rand(10, 3)


data = [np.random.rand(1, 3),

Garyfallidis

import sys
import numpy as np
from dipy.viz import actor, window, ui

from dipy.io.image import load_nifti

if __name__ == '__main__':

    #data, affine = load_nifti('resliced.nii.gz')

Garyfallidis

# Correct Boekel et. al public datasets
# The last b-vector is invalid as the norm is 0 when it should be 1.
# https://www.nitrc.org/projects/dwi_test-retest/
# 
# Run this using
# python correct_boekel_dwi.py pp01_dwi_run01_A.nii.gz bvals bvecs


import os
import sys