workflows.dmri.fsl.artifacts

all_fmb_pipeline()

Link to code

Builds a pipeline including three artifact corrections: head-motion correction (HMC), susceptibility-derived distortion correction (SDC), and Eddy currents-derived distortion correction (ECC).

The displacement fields from each kind of distortions are combined. Thus, only one interpolation occurs between input data and result.

Warning

this workflow rotates the gradients table (b-vectors) [Leemans09].

Examples

>>> from nipype.workflows.dmri.fsl.artifacts import all_fmb_pipeline
>>> allcorr = all_fmb_pipeline()
>>> allcorr.inputs.inputnode.in_file = 'epi.nii'
>>> allcorr.inputs.inputnode.in_bval = 'diffusion.bval'
>>> allcorr.inputs.inputnode.in_bvec = 'diffusion.bvec'
>>> allcorr.inputs.inputnode.bmap_mag = 'magnitude.nii'
>>> allcorr.inputs.inputnode.bmap_pha = 'phase.nii'
>>> allcorr.inputs.inputnode.epi_param = 'epi_param.txt'
>>> allcorr.run() 

Graph

digraph hmc_sdc_ecc{

  label="hmc_sdc_ecc";

  hmc_sdc_ecc_inputnode[label="inputnode (utility)"];

  hmc_sdc_ecc_B0indices[label="B0indices (utility)"];

  hmc_sdc_ecc_b0_avg_pre[label="b0_avg_pre (utility)"];

  hmc_sdc_ecc_bet_dwi_pre[label="bet_dwi_pre (fsl)"];

  hmc_sdc_ecc_b0_avg_post[label="b0_avg_post (utility)"];

  hmc_sdc_ecc_bet_dwi_post[label="bet_dwi_post (fsl)"];

  hmc_sdc_ecc_outputnode[label="outputnode (utility)"];

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_b0_avg_pre;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_B0indices;

  hmc_sdc_ecc_B0indices -> hmc_sdc_ecc_b0_avg_pre;

  hmc_sdc_ecc_B0indices -> hmc_sdc_ecc_b0_avg_post;

  hmc_sdc_ecc_b0_avg_pre -> hmc_sdc_ecc_bet_dwi_pre;

  subgraph cluster_hmc_sdc_ecc_motion_correct {

      label="motion_correct";

    hmc_sdc_ecc_motion_correct_inputnode[label="inputnode (utility)"];

    hmc_sdc_ecc_motion_correct_SplitDWI[label="SplitDWI (utility)"];

    hmc_sdc_ecc_motion_correct_InsertRefmat[label="InsertRefmat (utility)"];

    hmc_sdc_ecc_motion_correct_Rotate_Bvec[label="Rotate_Bvec (utility)"];

    hmc_sdc_ecc_motion_correct_outputnode[label="outputnode (utility)"];

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_Rotate_Bvec;

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_SplitDWI;

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_SplitDWI;

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_SplitDWI;

    hmc_sdc_ecc_motion_correct_SplitDWI -> hmc_sdc_ecc_motion_correct_InsertRefmat;

    subgraph cluster_hmc_sdc_ecc_motion_correct_DWICoregistration {

            label="DWICoregistration";

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode[label="inputnode (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_InitXforms[label="InitXforms (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate[label="MskDilate (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_SplitDWIs[label="SplitDWIs (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_DWEqualize[label="DWEqualize (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_Bias[label="Bias (ants)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_B0Equalize[label="B0Equalize (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration[label="CoRegistration (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_RemoveNegative[label="RemoveNegative (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_MergeDWIs[label="MergeDWIs (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode[label="outputnode (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_Bias;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_Bias;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_SplitDWIs;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_B0Equalize;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_InitXforms;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_InitXforms;

        hmc_sdc_ecc_motion_correct_DWICoregistration_InitXforms -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_motion_correct_DWICoregistration_DWEqualize;

        hmc_sdc_ecc_motion_correct_DWICoregistration_SplitDWIs -> hmc_sdc_ecc_motion_correct_DWICoregistration_DWEqualize;

        hmc_sdc_ecc_motion_correct_DWICoregistration_DWEqualize -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_Bias -> hmc_sdc_ecc_motion_correct_DWICoregistration_B0Equalize;

        hmc_sdc_ecc_motion_correct_DWICoregistration_B0Equalize -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration -> hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode;

        hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration -> hmc_sdc_ecc_motion_correct_DWICoregistration_RemoveNegative;

        hmc_sdc_ecc_motion_correct_DWICoregistration_RemoveNegative -> hmc_sdc_ecc_motion_correct_DWICoregistration_MergeDWIs;

        hmc_sdc_ecc_motion_correct_DWICoregistration_MergeDWIs -> hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode;

    }

    hmc_sdc_ecc_motion_correct_InsertRefmat -> hmc_sdc_ecc_motion_correct_Rotate_Bvec;

    hmc_sdc_ecc_motion_correct_InsertRefmat -> hmc_sdc_ecc_motion_correct_outputnode;

    hmc_sdc_ecc_motion_correct_Rotate_Bvec -> hmc_sdc_ecc_motion_correct_outputnode;

    hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_motion_correct_InsertRefmat;

    hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_motion_correct_outputnode;

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_motion_correct_SplitDWI -> hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_motion_correct_SplitDWI -> hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_motion_correct_SplitDWI -> hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode;

  }

  subgraph cluster_hmc_sdc_ecc_eddy_correct {

      label="eddy_correct";

    hmc_sdc_ecc_eddy_correct_inputnode[label="inputnode (utility)"];

    hmc_sdc_ecc_eddy_correct_b0_avg[label="b0_avg (utility)"];

    hmc_sdc_ecc_eddy_correct_ExtractDWI[label="ExtractDWI (utility)"];

    hmc_sdc_ecc_eddy_correct_SplitDWIs[label="SplitDWIs (fsl)"];

    hmc_sdc_ecc_eddy_correct_ModulateDWIs[label="ModulateDWIs (fsl)"];

    hmc_sdc_ecc_eddy_correct_RemoveNegative[label="RemoveNegative (fsl)"];

    hmc_sdc_ecc_eddy_correct_MergeDWIs[label="MergeDWIs (utility)"];

    hmc_sdc_ecc_eddy_correct_GatherMatrices[label="GatherMatrices (utility)"];

    hmc_sdc_ecc_eddy_correct_outputnode[label="outputnode (utility)"];

