UKF Tractography uses an unscented Kalman filter to perform tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model.

It can tract fibers 1-, 2-, or 3-tensor methods which uses a mixture of Gaussian tensors. There are two methods: One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation.



In [1]:

    
import nipype.interfaces.semtools.diffusion as ukf



In [23]:

    
from nipype.interfaces.semtools.diffusion import tractography



In [ ]:

    
import nipype



In [ ]:

    
import nipype.interfaces.semtools as tools



In [2]:

    
test = ukf.dtiestim(dwi_image = "Control258localeq.nii")



In [21]:

    
convert = ukf.DWIConvert()
convert.input_spec(allowLossyConversion=True, )









    Out[21]:





allowLossyConversion = True
args = <undefined>
conversionMode = <undefined>
environ = {}
fMRI = <undefined>
fslNIFTIFile = <undefined>
gradientVectorFile = <undefined>
ignore_exception = False
inputBValues = <undefined>
inputBVectors = <undefined>
inputDicomDirectory = <undefined>
inputVolume = <undefined>
outputBValues = <undefined>
outputBVectors = <undefined>
outputDirectory = <undefined>
outputVolume = <undefined>
smallGradientThreshold = <undefined>
terminal_output = <undefined>
transposeInputBVectors = <undefined>
useBMatrixGradientDirections = <undefined>
useIdentityMeaseurementFrame = <undefined>
writeProtocolGradientsFile = <undefined>



In [18]:

    
convert.output_spec()









    Out[18]:





gradientVectorFile = <undefined>
outputBValues = <undefined>
outputBVectors = <undefined>
outputDirectory = <undefined>
outputVolume = <undefined>



In [ ]:

    
from nipype.interfaces.freesurfer import MRIConvert



In [22]:

    
import nipype.interfaces.freesurfer.MRIConvert









    



---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-22-9e5a346ba86f> in <module>()
----> 1 import nipype.interfaces.freesurfer.MRIConvert

ImportError: No module named MRIConvert



In [24]:

    
a = tractography.UKFTractography()



In [26]:

    
a.input_spec()









    Out[26]:





Ql = <undefined>
Qm = <undefined>
Qw = <undefined>
Rs = <undefined>
args = <undefined>
dwiFile = <undefined>
environ = {}
freeWater = <undefined>
fullTensorModel = <undefined>
ignore_exception = False
labels = <undefined>
maskFile = <undefined>
maxBranchingAngle = <undefined>
maxHalfFiberLength = <undefined>
minBranchingAngle = <undefined>
minFA = <undefined>
minGA = <undefined>
numTensor = <undefined>
numThreads = <undefined>
recordCovariance = <undefined>
recordFA = <undefined>
recordFreeWater = <undefined>
recordLength = <undefined>
recordNMSE = <undefined>
recordState = <undefined>
recordTensors = <undefined>
recordTrace = <undefined>
seedFALimit = <undefined>
seedsFile = <undefined>
seedsPerVoxel = <undefined>
stepLength = <undefined>
storeGlyphs = <undefined>
terminal_output = <undefined>
tracts = <undefined>
tractsWithSecondTensor = <undefined>
writeAsciiTracts = <undefined>
writeUncompressedTracts = <undefined>



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