def RunDTIProcess(dti_image): import os from nipype.interfaces.semtools import dtiprocess DTIProcess = dtiprocess() DTIProcess.inputs.dti_image = dti_image DTIProcess.inputs.fa_output = 'FA.nrrd' DTIProcess.inputs.md_output = 'MD.nrrd' DTIProcess.inputs.RD_output = 'RD.nrrd' DTIProcess.inputs.frobenius_norm_output = 'frobenius_norm_output.nrrd' DTIProcess.inputs.lambda1_output = 'lambda1_output.nrrd' DTIProcess.inputs.lambda2_output = 'lambda2_output.nrrd' DTIProcess.inputs.lambda3_output = 'lambda3_output.nrrd' DTIProcess.inputs.correction = 'nearest' DTIProcess.inputs.scalar_float = True DTIProcess.inputs.ignore_exception = True DTIProcess.run() fa_output = os.path.join(os.getcwd(), 'FA.nrrd') md_output = os.path.join(os.getcwd(), 'MD.nrrd') RD_output = os.path.join(os.getcwd(), 'RD.nrrd') frobenius_norm_output = os.path.join(os.getcwd(), 'frobenius_norm_output.nrrd') lambda1_output = os.path.join(os.getcwd(), 'lambda1_output.nrrd') lambda2_output = os.path.join(os.getcwd(), 'lambda2_output.nrrd') lambda3_output = os.path.join(os.getcwd(), 'lambda3_output.nrrd') assert os.path.isfile(fa_output), "FA file is not found: %s" % fa_output assert os.path.isfile(md_output), "MD file is not found: %s" % md_output assert os.path.isfile(RD_output), "RD file is not found: %s" % RD_output assert os.path.isfile(frobenius_norm_output), "frobenius_norm file is not found: %s" % frobenius_norm_output assert os.path.isfile(lambda1_output), "lambda1 file is not found: %s" % lambda1_output assert os.path.isfile(lambda2_output), "lambda2 file is not found: %s" % lambda2_output assert os.path.isfile(lambda3_output), "lambda3 file is not found: %s" % lambda3_output return fa_output, md_output, RD_output, frobenius_norm_output, lambda1_output, lambda2_output, lambda3_output
def run_dti_process(dti_image): """ This Function takes in... :param dti_image: :return: """ import os from nipype.interfaces.semtools import dtiprocess DTIProcess = dtiprocess() DTIProcess.inputs.dti_image = dti_image DTIProcess.inputs.fa_output = "FA.nrrd" DTIProcess.inputs.md_output = "MD.nrrd" DTIProcess.inputs.RD_output = "RD.nrrd" DTIProcess.inputs.frobenius_norm_output = "frobenius_norm_output.nrrd" DTIProcess.inputs.lambda1_output = "lambda1_output.nrrd" DTIProcess.inputs.lambda2_output = "lambda2_output.nrrd" DTIProcess.inputs.lambda3_output = "lambda3_output.nrrd" DTIProcess.inputs.correction = "nearest" DTIProcess.inputs.scalar_float = True # DTIProcess.inputs.ignore_exception = True DTIProcess.run() fa_output = os.path.join(os.getcwd(), "FA.nrrd") md_output = os.path.join(os.getcwd(), "MD.nrrd") RD_output = os.path.join(os.getcwd(), "RD.nrrd") frobenius_norm_output = os.path.join(os.getcwd(), "frobenius_norm_output.nrrd") lambda1_output = os.path.join(os.getcwd(), "lambda1_output.nrrd") lambda2_output = os.path.join(os.getcwd(), "lambda2_output.nrrd") lambda3_output = os.path.join(os.getcwd(), "lambda3_output.nrrd") assert os.path.isfile(fa_output), "FA file is not found: %s" % fa_output assert os.path.isfile(md_output), "MD file is not found: %s" % md_output assert os.path.isfile(RD_output), "RD file is not found: %s" % RD_output assert os.path.isfile(frobenius_norm_output), ( "frobenius_norm file is not found: %s" % frobenius_norm_output ) assert os.path.isfile(lambda1_output), ( "lambda1 file is not found: %s" % lambda1_output ) assert os.path.isfile(lambda2_output), ( "lambda2 file is not found: %s" % lambda2_output ) assert os.path.isfile(lambda3_output), ( "lambda3 file is not found: %s" % lambda3_output ) return ( fa_output, md_output, RD_output, frobenius_norm_output, lambda1_output, lambda2_output, lambda3_output, )