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_ExtractDWI;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_ExtractDWI;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_MergeDWIs;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_MergeDWIs;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_b0_avg;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_b0_avg;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_GatherMatrices;

    subgraph cluster_hmc_sdc_ecc_eddy_correct_DWICoregistration {

            label="DWICoregistration";

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode[label="inputnode (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_SplitDWIs[label="SplitDWIs (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate[label="MskDilate (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_DWEqualize[label="DWEqualize (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_Bias[label="Bias (ants)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_B0Equalize[label="B0Equalize (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_InitXforms[label="InitXforms (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration[label="CoRegistration (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_RemoveNegative[label="RemoveNegative (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MergeDWIs[label="MergeDWIs (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode[label="outputnode (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_InitXforms;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_InitXforms;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_Bias;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_Bias;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_SplitDWIs;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_B0Equalize;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_SplitDWIs -> hmc_sdc_ecc_eddy_correct_DWICoregistration_DWEqualize;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_eddy_correct_DWICoregistration_DWEqualize;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_DWEqualize -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_Bias -> hmc_sdc_ecc_eddy_correct_DWICoregistration_B0Equalize;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_B0Equalize -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_InitXforms -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration -> hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration -> hmc_sdc_ecc_eddy_correct_DWICoregistration_RemoveNegative;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_RemoveNegative -> hmc_sdc_ecc_eddy_correct_DWICoregistration_MergeDWIs;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MergeDWIs -> hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode;

    }

    hmc_sdc_ecc_eddy_correct_SplitDWIs -> hmc_sdc_ecc_eddy_correct_ModulateDWIs;

    hmc_sdc_ecc_eddy_correct_ModulateDWIs -> hmc_sdc_ecc_eddy_correct_RemoveNegative;

    hmc_sdc_ecc_eddy_correct_RemoveNegative -> hmc_sdc_ecc_eddy_correct_MergeDWIs;

    hmc_sdc_ecc_eddy_correct_MergeDWIs -> hmc_sdc_ecc_eddy_correct_outputnode;

    hmc_sdc_ecc_eddy_correct_GatherMatrices -> hmc_sdc_ecc_eddy_correct_outputnode;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_eddy_correct_ExtractDWI -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_eddy_correct_b0_avg -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_eddy_correct_GatherMatrices;

    hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_eddy_correct_ModulateDWIs;

    hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_eddy_correct_SplitDWIs;

  }

  hmc_sdc_ecc_b0_avg_post -> hmc_sdc_ecc_bet_dwi_post;

  hmc_sdc_ecc_bet_dwi_post -> hmc_sdc_ecc_outputnode;

  subgraph cluster_hmc_sdc_ecc_fmb_correction {

      label="fmb_correction";

    hmc_sdc_ecc_fmb_correction_inputnode[label="inputnode (utility)"];

    hmc_sdc_ecc_fmb_correction_Baseline[label="Baseline (utility)"];

    hmc_sdc_ecc_fmb_correction_SplitDWIs[label="SplitDWIs (fsl)"];

    hmc_sdc_ecc_fmb_correction_GetFirst[label="GetFirst (fsl)"];

    hmc_sdc_ecc_fmb_correction_Bias[label="Bias (ants)"];

    hmc_sdc_ecc_fmb_correction_BrainExtraction[label="BrainExtraction (fsl)"];

    hmc_sdc_ecc_fmb_correction_MskDilate[label="MskDilate (fsl)"];

    hmc_sdc_ecc_fmb_correction_FMm_to_B0[label="FMm_to_B0 (ants)"];

    hmc_sdc_ecc_fmb_correction_SettingsGrabber[label="SettingsGrabber (io)"];

    hmc_sdc_ecc_fmb_correction_EffEcho[label="EffEcho (utility)"];

    hmc_sdc_ecc_fmb_correction_PreparePhase[label="PreparePhase (utility)"];

    hmc_sdc_ecc_fmb_correction_PhaseUnwrap[label="PhaseUnwrap (fsl)"];

    hmc_sdc_ecc_fmb_correction_ToRadSec[label="ToRadSec (utility)"];

    hmc_sdc_ecc_fmb_correction_FMp_to_B0[label="FMp_to_B0 (ants)"];

    hmc_sdc_ecc_fmb_correction_PreliminaryFugue[label="PreliminaryFugue (fsl)"];

    hmc_sdc_ecc_fmb_correction_DemeanFmap[label="DemeanFmap (utility)"];

    hmc_sdc_ecc_fmb_correction_AddEmptyVol[label="AddEmptyVol (utility)"];

    hmc_sdc_ecc_fmb_correction_ComputeVSM[label="ComputeVSM (fsl)"];

    hmc_sdc_ecc_fmb_correction_UnwarpDWIs[label="UnwarpDWIs (fsl)"];

    hmc_sdc_ecc_fmb_correction_RemoveNegative[label="RemoveNegative (fsl)"];

    hmc_sdc_ecc_fmb_correction_MergeDWIs[label="MergeDWIs (fsl)"];

    hmc_sdc_ecc_fmb_correction_outputnode[label="outputnode (utility)"];

