Python dtiprocess Examples

Example #1

File: EstimationWorkflow.py Project: Slicer/BRAINSTools

 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

Example #2

File: EstimationWorkflow.py Project: sjh26/BRAINSTools

    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,
        )

Example #3

 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

Example #4

File: DWIInACPCTest.py Project: NIRALUser/BRAINSTools

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')

Example #5

File: DWIInACPCTest.py Project: LunarMedic/BRAINSTools

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')