Workflows¶
SABRE¶
- sbl.sabre.workflows.SabreWorkflow(name='SABRE', TIV_template_type='T2', *args, **kwargs)¶
Create a SABRE workflow.
Parameters: - name – Name of workflow
- TIV_template_type – Type of head-from-brain template to use (‘T2’ or ‘PD’)
Inputs:
inputnode.T1_image : inputnode.T2_image : inputnode.PD_image : inputnode.T1_BET_threshold: inputnode.T2_BET_threshold: inputnode.PD_BET_threshold: inputnode.T2_TIV_threshold: inputnode.PD_TIV_threshold: inputnode.TIV_BET_threshold: inputnode.TIV_template : inputnode.TIV_template_mask : inputnode.TIV_cutoff : inputnode.ACPC_template : inputnode.T2_hyperintensity_threshold : inputnode.PD_hyperintensity_threshold :
Outputs:
outputnode.resliced_image :
Example:
>>> sabre = SabreWorkflow(TIV_template_type='T2') >>> sabre.inputs.inputnode.T1_image = 'mni_icbm152_T1.nii.gz' >>> sabre.inputs.inputnode.T2_image = 'mni_icbm152_T2.nii.gz' >>> sabre.inputs.inputnode.PD_image = 'mni_icbm152_PD.nii.gz' >>> sabre.inputs.inputnode.TIV_template = 'template_T2.nii.gz' >>> sabre.inputs.inputnode.TIV_template_mask = 'template_TIV.nii.gz' >>> sabre.run()
Sub-workflows¶
Overview¶
![digraph SABRE{
label="SABRE";
SABRE_inputnode[label="inputnode (utility)"];
SABRE_Thresholds[label="Thresholds (utility)"];
SABRE_Images[label="Images (utility)"];
SABRE_BET[label="BET (fsl)"];
SABRE_SelectReference[label="SelectReference (utility)"];
SABRE_SelectRegister[label="SelectRegister (utility)"];
SABRE_SelectReslice[label="SelectReslice (utility)"];
SABRE_SelectPD[label="SelectPD (utility)"];
SABRE_SelectT2[label="SelectT2 (utility)"];
SABRE_inputnode -> SABRE_Images;
SABRE_inputnode -> SABRE_Images;
SABRE_inputnode -> SABRE_Images;
SABRE_inputnode -> SABRE_Thresholds;
SABRE_inputnode -> SABRE_Thresholds;
SABRE_inputnode -> SABRE_Thresholds;
SABRE_Thresholds -> SABRE_BET;
subgraph cluster_SABRE_AcpcAlignment {
label="AcpcAlignment";
SABRE_AcpcAlignment_inputnode[label="inputnode (utility)"];
SABRE_AcpcAlignment_BET[label="BET (fsl)"];
SABRE_AcpcAlignment_N4CorrectT1[label="N4CorrectT1 (ants)"];
SABRE_AcpcAlignment_MakeIsotropic[label="MakeIsotropic (interfaces)"];
SABRE_AcpcAlignment_LinearRegistration[label="LinearRegistration (fsl)"];
SABRE_AcpcAlignment_AlignToAcpc[label="AlignToAcpc (interfaces)"];
SABRE_AcpcAlignment_inputnode -> SABRE_AcpcAlignment_AlignToAcpc;
SABRE_AcpcAlignment_inputnode -> SABRE_AcpcAlignment_LinearRegistration;
SABRE_AcpcAlignment_inputnode -> SABRE_AcpcAlignment_BET;
SABRE_AcpcAlignment_inputnode -> SABRE_AcpcAlignment_BET;
SABRE_AcpcAlignment_inputnode -> SABRE_AcpcAlignment_BET;
SABRE_AcpcAlignment_inputnode -> SABRE_AcpcAlignment_N4CorrectT1;
SABRE_AcpcAlignment_inputnode -> SABRE_AcpcAlignment_N4CorrectT1;
SABRE_AcpcAlignment_BET -> SABRE_AcpcAlignment_N4CorrectT1;
SABRE_AcpcAlignment_N4CorrectT1 -> SABRE_AcpcAlignment_MakeIsotropic;
SABRE_AcpcAlignment_MakeIsotropic -> SABRE_AcpcAlignment_LinearRegistration;
SABRE_AcpcAlignment_MakeIsotropic -> SABRE_AcpcAlignment_LinearRegistration;
SABRE_AcpcAlignment_MakeIsotropic -> SABRE_AcpcAlignment_AlignToAcpc;
SABRE_AcpcAlignment_LinearRegistration -> SABRE_AcpcAlignment_AlignToAcpc;
}
SABRE_Images -> SABRE_BET;
SABRE_Images -> SABRE_BET;
SABRE_Images -> SABRE_SelectReslice;
SABRE_BET -> SABRE_SelectReference;
SABRE_BET -> SABRE_SelectRegister;
subgraph cluster_SABRE_Coregister {
label="Coregister";
SABRE_Coregister_inputnode[label="inputnode (utility)"];
SABRE_Coregister_LinearRegistration[label="LinearRegistration (fsl)"];
SABRE_Coregister_ApplyTransformation[label="ApplyTransformation (fsl)"];
SABRE_Coregister_outputnode[label="outputnode (utility)"];
SABRE_Coregister_inputnode -> SABRE_Coregister_LinearRegistration;