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_ComputeVSM;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_DemeanFmap;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_FMm_to_B0;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_PreparePhase;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_SettingsGrabber;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_PreliminaryFugue;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_GetFirst;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_SplitDWIs;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_Baseline;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_Baseline;

    hmc_sdc_ecc_fmb_correction_Baseline -> hmc_sdc_ecc_fmb_correction_FMp_to_B0;

    hmc_sdc_ecc_fmb_correction_Baseline -> hmc_sdc_ecc_fmb_correction_FMm_to_B0;

    hmc_sdc_ecc_fmb_correction_SplitDWIs -> hmc_sdc_ecc_fmb_correction_UnwarpDWIs;

    hmc_sdc_ecc_fmb_correction_GetFirst -> hmc_sdc_ecc_fmb_correction_Bias;

    hmc_sdc_ecc_fmb_correction_Bias -> hmc_sdc_ecc_fmb_correction_BrainExtraction;

    hmc_sdc_ecc_fmb_correction_Bias -> hmc_sdc_ecc_fmb_correction_PhaseUnwrap;

    hmc_sdc_ecc_fmb_correction_Bias -> hmc_sdc_ecc_fmb_correction_FMm_to_B0;

    hmc_sdc_ecc_fmb_correction_BrainExtraction -> hmc_sdc_ecc_fmb_correction_MskDilate;

    hmc_sdc_ecc_fmb_correction_MskDilate -> hmc_sdc_ecc_fmb_correction_PhaseUnwrap;

    hmc_sdc_ecc_fmb_correction_MskDilate -> hmc_sdc_ecc_fmb_correction_FMm_to_B0;

    hmc_sdc_ecc_fmb_correction_FMm_to_B0 -> hmc_sdc_ecc_fmb_correction_FMp_to_B0;

    hmc_sdc_ecc_fmb_correction_FMm_to_B0 -> hmc_sdc_ecc_fmb_correction_FMp_to_B0;

    hmc_sdc_ecc_fmb_correction_SettingsGrabber -> hmc_sdc_ecc_fmb_correction_EffEcho;

    hmc_sdc_ecc_fmb_correction_SettingsGrabber -> hmc_sdc_ecc_fmb_correction_EffEcho;

    hmc_sdc_ecc_fmb_correction_SettingsGrabber -> hmc_sdc_ecc_fmb_correction_UnwarpDWIs;

    hmc_sdc_ecc_fmb_correction_SettingsGrabber -> hmc_sdc_ecc_fmb_correction_ComputeVSM;

    hmc_sdc_ecc_fmb_correction_SettingsGrabber -> hmc_sdc_ecc_fmb_correction_ToRadSec;

    hmc_sdc_ecc_fmb_correction_EffEcho -> hmc_sdc_ecc_fmb_correction_ComputeVSM;

    hmc_sdc_ecc_fmb_correction_PreparePhase -> hmc_sdc_ecc_fmb_correction_PhaseUnwrap;

    hmc_sdc_ecc_fmb_correction_PhaseUnwrap -> hmc_sdc_ecc_fmb_correction_ToRadSec;

    hmc_sdc_ecc_fmb_correction_ToRadSec -> hmc_sdc_ecc_fmb_correction_FMp_to_B0;

    hmc_sdc_ecc_fmb_correction_FMp_to_B0 -> hmc_sdc_ecc_fmb_correction_PreliminaryFugue;

    hmc_sdc_ecc_fmb_correction_PreliminaryFugue -> hmc_sdc_ecc_fmb_correction_DemeanFmap;

    subgraph cluster_hmc_sdc_ecc_fmb_correction_Cleanup {

            label="Cleanup";

        hmc_sdc_ecc_fmb_correction_Cleanup_inputnode[label="inputnode (utility)"];

        hmc_sdc_ecc_fmb_correction_Cleanup_MskErode[label="MskErode (fsl)"];

        hmc_sdc_ecc_fmb_correction_Cleanup_NewMask[label="NewMask (fsl)"];

        hmc_sdc_ecc_fmb_correction_Cleanup_Despike[label="Despike (fsl)"];

        hmc_sdc_ecc_fmb_correction_Cleanup_ApplyMask[label="ApplyMask (fsl)"];

        hmc_sdc_ecc_fmb_correction_Cleanup_Merge[label="Merge (utility)"];

        hmc_sdc_ecc_fmb_correction_Cleanup_AddEdge[label="AddEdge (fsl)"];

        hmc_sdc_ecc_fmb_correction_Cleanup_outputnode[label="outputnode (utility)"];

        hmc_sdc_ecc_fmb_correction_Cleanup_inputnode -> hmc_sdc_ecc_fmb_correction_Cleanup_NewMask;

        hmc_sdc_ecc_fmb_correction_Cleanup_inputnode -> hmc_sdc_ecc_fmb_correction_Cleanup_Despike;

        hmc_sdc_ecc_fmb_correction_Cleanup_inputnode -> hmc_sdc_ecc_fmb_correction_Cleanup_Despike;

        hmc_sdc_ecc_fmb_correction_Cleanup_inputnode -> hmc_sdc_ecc_fmb_correction_Cleanup_MskErode;

        hmc_sdc_ecc_fmb_correction_Cleanup_inputnode -> hmc_sdc_ecc_fmb_correction_Cleanup_AddEdge;

        hmc_sdc_ecc_fmb_correction_Cleanup_MskErode -> hmc_sdc_ecc_fmb_correction_Cleanup_NewMask;

        hmc_sdc_ecc_fmb_correction_Cleanup_MskErode -> hmc_sdc_ecc_fmb_correction_Cleanup_Merge;

        hmc_sdc_ecc_fmb_correction_Cleanup_NewMask -> hmc_sdc_ecc_fmb_correction_Cleanup_ApplyMask;

        hmc_sdc_ecc_fmb_correction_Cleanup_Despike -> hmc_sdc_ecc_fmb_correction_Cleanup_ApplyMask;

        hmc_sdc_ecc_fmb_correction_Cleanup_ApplyMask -> hmc_sdc_ecc_fmb_correction_Cleanup_Merge;

        hmc_sdc_ecc_fmb_correction_Cleanup_Merge -> hmc_sdc_ecc_fmb_correction_Cleanup_AddEdge;

        hmc_sdc_ecc_fmb_correction_Cleanup_AddEdge -> hmc_sdc_ecc_fmb_correction_Cleanup_outputnode;

