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Copy pathNODDI_Preprocessing.py
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NODDI_Preprocessing.py
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import os, json, sys, shutil
import numpy as np
import nibabel as nib
import matplotlib.pyplot as plt
from time import time
# DIPY Local PCA Denoising
from dipy.denoise.localpca import mppca
from dipy.core.gradients import gradient_table
from dipy.io.image import load_nifti
import dipy.reconst.dki as dki
sys.path.insert( 0, os.path.join( os.sep, 'usr', 'share', 'gkg', 'python' ) )
from CopyFileDirectoryRm import *
def runNoddiProcessing( Dir,
subject,
template,
mask,
diff_to_anat_affine,
diff_to_anat_direct,
diff_to_anat_inverse,
rot_tracto,
group,
sex,
verbose ):
if ( verbose == True ):
#-----------------------------------------------------------------------------
# Make Directories & Inputs
#-----------------------------------------------------------------------------
makedir( os.path.join( Dir,
subject,
'03-Diffusion' ) )
makedir( os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection' ) )
makedir( os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis' ) )
makedir( os.path.join( Dir,
subject,
'03-Diffusion',
'03-DWIAndQSpace' ) )
makedir( os.path.join( Dir,
subject,
'03-Diffusion',
'04-LocalModelling_DTI ' ) )
makedir( os.path.join( Dir,
subject,
'03-Diffusion',
'05-NODDI' ) )
makedir( os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData' ) )
makedir( os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed' ) )
rawDataDir = os.path.join( Dir,
'Turone_Equine_Social_Brain_Dataset' )
topUpParameters = os.path.join( rawDataDir,
'topup_parameters_dw.txt' )
epi_resolution = [2, 2, 2.4]
epi_matrix = [128, 128, 56]
trm = os.path.join( rawDataDir,
'ID_Matrix.trm' )
template_tracto = os.path.join( rawDataDir,
'Turone_Equine_Brain_Atlas_and_Templates',
'diff',
'tractogram',
'template.ima' )
mask_tracto = os.path.join( Dir,
'Turone_Equine_Social_Brain_Dataset',
'Turone_Equine_Brain_Atlas_and_Templates',
'diff',
'tractogram',
'mask.ima' )
#-------------------------------------------------------------------------
# NODDI preprocessing
#-------------------------------------------------------------------------
#-----------------------------------------------------------------------
# Data Collecting
#-----------------------------------------------------------------------
print( 'Data Collecting ' + subject)
directions = { '_acq-RL_dir-6_dwi':{ 'nbDir':'dw_01',
'index':'index_6',
'nbVolumes':'7' },
'_acq-RL_dir-30_dwi':{ 'nbDir':'dw_02',
'index':'index_30',
'nbVolumes':'31' },
'_acq-RL_dir-64_dwi':{ 'nbDir':'dw_03',
'index':'index_64',
'nbVolumes':'65' } }
for key in directions.keys():
"""
command = 'AimsSubVolume ' + \
'-i ' + os.path.join( rawDataDir,
subject,
'dwi',
subject + str( key ) + '.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '.nii.gz ' ) + \
'-z 0 ' + \
'-Z 55'
os.system( command )
command = 'cp -f ' + \
os.path.join( rawDataDir,
subject,
'dwi',
subject + str( key ) + '.bvec ' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '.bvec ' )
os.system( command )
command = 'cp -f ' + \
os.path.join( rawDataDir,
subject,
'dwi',
subject + str( key ) + '.bval ' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '.bval ' )
os.system( command )
encoding = { '_acq-topupRL_dir-6_dwi':'dw_BlipUp',
'_acq-topupLR_dir-6_dwi':'dw_BlipDown' }
for key in encoding.keys():
command = 'AimsSubVolume ' + \
'-i ' + os.path.join( rawDataDir,
subject,
'dwi',
subject + str( key ) + '.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( encoding[ key ] ) + '.nii.gz ' ) + \
'-z 0 ' + \
'-Z 55'
os.system( command )
print( 'Done' )
#-----------------------------------------------------------------------
# TopUp Correction
#-----------------------------------------------------------------------
print( 'TopUp Correction ' + subject)
command = 'fslmerge ' + \
'-t ' + \
os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