SABRE_Coregister_inputnode -> SABRE_Coregister_LinearRegistration;
SABRE_Coregister_inputnode -> SABRE_Coregister_LinearRegistration;
SABRE_Coregister_inputnode -> SABRE_Coregister_ApplyTransformation;
SABRE_Coregister_inputnode -> SABRE_Coregister_ApplyTransformation;
SABRE_Coregister_inputnode -> SABRE_Coregister_ApplyTransformation;
SABRE_Coregister_LinearRegistration -> SABRE_Coregister_outputnode;
SABRE_Coregister_LinearRegistration -> SABRE_Coregister_ApplyTransformation;
SABRE_Coregister_ApplyTransformation -> SABRE_Coregister_outputnode;
}
subgraph cluster_SABRE_HeadFromBrain {
label="HeadFromBrain";
SABRE_HeadFromBrain_inputnode[label="inputnode (utility)"];
SABRE_HeadFromBrain_BET[label="BET (fsl)"];
SABRE_HeadFromBrain_N4CorrectT2[label="N4CorrectT2 (ants)"];
SABRE_HeadFromBrain_N4CorrectPD[label="N4CorrectPD (ants)"];
SABRE_HeadFromBrain_LinearRegistration[label="LinearRegistration (fsl)"];
SABRE_HeadFromBrain_InvertTransformation[label="InvertTransformation (fsl)"];
SABRE_HeadFromBrain_ApplyTransformation[label="ApplyTransformation (fsl)"];
SABRE_HeadFromBrain_HeadFromBrain[label="HeadFromBrain (interfaces)"];
SABRE_HeadFromBrain_outputnode[label="outputnode (utility)"];
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_LinearRegistration;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_LinearRegistration;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_HeadFromBrain;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_HeadFromBrain;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_HeadFromBrain;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_HeadFromBrain;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_ApplyTransformation;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_ApplyTransformation;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_BET;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_BET;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_BET;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_N4CorrectPD;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_N4CorrectPD;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_N4CorrectT2;
SABRE_HeadFromBrain_inputnode -> SABRE_HeadFromBrain_N4CorrectT2;
SABRE_HeadFromBrain_BET -> SABRE_HeadFromBrain_ApplyTransformation;
SABRE_HeadFromBrain_BET -> SABRE_HeadFromBrain_N4CorrectPD;
SABRE_HeadFromBrain_BET -> SABRE_HeadFromBrain_N4CorrectT2;
SABRE_HeadFromBrain_BET -> SABRE_HeadFromBrain_LinearRegistration;
SABRE_HeadFromBrain_N4CorrectT2 -> SABRE_HeadFromBrain_HeadFromBrain;
SABRE_HeadFromBrain_N4CorrectPD -> SABRE_HeadFromBrain_HeadFromBrain;
SABRE_HeadFromBrain_LinearRegistration -> SABRE_HeadFromBrain_InvertTransformation;
SABRE_HeadFromBrain_InvertTransformation -> SABRE_HeadFromBrain_ApplyTransformation;
SABRE_HeadFromBrain_ApplyTransformation -> SABRE_HeadFromBrain_HeadFromBrain;
SABRE_HeadFromBrain_HeadFromBrain -> SABRE_HeadFromBrain_outputnode;
}
SABRE_SelectRegister -> SABRE_Coregister_inputnode;
SABRE_SelectReslice -> SABRE_Coregister_inputnode;
SABRE_Coregister_outputnode -> SABRE_SelectPD;
SABRE_Coregister_outputnode -> SABRE_SelectT2;
SABRE_SelectReference -> SABRE_Coregister_inputnode;
SABRE_SelectPD -> SABRE_HeadFromBrain_inputnode;
SABRE_inputnode -> SABRE_HeadFromBrain_inputnode;
SABRE_inputnode -> SABRE_HeadFromBrain_inputnode;
SABRE_inputnode -> SABRE_HeadFromBrain_inputnode;
SABRE_inputnode -> SABRE_HeadFromBrain_inputnode;
SABRE_inputnode -> SABRE_AcpcAlignment_inputnode;
SABRE_inputnode -> SABRE_AcpcAlignment_inputnode;
SABRE_inputnode -> SABRE_AcpcAlignment_inputnode;
SABRE_SelectT2 -> SABRE_HeadFromBrain_inputnode;
}](../../_images/graphviz-c07d4431e140581d260a7e959c665772d71063b2.png)