    }

    hmc_sdc_ecc_fmb_correction_AddEmptyVol -> hmc_sdc_ecc_fmb_correction_ComputeVSM;

    hmc_sdc_ecc_fmb_correction_ComputeVSM -> hmc_sdc_ecc_fmb_correction_outputnode;

    hmc_sdc_ecc_fmb_correction_ComputeVSM -> hmc_sdc_ecc_fmb_correction_UnwarpDWIs;

    hmc_sdc_ecc_fmb_correction_UnwarpDWIs -> hmc_sdc_ecc_fmb_correction_RemoveNegative;

    hmc_sdc_ecc_fmb_correction_RemoveNegative -> hmc_sdc_ecc_fmb_correction_MergeDWIs;

    hmc_sdc_ecc_fmb_correction_MergeDWIs -> hmc_sdc_ecc_fmb_correction_outputnode;

    subgraph cluster_hmc_sdc_ecc_fmb_correction_Shiftmap2Warping {

            label="Shiftmap2Warping";

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_inputnode[label="inputnode (utility)"];

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_Fix_hdr[label="Fix_hdr (utility)"];

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_ScaleField[label="ScaleField (fsl)"];

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_vsm2dfm[label="vsm2dfm (fsl)"];

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_outputnode[label="outputnode (utility)"];

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_Fix_hdr;

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_Fix_hdr;

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_ScaleField;

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_vsm2dfm;

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_vsm2dfm;

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_Fix_hdr -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_ScaleField;

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_ScaleField -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_vsm2dfm;

        hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_vsm2dfm -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_outputnode;

    }

    hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_outputnode -> hmc_sdc_ecc_fmb_correction_outputnode;

    hmc_sdc_ecc_fmb_correction_ComputeVSM -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_inputnode;

    hmc_sdc_ecc_fmb_correction_DemeanFmap -> hmc_sdc_ecc_fmb_correction_Cleanup_inputnode;

    hmc_sdc_ecc_fmb_correction_SettingsGrabber -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_inputnode;

    hmc_sdc_ecc_fmb_correction_Cleanup_outputnode -> hmc_sdc_ecc_fmb_correction_AddEmptyVol;

    hmc_sdc_ecc_fmb_correction_inputnode -> hmc_sdc_ecc_fmb_correction_Cleanup_inputnode;

    hmc_sdc_ecc_fmb_correction_MergeDWIs -> hmc_sdc_ecc_fmb_correction_Shiftmap2Warping_inputnode;

  }

  subgraph cluster_hmc_sdc_ecc_UnwarpArtifacts {

      label="UnwarpArtifacts";

    hmc_sdc_ecc_UnwarpArtifacts_inputnode[label="inputnode (utility)"];

    hmc_sdc_ecc_UnwarpArtifacts_SplitDWIs[label="SplitDWIs (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_Reference[label="Reference (utility)"];

    hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp[label="ConvertWarp (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_CoeffComp[label="CoeffComp (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_JacobianComp[label="JacobianComp (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs[label="UnwarpDWIs (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_ModulateDWIs[label="ModulateDWIs (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_RemoveNegative[label="RemoveNegative (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_MergeDWIs[label="MergeDWIs (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_outputnode[label="outputnode (utility)"];

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp;

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp;

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp;

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp;

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_SplitDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_SplitDWIs -> hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_SplitDWIs -> hmc_sdc_ecc_UnwarpArtifacts_Reference;

    hmc_sdc_ecc_UnwarpArtifacts_Reference -> hmc_sdc_ecc_UnwarpArtifacts_JacobianComp;

    hmc_sdc_ecc_UnwarpArtifacts_Reference -> hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_Reference -> hmc_sdc_ecc_UnwarpArtifacts_CoeffComp;

    hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp -> hmc_sdc_ecc_UnwarpArtifacts_outputnode;

    hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp -> hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp -> hmc_sdc_ecc_UnwarpArtifacts_CoeffComp;

    hmc_sdc_ecc_UnwarpArtifacts_CoeffComp -> hmc_sdc_ecc_UnwarpArtifacts_JacobianComp;

    hmc_sdc_ecc_UnwarpArtifacts_CoeffComp -> hmc_sdc_ecc_UnwarpArtifacts_outputnode;

    hmc_sdc_ecc_UnwarpArtifacts_JacobianComp -> hmc_sdc_ecc_UnwarpArtifacts_outputnode;

    hmc_sdc_ecc_UnwarpArtifacts_JacobianComp -> hmc_sdc_ecc_UnwarpArtifacts_ModulateDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs -> hmc_sdc_ecc_UnwarpArtifacts_ModulateDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_ModulateDWIs -> hmc_sdc_ecc_UnwarpArtifacts_RemoveNegative;

    hmc_sdc_ecc_UnwarpArtifacts_RemoveNegative -> hmc_sdc_ecc_UnwarpArtifacts_MergeDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_MergeDWIs -> hmc_sdc_ecc_UnwarpArtifacts_outputnode;

  }

  hmc_sdc_ecc_B0indices -> hmc_sdc_ecc_fmb_correction_inputnode;

  hmc_sdc_ecc_eddy_correct_outputnode -> hmc_sdc_ecc_UnwarpArtifacts_inputnode;

  hmc_sdc_ecc_eddy_correct_outputnode -> hmc_sdc_ecc_b0_avg_post;

  hmc_sdc_ecc_motion_correct_outputnode -> hmc_sdc_ecc_UnwarpArtifacts_inputnode;

  hmc_sdc_ecc_motion_correct_outputnode -> hmc_sdc_ecc_fmb_correction_inputnode;

  hmc_sdc_ecc_motion_correct_outputnode -> hmc_sdc_ecc_outputnode;

  hmc_sdc_ecc_motion_correct_outputnode -> hmc_sdc_ecc_eddy_correct_inputnode;

  hmc_sdc_ecc_fmb_correction_outputnode -> hmc_sdc_ecc_UnwarpArtifacts_inputnode;

  hmc_sdc_ecc_UnwarpArtifacts_outputnode -> hmc_sdc_ecc_outputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_eddy_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_eddy_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_motion_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_motion_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_motion_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_fmb_correction_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_fmb_correction_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_fmb_correction_inputnode;

  hmc_sdc_ecc_bet_dwi_pre -> hmc_sdc_ecc_fmb_correction_inputnode;

  hmc_sdc_ecc_bet_dwi_pre -> hmc_sdc_ecc_eddy_correct_inputnode;

  hmc_sdc_ecc_bet_dwi_pre -> hmc_sdc_ecc_motion_correct_inputnode;

}

all_fsl_pipeline()

Link to code

Workflow that integrates FSL topup and eddy.

