Lesion segmentation¶
- sbl.sabre.workflows.LesionWorkflow(name='Lesions', *args, **kwargs)¶
Create a Lesion Explorer workflow
Parameters: name – Name of workflow (default: “Lesions”) Inputs:
inputnode.T1_image : T1 image inputnode.T2_image : T2 image in T1 acquisition space inputnode.PD_image : PD image in T1 acquisition space inputnode.T1_segmentation : T1 segmentation with relabeled ventricular CSF inputnode.T1_CSF_threshold : cutoff value for CSF segmentation from T1 image inputnode.T2_hyperintensity_threshold : Cutoff value for hyperintensity segmentation from T2 image inputnode.PD_hyperintensity_threshold : Cutoff value for hyperintensity segmentation from PD image inputnode.min_objectsize : Minimum 3D object size to keep inputnode.VCSF_value : Value assigned to ventricular CSV voxels in relabeled T1 segmentation inputnode.VCSF_dilate_radius : Dilation radius for ventricular CSF (vCSF) inputnode.FCM_exponent : Fuzzy C-Means clustering - exponent inputnode.FCM_max_iterations : Fuzzy C-Means clustering - maximum number of iterations inputnode.FCM_min_improvement : Fuzzy C-Means clustering - minimum improvement
Outputs:
outputnode.lesions : outputnode.lesions_juxtacortical :
![digraph Lesions{
label="Lesions";
Lesions_inputnode[label="inputnode (utility)"];
Lesions_MaskT1[label="MaskT1 (fsl)"];
Lesions_FuzzyClusterCSF[label="FuzzyClusterCSF (interfaces)"];
Lesions_SegmentLesionZone[label="SegmentLesionZone (interfaces)"];
Lesions_DilateVentricularCSF[label="DilateVentricularCSF (interfaces)"];
Lesions_MaskT2VentricularCSF[label="MaskT2VentricularCSF (interfaces)"];
Lesions_SegmentLesionsT2[label="SegmentLesionsT2 (interfaces)"];
Lesions_MaskPDVentricularCSF[label="MaskPDVentricularCSF (interfaces)"];
Lesions_SegmentLesionsPD[label="SegmentLesionsPD (interfaces)"];
Lesions_CombineLesions[label="CombineLesions (fsl)"];
Lesions_MaskLesionZone[label="MaskLesionZone (interfaces)"];
Lesions_ThresholdLesionVolumes[label="ThresholdLesionVolumes (interfaces)"];
Lesions_CombineLesionsAndCandidates[label="CombineLesionsAndCandidates (fsl)"];
Lesions_outputnode[label="outputnode (utility)"];
Lesions_inputnode -> Lesions_MaskT2VentricularCSF;
Lesions_inputnode -> Lesions_MaskT2VentricularCSF;
Lesions_inputnode -> Lesions_SegmentLesionZone;
Lesions_inputnode -> Lesions_SegmentLesionZone;
Lesions_inputnode -> Lesions_FuzzyClusterCSF;
Lesions_inputnode -> Lesions_FuzzyClusterCSF;
Lesions_inputnode -> Lesions_FuzzyClusterCSF;
Lesions_inputnode -> Lesions_MaskT1;
Lesions_inputnode -> Lesions_MaskT1;
Lesions_inputnode -> Lesions_SegmentLesionsT2;
Lesions_inputnode -> Lesions_SegmentLesionsPD;
Lesions_inputnode -> Lesions_DilateVentricularCSF;
Lesions_inputnode -> Lesions_DilateVentricularCSF;
Lesions_inputnode -> Lesions_DilateVentricularCSF;
Lesions_inputnode -> Lesions_ThresholdLesionVolumes;
Lesions_inputnode -> Lesions_MaskPDVentricularCSF;
Lesions_inputnode -> Lesions_MaskPDVentricularCSF;
Lesions_MaskT1 -> Lesions_FuzzyClusterCSF;
Lesions_FuzzyClusterCSF -> Lesions_outputnode;
Lesions_FuzzyClusterCSF -> Lesions_SegmentLesionZone;
Lesions_SegmentLesionZone -> Lesions_MaskLesionZone;
Lesions_DilateVentricularCSF -> Lesions_MaskT2VentricularCSF;
Lesions_DilateVentricularCSF -> Lesions_MaskPDVentricularCSF;
Lesions_MaskT2VentricularCSF -> Lesions_SegmentLesionsT2;
Lesions_SegmentLesionsT2 -> Lesions_CombineLesions;
Lesions_MaskPDVentricularCSF -> Lesions_SegmentLesionsPD;
Lesions_SegmentLesionsPD -> Lesions_CombineLesions;
Lesions_CombineLesions -> Lesions_MaskLesionZone;
Lesions_CombineLesions -> Lesions_CombineLesionsAndCandidates;
Lesions_CombineLesions -> Lesions_outputnode;
Lesions_MaskLesionZone -> Lesions_ThresholdLesionVolumes;
Lesions_ThresholdLesionVolumes -> Lesions_outputnode;
Lesions_ThresholdLesionVolumes -> Lesions_CombineLesionsAndCandidates;
Lesions_CombineLesionsAndCandidates -> Lesions_outputnode;
}](../../_images/graphviz-f53ff25f52fc8509f22c9705c31ab41ad71466c9.png)