'dw_TopUp.nii.gz ' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
'dw_BlipUp.nii.gz ' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
'dw_BlipDown.nii.gz ' )
os.system( command )
"""
for key in directions.keys():
"""
command = 'topup ' + \
'--imain=' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
'dw_TopUp.nii.gz ' ) + \
'--datain=' + topUpParameters + \
' --fwhm=0 ' + \
'--config=b02b0.cnf ' + \
'--out=' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
'TopUp_results' )
print( command )
os.system( command )
print( 'TopUp Correction ' + str( directions[ key ]['nbDir'] ) + ' : Done! ' )
command = 'antsApplyTransforms ' + \
'-d 3 ' + \
'-e 0 ' + \
'-i ' + mask + \
' -o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_mask.nii.gz ' ) + \
'-r ' + os.path.join( Dir,
'Turone_Equine_Social_Brain_Dataset',
'transformations',
'diff',
subject + '_' + str( directions[ key ]['nbDir'] ) + '.nii.gz ' ) + \
'-n Linear ' + \
'-t ' + os.path.join( Dir,
'Turone_Equine_Social_Brain_Dataset',
'transformations',
'diff',
subject + '_' + str( directions[ key ]['nbDir'] ) + "_1InverseWarp.nii.gz [" ) + \
os.path.join( Dir,
'Turone_Equine_Social_Brain_Dataset',
'transformations',
'diff',
subject + '_' + str( directions[ key ]['nbDir'] ) + "_0GenericAffine.mat, 1]" )
os.system( command )
command = 'eddy' + \
' --imain=' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '.nii.gz ' ) + \
' --mask=' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_mask.nii.gz ' ) + \
' --acqp=' + topUpParameters + \
' --index=' + os.path.join( rawDataDir,
str( directions[ key ]['index'] ) + '.txt' ) + \
' --bvecs=' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '.bvec ' ) + \
' --bvals=' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '.bval ' ) + \
' --topup=' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
'TopUp_results ' ) + \
' --niter=8 ' + \
' --fwhm=10,8,4,2,0,0,0,0 ' + \
' --repol ' + \
' --out=' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_corrected' ) + \
' --verbose'
print( command )
os.system( command )
command = 'N4BiasFieldCorrection ' + \
'-d 4 ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_corrected.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_corrected_N4.nii.gz' )
os.system( command )
data, affine = load_nifti(os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_corrected_N4.nii.gz' ))
denoised = mppca( data,patch_radius=6)
nib.save(nib.Nifti1Image( denoised,
affine),
os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_corrected_N4_Denoised.nii.gz' ))
#-----------------------------------------------------------------------
# Nifti to Gis Conversion
#-----------------------------------------------------------------------
print( 'Nifti to Gis Conversion ' + str( directions[ key ]['nbDir'] ) )
command = 'AimsFileConvert ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_corrected_N4_Denoised.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
str( directions[ key ]['nbDir'] ) + '.ima ' )
os.system( command )
my_file = open(os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
str( directions[ key ]['nbDir'] ) + '.dim' ),
"w")
string_list = [str(epi_matrix[0]) + \
' ' + \
str(epi_matrix[1]) + \
' ' + \
str(epi_matrix[2]) + \
' ' + str( directions[ key ]['nbVolumes'] ) + '\n' + \
'-type FLOAT\n' + \
'-dx ' + str(epi_resolution[0]) + \
' ' + \
'-dy ' + str(epi_resolution[1]) + \
' ' + \
'-dz ' + str(epi_resolution[2]) + \
' -dt ' + str( directions[ key ]['nbVolumes'] ) + '\n' + \
'-bo DCBA\n' + \
'-om binar\n']
new_file_contents = "".join(string_list)
my_file.write(new_file_contents)
my_file.close()
command = 'AimsFileConvert ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_mask.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
str( directions[ key ]['nbDir'] ) + '_mask.ima ' ) + \
'-t S16'
os.system( command )
my_file = open(os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
str( directions[ key ]['nbDir'] ) + '_mask.dim' ),
"w")
string_list = [str(epi_matrix[0]) + \
' ' + \
str(epi_matrix[1]) + \
' ' + \