Warning

this workflow rotates the gradients table (b-vectors) [Leemans09].

Warning

this workflow does not perform jacobian modulation of each DWI [Jones10].

Examples

>>> from nipype.workflows.dmri.fsl.artifacts import all_fsl_pipeline
>>> allcorr = all_fsl_pipeline()
>>> allcorr.inputs.inputnode.in_file = 'epi.nii'
>>> allcorr.inputs.inputnode.alt_file = 'epi_rev.nii'
>>> allcorr.inputs.inputnode.in_bval = 'diffusion.bval'
>>> allcorr.inputs.inputnode.in_bvec = 'diffusion.bvec'
>>> allcorr.run() 

Graph

digraph fsl_all_correct{

  label="fsl_all_correct";

  fsl_all_correct_inputnode[label="inputnode (utility)"];

  fsl_all_correct_gen_index[label="gen_index (utility)"];

  fsl_all_correct_b0_avg_pre[label="b0_avg_pre (utility)"];

  fsl_all_correct_bet_dwi_pre[label="bet_dwi_pre (fsl)"];

  fsl_all_correct_fsl_eddy[label="fsl_eddy (fsl)"];

  fsl_all_correct_b0_avg_post[label="b0_avg_post (utility)"];

  fsl_all_correct_bet_dwi_post[label="bet_dwi_post (fsl)"];

  fsl_all_correct_Rotate_Bvec[label="Rotate_Bvec (utility)"];

  fsl_all_correct_outputnode[label="outputnode (utility)"];

  fsl_all_correct_inputnode -> fsl_all_correct_Rotate_Bvec;

  fsl_all_correct_inputnode -> fsl_all_correct_fsl_eddy;

  fsl_all_correct_inputnode -> fsl_all_correct_fsl_eddy;

  fsl_all_correct_inputnode -> fsl_all_correct_fsl_eddy;

  fsl_all_correct_inputnode -> fsl_all_correct_b0_avg_pre;

  fsl_all_correct_inputnode -> fsl_all_correct_b0_avg_pre;

  fsl_all_correct_inputnode -> fsl_all_correct_gen_index;

  fsl_all_correct_inputnode -> fsl_all_correct_b0_avg_post;

  fsl_all_correct_gen_index -> fsl_all_correct_fsl_eddy;

  fsl_all_correct_b0_avg_pre -> fsl_all_correct_bet_dwi_pre;

  fsl_all_correct_bet_dwi_pre -> fsl_all_correct_fsl_eddy;

  subgraph cluster_fsl_all_correct_peb_correction {

      label="peb_correction";

    fsl_all_correct_peb_correction_inputnode[label="inputnode (utility)"];

    fsl_all_correct_peb_correction_b0_ref[label="b0_ref (fsl)"];

    fsl_all_correct_peb_correction_b0_alt[label="b0_alt (fsl)"];

    fsl_all_correct_peb_correction_b0_list[label="b0_list (utility)"];

    fsl_all_correct_peb_correction_b0_merged[label="b0_merged (fsl)"];

    fsl_all_correct_peb_correction_topup[label="topup (fsl)"];

    fsl_all_correct_peb_correction_unwarp[label="unwarp (fsl)"];

    fsl_all_correct_peb_correction_outputnode[label="outputnode (utility)"];

    fsl_all_correct_peb_correction_inputnode -> fsl_all_correct_peb_correction_b0_alt;

    fsl_all_correct_peb_correction_inputnode -> fsl_all_correct_peb_correction_b0_alt;

    fsl_all_correct_peb_correction_inputnode -> fsl_all_correct_peb_correction_unwarp;

    fsl_all_correct_peb_correction_inputnode -> fsl_all_correct_peb_correction_b0_ref;

    fsl_all_correct_peb_correction_inputnode -> fsl_all_correct_peb_correction_b0_ref;

    fsl_all_correct_peb_correction_b0_ref -> fsl_all_correct_peb_correction_b0_list;

    fsl_all_correct_peb_correction_b0_alt -> fsl_all_correct_peb_correction_b0_list;

    fsl_all_correct_peb_correction_b0_list -> fsl_all_correct_peb_correction_b0_merged;

    fsl_all_correct_peb_correction_b0_merged -> fsl_all_correct_peb_correction_topup;

    fsl_all_correct_peb_correction_topup -> fsl_all_correct_peb_correction_outputnode;

    fsl_all_correct_peb_correction_topup -> fsl_all_correct_peb_correction_unwarp;

    fsl_all_correct_peb_correction_topup -> fsl_all_correct_peb_correction_unwarp;

    fsl_all_correct_peb_correction_topup -> fsl_all_correct_peb_correction_unwarp;

    subgraph cluster_fsl_all_correct_peb_correction_Shiftmap2Warping {

            label="Shiftmap2Warping";

        fsl_all_correct_peb_correction_Shiftmap2Warping_inputnode[label="inputnode (utility)"];

        fsl_all_correct_peb_correction_Shiftmap2Warping_Fix_hdr[label="Fix_hdr (utility)"];

        fsl_all_correct_peb_correction_Shiftmap2Warping_ScaleField[label="ScaleField (fsl)"];

        fsl_all_correct_peb_correction_Shiftmap2Warping_vsm2dfm[label="vsm2dfm (fsl)"];

        fsl_all_correct_peb_correction_Shiftmap2Warping_outputnode[label="outputnode (utility)"];

        fsl_all_correct_peb_correction_Shiftmap2Warping_inputnode -> fsl_all_correct_peb_correction_Shiftmap2Warping_Fix_hdr;