def RunDTIProcess(dti_image): import os from nipype.interfaces.semtools import dtiprocess DTIProcess = dtiprocess() DTIProcess.inputs.dti_image = dti_image DTIProcess.inputs.fa_output = 'FA.nrrd' DTIProcess.inputs.md_output = 'MD.nrrd' DTIProcess.inputs.RD_output = 'RD.nrrd' DTIProcess.inputs.frobenius_norm_output = 'frobenius_norm_output.nrrd' DTIProcess.inputs.lambda1_output = 'lambda1_output.nrrd' DTIProcess.inputs.lambda2_output = 'lambda2_output.nrrd' DTIProcess.inputs.lambda3_output = 'lambda3_output.nrrd' DTIProcess.inputs.correction = 'nearest' DTIProcess.inputs.scalar_float = True DTIProcess.inputs.ignore_exception = True DTIProcess.run() fa_output = os.path.join(os.getcwd(), 'FA.nrrd') md_output = os.path.join(os.getcwd(), 'MD.nrrd') RD_output = os.path.join(os.getcwd(), 'RD.nrrd') frobenius_norm_output = os.path.join(os.getcwd(), 'frobenius_norm_output.nrrd') lambda1_output = os.path.join(os.getcwd(), 'lambda1_output.nrrd') lambda2_output = os.path.join(os.getcwd(), 'lambda2_output.nrrd') lambda3_output = os.path.join(os.getcwd(), 'lambda3_output.nrrd') assert os.path.isfile( fa_output), "FA file is not found: %s" % fa_output assert os.path.isfile( md_output), "MD file is not found: %s" % md_output assert os.path.isfile( RD_output), "RD file is not found: %s" % RD_output assert os.path.isfile( frobenius_norm_output ), "frobenius_norm file is not found: %s" % frobenius_norm_output assert os.path.isfile( lambda1_output), "lambda1 file is not found: %s" % lambda1_output assert os.path.isfile( lambda2_output), "lambda2 file is not found: %s" % lambda2_output assert os.path.isfile( lambda3_output), "lambda3 file is not found: %s" % lambda3_output return fa_output, md_output, RD_output, frobenius_norm_output, lambda1_output, lambda2_output, lambda3_output
RESAMPLE_BRAINMASK.inputs.interpolationMode = 'NearestNeighbor' # This needs to be debugged'Binary' RESAMPLE_BRAINMASK.inputs.outputVolume = 'DeformedBrainMaskDWIRIP.nrrd' RESAMPLE_BRAINMASK.inputs.pixelType = 'binary' MasterDWIWorkflow.connect(BSPLINE_T2_TO_RIPB0, 'bsplineTransform', RESAMPLE_BRAINMASK, 'warpTransform') ### MasterDWIWorkflow.connect(inputsSpec, 'BrainMask',RESAMPLE_BRAINMASK,'inputVolume') MasterDWIWorkflow.connect(GetFileNamesNode, 'FixMaskImage', RESAMPLE_BRAINMASK, 'inputVolume') MasterDWIWorkflow.connect(DWIRIP_lowRes, 'outputResampledB0', RESAMPLE_BRAINMASK, 'referenceVolume') DTIEstim = pe.Node(interface=dtiestim(), name='DTIEstim_Process') DTIEstim.inputs.method = 'wls' DTIEstim.inputs.tensor_output = 'DTI_Output.nrrd' MasterDWIWorkflow.connect(DWIRIP_lowRes, 'outputVolume', DTIEstim, 'dwi_image') MasterDWIWorkflow.connect(RESAMPLE_BRAINMASK, 'outputVolume', DTIEstim, 'brain_mask') DTIProcess = pe.Node(interface=dtiprocess(), name='DTIProcess') DTIProcess.inputs.fa_output = 'FA.nrrd' DTIProcess.inputs.md_output = 'MD.nrrd' DTIProcess.inputs.RD_output = 'RD.nrrd' DTIProcess.inputs.frobenius_norm_output = 'frobenius_norm_output.nrrd' DTIProcess.inputs.lambda1_output = 'lambda1_output.nrrd' DTIProcess.inputs.lambda2_output = 'lambda2_output.nrrd' DTIProcess.inputs.lambda3_output = 'lambda3_output.nrrd' DTIProcess.inputs.scalar_float = True MasterDWIWorkflow.connect(DTIEstim, 'tensor_output', DTIProcess, 'dti_image') MasterDWIWorkflow.connect(DTIEstim, 'tensor_output', outputsSpec, 'tensor_image') MasterDWIWorkflow.connect(DTIProcess, 'fa_output', outputsSpec, 'FAImage') MasterDWIWorkflow.connect(DTIProcess, 'md_output', outputsSpec, 'MDImage') MasterDWIWorkflow.connect(DTIProcess, 'RD_output', outputsSpec, 'RDImage') MasterDWIWorkflow.connect(DTIProcess, 'frobenius_norm_output', outputsSpec, 'FrobeniusNormImage')