str(epi_matrix[2]) + \
' 1\n' + \
'-type S16\n' + \
'-dx ' + str(epi_resolution[0]) + \
' ' + \
'-dy ' + str(epi_resolution[1]) + \
' ' + \
'-dz ' + str(epi_resolution[2]) + \
' -dt 1\n' + \
'-bo DCBA\n' + \
'-om binar\n']
new_file_contents = "".join(string_list)
my_file.write(new_file_contents)
my_file.close()
command = 'cp -f ' + \
os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '_corrected.eddy_rotated_bvecs ' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
str( directions[ key ]['nbDir'] ) + '.bvec' )
os.system( command )
command = 'cp -f ' + \
os.path.join( Dir,
subject,
'03-Diffusion',
'01-TopUpCorrection',
str( directions[ key ]['nbDir'] ) + '.bval ' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
str( directions[ key ]['nbDir'] ) + '.bval' )
os.system( command )
command = 'rm -rf ' + \
os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'*.minf' )
os.system( command )
print( 'Nifti to Gis Conversion ' + str( directions[ key ]['nbDir'] ) + ' : Done! ' )
#-----------------------------------------------------------------------------
# DWIAndQSpace
#-----------------------------------------------------------------------------
parameterValues = {
'_algorithmName' : 'DWI-Data-Import-And-QSpace-Sampling',
'_subjectName' : '',
'acqpFileNames' : '',
'applyVisuCoreTransformation' : 0,
'bValFileNames' : '',
'bValueStdDev' : 10.0,
'bValueThreshold' : 10.0,
'bVecFileNames' : '',
'fileNameDwi' : '',
'gradientCharacteristicsFileNames' : '',
'invertXAxis' : 0,
'invertYAxis' : 0,
'invertZAxis' : 0,
'manufacturer' : 3,
'methodFileNames' : '',
'outputWorkDirectory' : '',
'phaseAxis' :0,
'qSpaceSamplingType' : 3,
'sliceAxis' : 0,
'visuParsFileNames' : ''
}
dwiFile = os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_01.ima;' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_02.ima;' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_03.ima' )
bvalFile = os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_01.bval;' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_02.bval;' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_03.bval' )
bvecFile = os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_01.bvec;' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_02.bvec;' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_03.bvec' )
outputFolder = os.path.join( Dir,
subject,
'03-Diffusion',
'03-DWIAndQSpace' )
parameterValues[ 'fileNameDwi' ] = dwiFile
parameterValues[ 'bValFileNames' ] = bvalFile
parameterValues[ 'bVecFileNames' ] = bvecFile
runGinkgo( parameterValues, outputFolder )
print( 'QSpace Sampling ' + subject + ' : Done! ' )
#-----------------------------------------------------------------------------
# NODDI analysis
#-----------------------------------------------------------------------------
t2 = os.path.join( Dir,
subject,
'03-Diffusion',
'03-DWIAndQSpace',
't2.ima ' )
data = os.path.join( Dir,
subject,
'03-Diffusion',
'03-DWIAndQSpace',
'dw.ima ' )
mask = os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_01_mask.ima ' )
outputDir = os.path.join( Dir,
subject,
'03-Diffusion',
'05-NODDI' )
command = 'GkgExecuteCommand DwiMicrostructureField ' + \
'-t2 ' + t2 + \
'-dw ' + data + \
'-m '+ mask + \
'-type noddi_microstructure_cartesian_field ' + \
'-f gfa ' + \
' intracellular_fraction ' + \
' isotropic_fraction ' + \
' kappa ' + \
' orientation_dispersion ' + \
' rgb ' + \
' stationary_fraction ' + \
' -o ' + os.path.join( outputDir,
subject + '_gfa.ima ' ) + \
os.path.join( outputDir,
subject + '_intracellular_fraction.ima ' ) + \
os.path.join( outputDir,
subject + '_isotropic_fraction.ima ' ) + \
os.path.join( outputDir,
subject + '_kappa.ima ' ) + \
os.path.join( outputDir,
subject + '_orientation_dispersion.ima ' ) + \
os.path.join( outputDir,
subject + '_rgb.ima ' ) + \
os.path.join( outputDir,
subject + '_stationary_fraction.ima ' ) + \
' -scalarParameters 0.0 0.5 0.0 1.7e-9 3.0e-9 0.0 ' + \
'0.0 0.0 0.0 0.0, 0.0, 0.0 ' + \
'1.0 1.0 100 3.0e-9 4.0e-9 1.0 ' + \
'0.1 0.1 1.0 0.2e-9 0.2e-9 0.1 ' + \
'0 0 0 1 1 1 0 ' + \