        fsl_all_correct_peb_correction_Shiftmap2Warping_inputnode -> fsl_all_correct_peb_correction_Shiftmap2Warping_Fix_hdr;

        fsl_all_correct_peb_correction_Shiftmap2Warping_inputnode -> fsl_all_correct_peb_correction_Shiftmap2Warping_vsm2dfm;

        fsl_all_correct_peb_correction_Shiftmap2Warping_inputnode -> fsl_all_correct_peb_correction_Shiftmap2Warping_vsm2dfm;

        fsl_all_correct_peb_correction_Shiftmap2Warping_inputnode -> fsl_all_correct_peb_correction_Shiftmap2Warping_ScaleField;

        fsl_all_correct_peb_correction_Shiftmap2Warping_Fix_hdr -> fsl_all_correct_peb_correction_Shiftmap2Warping_ScaleField;

        fsl_all_correct_peb_correction_Shiftmap2Warping_ScaleField -> fsl_all_correct_peb_correction_Shiftmap2Warping_vsm2dfm;

        fsl_all_correct_peb_correction_Shiftmap2Warping_vsm2dfm -> fsl_all_correct_peb_correction_Shiftmap2Warping_outputnode;

    }

    fsl_all_correct_peb_correction_unwarp -> fsl_all_correct_peb_correction_outputnode;

    fsl_all_correct_peb_correction_topup -> fsl_all_correct_peb_correction_Shiftmap2Warping_inputnode;

    fsl_all_correct_peb_correction_Shiftmap2Warping_outputnode -> fsl_all_correct_peb_correction_outputnode;

    fsl_all_correct_peb_correction_b0_ref -> fsl_all_correct_peb_correction_Shiftmap2Warping_inputnode;

  }

  fsl_all_correct_fsl_eddy -> fsl_all_correct_Rotate_Bvec;

  fsl_all_correct_fsl_eddy -> fsl_all_correct_b0_avg_post;

  fsl_all_correct_fsl_eddy -> fsl_all_correct_outputnode;

  fsl_all_correct_b0_avg_post -> fsl_all_correct_bet_dwi_post;

  fsl_all_correct_bet_dwi_post -> fsl_all_correct_outputnode;

  fsl_all_correct_Rotate_Bvec -> fsl_all_correct_outputnode;

  fsl_all_correct_inputnode -> fsl_all_correct_peb_correction_inputnode;

  fsl_all_correct_inputnode -> fsl_all_correct_peb_correction_inputnode;

  fsl_all_correct_inputnode -> fsl_all_correct_peb_correction_inputnode;

  fsl_all_correct_peb_correction_topup -> fsl_all_correct_fsl_eddy;

  fsl_all_correct_peb_correction_topup -> fsl_all_correct_fsl_eddy;

  fsl_all_correct_peb_correction_topup -> fsl_all_correct_fsl_eddy;

  fsl_all_correct_bet_dwi_pre -> fsl_all_correct_peb_correction_inputnode;

}

all_peb_pipeline()

Link to code

Builds a pipeline including three artifact corrections: head-motion correction (HMC), susceptibility-derived distortion correction (SDC), and Eddy currents-derived distortion correction (ECC).

Warning

this workflow rotates the gradients table (b-vectors) [Leemans09].

Examples

>>> from nipype.workflows.dmri.fsl.artifacts import all_peb_pipeline
>>> allcorr = all_peb_pipeline()
>>> allcorr.inputs.inputnode.in_file = 'epi.nii'
>>> allcorr.inputs.inputnode.alt_file = 'epi_rev.nii'
>>> allcorr.inputs.inputnode.in_bval = 'diffusion.bval'
>>> allcorr.inputs.inputnode.in_bvec = 'diffusion.bvec'
>>> allcorr.run() 

Graph

digraph hmc_sdc_ecc{

  label="hmc_sdc_ecc";

  hmc_sdc_ecc_inputnode[label="inputnode (utility)"];

  hmc_sdc_ecc_b0_avg_pre[label="b0_avg_pre (utility)"];

  hmc_sdc_ecc_bet_dwi_pre[label="bet_dwi_pre (fsl)"];

  hmc_sdc_ecc_b0_avg_post[label="b0_avg_post (utility)"];

  hmc_sdc_ecc_bet_dwi_post[label="bet_dwi_post (fsl)"];

  hmc_sdc_ecc_outputnode[label="outputnode (utility)"];

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_b0_avg_post;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_b0_avg_pre;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_b0_avg_pre;

  hmc_sdc_ecc_b0_avg_pre -> hmc_sdc_ecc_bet_dwi_pre;

  subgraph cluster_hmc_sdc_ecc_motion_correct {

      label="motion_correct";

    hmc_sdc_ecc_motion_correct_inputnode[label="inputnode (utility)"];

    hmc_sdc_ecc_motion_correct_SplitDWI[label="SplitDWI (utility)"];

    hmc_sdc_ecc_motion_correct_InsertRefmat[label="InsertRefmat (utility)"];

    hmc_sdc_ecc_motion_correct_Rotate_Bvec[label="Rotate_Bvec (utility)"];

    hmc_sdc_ecc_motion_correct_outputnode[label="outputnode (utility)"];

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_SplitDWI;

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_SplitDWI;

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_SplitDWI;

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_Rotate_Bvec;

    hmc_sdc_ecc_motion_correct_SplitDWI -> hmc_sdc_ecc_motion_correct_InsertRefmat;

    subgraph cluster_hmc_sdc_ecc_motion_correct_DWICoregistration {

            label="DWICoregistration";

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode[label="inputnode (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_InitXforms[label="InitXforms (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate[label="MskDilate (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_Bias[label="Bias (ants)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_B0Equalize[label="B0Equalize (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_SplitDWIs[label="SplitDWIs (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_DWEqualize[label="DWEqualize (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration[label="CoRegistration (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_RemoveNegative[label="RemoveNegative (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_MergeDWIs[label="MergeDWIs (fsl)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode[label="outputnode (utility)"];

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_SplitDWIs;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_Bias;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_Bias;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_B0Equalize;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_InitXforms;

        hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_InitXforms;

        hmc_sdc_ecc_motion_correct_DWICoregistration_InitXforms -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_motion_correct_DWICoregistration_DWEqualize;

        hmc_sdc_ecc_motion_correct_DWICoregistration_Bias -> hmc_sdc_ecc_motion_correct_DWICoregistration_B0Equalize;

        hmc_sdc_ecc_motion_correct_DWICoregistration_B0Equalize -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_SplitDWIs -> hmc_sdc_ecc_motion_correct_DWICoregistration_DWEqualize;

        hmc_sdc_ecc_motion_correct_DWICoregistration_DWEqualize -> hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration -> hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode;

        hmc_sdc_ecc_motion_correct_DWICoregistration_CoRegistration -> hmc_sdc_ecc_motion_correct_DWICoregistration_RemoveNegative;

        hmc_sdc_ecc_motion_correct_DWICoregistration_RemoveNegative -> hmc_sdc_ecc_motion_correct_DWICoregistration_MergeDWIs;

        hmc_sdc_ecc_motion_correct_DWICoregistration_MergeDWIs -> hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode;

    }

    hmc_sdc_ecc_motion_correct_InsertRefmat -> hmc_sdc_ecc_motion_correct_Rotate_Bvec;

    hmc_sdc_ecc_motion_correct_InsertRefmat -> hmc_sdc_ecc_motion_correct_outputnode;

    hmc_sdc_ecc_motion_correct_Rotate_Bvec -> hmc_sdc_ecc_motion_correct_outputnode;

    hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_motion_correct_outputnode;

    hmc_sdc_ecc_motion_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_motion_correct_InsertRefmat;

    hmc_sdc_ecc_motion_correct_inputnode -> hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_motion_correct_SplitDWI -> hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_motion_correct_SplitDWI -> hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_motion_correct_SplitDWI -> hmc_sdc_ecc_motion_correct_DWICoregistration_inputnode;

  }

  subgraph cluster_hmc_sdc_ecc_eddy_correct {

      label="eddy_correct";

    hmc_sdc_ecc_eddy_correct_inputnode[label="inputnode (utility)"];

    hmc_sdc_ecc_eddy_correct_ExtractDWI[label="ExtractDWI (utility)"];

    hmc_sdc_ecc_eddy_correct_b0_avg[label="b0_avg (utility)"];

    hmc_sdc_ecc_eddy_correct_GatherMatrices[label="GatherMatrices (utility)"];

    hmc_sdc_ecc_eddy_correct_SplitDWIs[label="SplitDWIs (fsl)"];

    hmc_sdc_ecc_eddy_correct_ModulateDWIs[label="ModulateDWIs (fsl)"];

    hmc_sdc_ecc_eddy_correct_RemoveNegative[label="RemoveNegative (fsl)"];

    hmc_sdc_ecc_eddy_correct_MergeDWIs[label="MergeDWIs (utility)"];

    hmc_sdc_ecc_eddy_correct_outputnode[label="outputnode (utility)"];

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_b0_avg;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_b0_avg;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_ExtractDWI;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_ExtractDWI;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_MergeDWIs;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_MergeDWIs;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_GatherMatrices;

    subgraph cluster_hmc_sdc_ecc_eddy_correct_DWICoregistration {

            label="DWICoregistration";

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode[label="inputnode (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_Bias[label="Bias (ants)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_B0Equalize[label="B0Equalize (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_SplitDWIs[label="SplitDWIs (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate[label="MskDilate (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_DWEqualize[label="DWEqualize (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_InitXforms[label="InitXforms (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration[label="CoRegistration (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_RemoveNegative[label="RemoveNegative (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MergeDWIs[label="MergeDWIs (fsl)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode[label="outputnode (utility)"];

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_InitXforms;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_InitXforms;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_B0Equalize;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_SplitDWIs;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_Bias;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_Bias;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_Bias -> hmc_sdc_ecc_eddy_correct_DWICoregistration_B0Equalize;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_B0Equalize -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_SplitDWIs -> hmc_sdc_ecc_eddy_correct_DWICoregistration_DWEqualize;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_eddy_correct_DWICoregistration_DWEqualize;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MskDilate -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_DWEqualize -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_InitXforms -> hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration -> hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_CoRegistration -> hmc_sdc_ecc_eddy_correct_DWICoregistration_RemoveNegative;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_RemoveNegative -> hmc_sdc_ecc_eddy_correct_DWICoregistration_MergeDWIs;

        hmc_sdc_ecc_eddy_correct_DWICoregistration_MergeDWIs -> hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode;

    }

    hmc_sdc_ecc_eddy_correct_GatherMatrices -> hmc_sdc_ecc_eddy_correct_outputnode;

    hmc_sdc_ecc_eddy_correct_SplitDWIs -> hmc_sdc_ecc_eddy_correct_ModulateDWIs;

    hmc_sdc_ecc_eddy_correct_ModulateDWIs -> hmc_sdc_ecc_eddy_correct_RemoveNegative;

    hmc_sdc_ecc_eddy_correct_RemoveNegative -> hmc_sdc_ecc_eddy_correct_MergeDWIs;

    hmc_sdc_ecc_eddy_correct_MergeDWIs -> hmc_sdc_ecc_eddy_correct_outputnode;

    hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_eddy_correct_SplitDWIs;

    hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_eddy_correct_ModulateDWIs;

    hmc_sdc_ecc_eddy_correct_DWICoregistration_outputnode -> hmc_sdc_ecc_eddy_correct_GatherMatrices;

    hmc_sdc_ecc_eddy_correct_b0_avg -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_eddy_correct_ExtractDWI -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

    hmc_sdc_ecc_eddy_correct_inputnode -> hmc_sdc_ecc_eddy_correct_DWICoregistration_inputnode;