'0.03 ' + \
'1 5 ' + \
'1 1000 0.001 ' + \
'0 500 500 50 1000 ' + \
' -stringParameters watson ' + \
' -verbose true '
os.system( command )
print( 'NODDI Analysis ' + subject + ' : Done! ' )
#-----------------------------------------------------------------------------
# Normalize data
#-----------------------------------------------------------------------------
contrasts = [ 'gfa', 'intracellular_fraction',
'isotropic_fraction', 'kappa',
'orientation_dispersion', 'rgb',
'stationary_fraction' ]
command = 'GkgExecuteCommand Gis2NiftiConverter ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'04-LocalModelling_DTI',
'dti_diffusion_weighted_t2.ima ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_t2.nii.gz ' )
os.system( command )
command = 'GkgExecuteCommand Flipper ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_t2.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_t2.nii.gz ' ) + \
'-t yz '
os.system( command )
command = 'GkgExecuteCommand Flipper ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_t2.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_t2.nii.gz ' ) + \
'-t z '
os.system( command )
for con in contrasts:
print( 'conversion and normalization of ' + con + ' ' + subject )
if con == 'rgb':
command = 'AimsSplitRgb ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'05-NODDI',
subject + '_' + str(con) + '.ima ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) )
os.system( command )
channels = ['r', 'g', 'b']
for cha in channels:
command = 'GkgExecuteCommand Gis2NiftiConverter ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '_' + cha + '.ima ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '_' + cha + '.nii.gz ' )
os.system( command )
command = 'GkgExecuteCommand Flipper ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '_' + cha + '.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '_' + cha + '.nii.gz ' ) + \
'-t yz '
os.system( command )
command = 'GkgExecuteCommand Flipper ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '_' + cha + '.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '_' + cha + '.nii.gz ' ) + \
'-t z '
os.system( command )
else:
command = 'GkgExecuteCommand Gis2NiftiConverter ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'05-NODDI',
subject + '_' + str(con) + '.ima ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '.nii.gz ' )
os.system( command )
command = 'GkgExecuteCommand Flipper ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '.nii.gz ' ) + \
'-t yz '
os.system( command )
command = 'GkgExecuteCommand Flipper ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '.nii.gz ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
subject + '_' + str(con) + '.nii.gz ' ) + \
'-t z '
os.system( command )
command = 'rm -rf ' + \
os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
'*.ima ' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
'*.ima.minf ' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'06-ProcessedData',
'*.dim ' )
os.system( command )
#-----------------------------------------------------------------------------
# Local Modelling Make Directories and Inputs
#-----------------------------------------------------------------------------
parameterValues ={
'_algorithmName' : 'DWI-Local-Modeling',
'_subjectName' : '',
'aqbiLaplaceBeltramiSharpeningFactor' : 0.0,
'aqbiMaximumSHOrder' : 8,
'aqbiRegularizationLcurveFactor' : 0.006,
'computeOdfVolume' : 0,
'dotEffectiveDiffusionTime' : 25.0,
'dotMaximumSHOrder' : 8,
'dotOdfComputation' : 2,
'dotR0' : 12.0,
'dsiFilteringDataBeforeFFT' : 2,
'dsiMarginalOdf' : 2,
'dsiMaximumR0' : 15.0,
'dsiMinimumR0' : 1.0,
'dtiEstimatorType' : 0,
'fileNameDw' : '',
'fileNameMask' : '',
'fileNameT1' : '',
'fileNameT2' : '',
'fileNameTransformationDwToT1' : '',
'odfType' : 7,
'outputOrientationCount' : 500,
'outputWorkDirectory' : '',
'qbiEquatorPointCount' : 50,
'qbiPhiFunctionAngle' : 0.0,
'qbiPhiFunctionMaximumAngle' : 0.0,
'qbiPhiFunctionType' : 0,
'rgbScale' : 1.0,
'saAqbiLaplaceBeltramiSharpeningFactor' : 0.0,
'saAqbiMaximumSHOrder' : 8,
'saAqbiRegularizationLcurveFactor' : 0.006,
'sdFilterCoefficients' : '1 1 1 0.5 0.1 0.02 0.002 0.0005 0.0001 0.0001 0.00001 0.00001 0.00001 0.00001 0.00001 0.00001 0.00001',
'sdKernelLowerFAThreshold' : 0,
'sdKernelType' : 0,
'sdKernelUpperFAThreshold' : 1,
'sdKernelVoxelCount' : 300,
'sdMaximumSHOrder' : 8,
'sdUseCSD' : 0,
'sdtKernelLowerFAThreshold' : 0,
'sdtKernelType' : 0,
'sdtKernelUpperFAThreshold' : 1,
'sdtKernelVoxelCount' : 300,
'sdtMaximumSHOrder' : 8,
'sdtRegularizationLcurveFactor' : 0.006,
'sdtUseCSD' : 0,
'viewType' : 5
}
mask = os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_01_mask.ima' )
t1 = os.path.join( Dir,
subject,
'03-Diffusion',
'03-DWIAndQSpace',
't2.ima ' )
t2 = os.path.join( Dir,
subject,
'03-Diffusion',
'03-DWIAndQSpace',
't2.ima ' )
data = os.path.join( Dir,
subject,
'03-Diffusion',
'03-DWIAndQSpace',
'dw.ima ' )
outputFolder = os.path.join( Dir,
subject,
'03-Diffusion',
'04-LocalModelling_DTI' )
parameterValues[ 'fileNameDw' ] = data
parameterValues[ 'fileNameMask' ] = mask
parameterValues[ 'fileNameT1' ] = t1
parameterValues[ 'fileNameT2' ] = t2
parameterValues[ 'fileNameTransformationDwToT1' ] = trm
parameterValues[ 'outputWorkDirectory' ] = outputFolder
runGinkgo( parameterValues, outputFolder )
print( 'Local Modelling ' + subject + ' : Done! ' )
#-----------------------------------------------------------------------------
# Tractography SRD 1 Seeds Make Directories and Inputs
#-----------------------------------------------------------------------------
command = 'GkgExecuteCommand Binarizer ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'05-NODDI',
subject +'_isotropic_fraction.ima ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'isotropic_fraction_bin.ima ' ) + \
'-m ge ' + \
'-t1 0.1'
os.system( command )
command = 'AimsReplaceLevel ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'isotropic_fraction_bin.ima ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'isotropic_fraction_bin.ima ' ) + \
'-g 0 1 ' + \
'-n 1 0'
os.system( command )
command = 'cartoLinearComb.py ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'02-Dicom-to-Gis',
'dw_01_mask.ima ' ) + \
os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'isotropic_fraction_bin.ima ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'tractoMask.ima ' ) + \
'-f I1*I2'
os.system( command )
command = 'AimsFileConvert ' + \
'-i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'tractoMask.ima ' ) + \
'-o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'tractoMask.ima ' ) + \
'-t S16'
os.system( command )
command = 'GkgExecuteCommand DwiTractography' + \
' -s ' + os.path.join( Dir,
subject,
'03-Diffusion',
'04-LocalModelling_DTI',
'dti_odf_site_map.sitemap' ) + \
' -o ' + os.path.join( Dir,
subject,
'03-Diffusion',
'04-LocalModelling_DTI',
'dti_odf_texture_map.texturemap' ) + \
' -r ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'tractoMask.ima ' ) + \
' -m ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'tractoMask.ima ' ) + \
' -type streamline-regularized-deterministic ' + \
' -b ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
subject ) + \
' -scalarParameters 8 0.4 10 5 300.0 30.0 0.0 0.001 ' + \
' -outputOrientationCount 500 ' + \
' -stepCount 1 ' + \
' -bundleMapFormat aimsbundlemap ' + \
' -verbose '
print( command )
os.system( command )
command = 'GkgAntsRegistration3d' + \
' -r ' + template_tracto + \
' -m ' + mask_tracto + \
' -f ' + os.path.join( Dir,
subject,
'03-Diffusion',
'03-DWIAndQSpace',
't2.ima' ) + \
' -M ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'tractoMask.ima ' ) + \
' -d ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'direct') + \
' -i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
'inverse') + \
' -t affine_and_diffeomorphic'
os.system( command )
command = 'GkgExecuteCommand DwiBundleOperator' + \
' -i ' + os.path.join( Dir,
subject,
'03-Diffusion',
'07-Tractography_SRD_1seed',
subject + '.bundles' ) + \
' -o ' + os.path.join( Dir,
subject,