  }

  hmc_sdc_ecc_b0_avg_post -> hmc_sdc_ecc_bet_dwi_post;

  hmc_sdc_ecc_bet_dwi_post -> hmc_sdc_ecc_outputnode;

  subgraph cluster_hmc_sdc_ecc_peb_correction {

      label="peb_correction";

    hmc_sdc_ecc_peb_correction_inputnode[label="inputnode (utility)"];

    hmc_sdc_ecc_peb_correction_b0_ref[label="b0_ref (fsl)"];

    hmc_sdc_ecc_peb_correction_b0_alt[label="b0_alt (fsl)"];

    hmc_sdc_ecc_peb_correction_b0_list[label="b0_list (utility)"];

    hmc_sdc_ecc_peb_correction_b0_merged[label="b0_merged (fsl)"];

    hmc_sdc_ecc_peb_correction_topup[label="topup (fsl)"];

    hmc_sdc_ecc_peb_correction_unwarp[label="unwarp (fsl)"];

    hmc_sdc_ecc_peb_correction_outputnode[label="outputnode (utility)"];

    hmc_sdc_ecc_peb_correction_inputnode -> hmc_sdc_ecc_peb_correction_b0_alt;

    hmc_sdc_ecc_peb_correction_inputnode -> hmc_sdc_ecc_peb_correction_b0_alt;

    hmc_sdc_ecc_peb_correction_inputnode -> hmc_sdc_ecc_peb_correction_b0_ref;

    hmc_sdc_ecc_peb_correction_inputnode -> hmc_sdc_ecc_peb_correction_b0_ref;

    hmc_sdc_ecc_peb_correction_inputnode -> hmc_sdc_ecc_peb_correction_unwarp;

    hmc_sdc_ecc_peb_correction_b0_ref -> hmc_sdc_ecc_peb_correction_b0_list;

    hmc_sdc_ecc_peb_correction_b0_alt -> hmc_sdc_ecc_peb_correction_b0_list;

    hmc_sdc_ecc_peb_correction_b0_list -> hmc_sdc_ecc_peb_correction_b0_merged;

    hmc_sdc_ecc_peb_correction_b0_merged -> hmc_sdc_ecc_peb_correction_topup;

    hmc_sdc_ecc_peb_correction_topup -> hmc_sdc_ecc_peb_correction_outputnode;

    hmc_sdc_ecc_peb_correction_topup -> hmc_sdc_ecc_peb_correction_unwarp;

    hmc_sdc_ecc_peb_correction_topup -> hmc_sdc_ecc_peb_correction_unwarp;

    hmc_sdc_ecc_peb_correction_topup -> hmc_sdc_ecc_peb_correction_unwarp;

    hmc_sdc_ecc_peb_correction_unwarp -> hmc_sdc_ecc_peb_correction_outputnode;

    subgraph cluster_hmc_sdc_ecc_peb_correction_Shiftmap2Warping {

            label="Shiftmap2Warping";

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_inputnode[label="inputnode (utility)"];

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_Fix_hdr[label="Fix_hdr (utility)"];

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_ScaleField[label="ScaleField (fsl)"];

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_vsm2dfm[label="vsm2dfm (fsl)"];

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_outputnode[label="outputnode (utility)"];

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_ScaleField;

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_vsm2dfm;

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_vsm2dfm;

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_Fix_hdr;

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_inputnode -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_Fix_hdr;

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_Fix_hdr -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_ScaleField;

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_ScaleField -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_vsm2dfm;

        hmc_sdc_ecc_peb_correction_Shiftmap2Warping_vsm2dfm -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_outputnode;

    }

    hmc_sdc_ecc_peb_correction_Shiftmap2Warping_outputnode -> hmc_sdc_ecc_peb_correction_outputnode;

    hmc_sdc_ecc_peb_correction_topup -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_inputnode;

    hmc_sdc_ecc_peb_correction_b0_ref -> hmc_sdc_ecc_peb_correction_Shiftmap2Warping_inputnode;

  }

  subgraph cluster_hmc_sdc_ecc_UnwarpArtifacts {

      label="UnwarpArtifacts";

    hmc_sdc_ecc_UnwarpArtifacts_inputnode[label="inputnode (utility)"];

    hmc_sdc_ecc_UnwarpArtifacts_SplitDWIs[label="SplitDWIs (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_Reference[label="Reference (utility)"];

    hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp[label="ConvertWarp (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_CoeffComp[label="CoeffComp (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_JacobianComp[label="JacobianComp (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs[label="UnwarpDWIs (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_ModulateDWIs[label="ModulateDWIs (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_RemoveNegative[label="RemoveNegative (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_MergeDWIs[label="MergeDWIs (fsl)"];

    hmc_sdc_ecc_UnwarpArtifacts_outputnode[label="outputnode (utility)"];

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp;

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp;

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp;

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp;

    hmc_sdc_ecc_UnwarpArtifacts_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_SplitDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_SplitDWIs -> hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_SplitDWIs -> hmc_sdc_ecc_UnwarpArtifacts_Reference;

    hmc_sdc_ecc_UnwarpArtifacts_Reference -> hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_Reference -> hmc_sdc_ecc_UnwarpArtifacts_CoeffComp;

    hmc_sdc_ecc_UnwarpArtifacts_Reference -> hmc_sdc_ecc_UnwarpArtifacts_JacobianComp;

    hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp -> hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp -> hmc_sdc_ecc_UnwarpArtifacts_CoeffComp;

    hmc_sdc_ecc_UnwarpArtifacts_ConvertWarp -> hmc_sdc_ecc_UnwarpArtifacts_outputnode;

    hmc_sdc_ecc_UnwarpArtifacts_CoeffComp -> hmc_sdc_ecc_UnwarpArtifacts_outputnode;

    hmc_sdc_ecc_UnwarpArtifacts_CoeffComp -> hmc_sdc_ecc_UnwarpArtifacts_JacobianComp;

    hmc_sdc_ecc_UnwarpArtifacts_JacobianComp -> hmc_sdc_ecc_UnwarpArtifacts_outputnode;

    hmc_sdc_ecc_UnwarpArtifacts_JacobianComp -> hmc_sdc_ecc_UnwarpArtifacts_ModulateDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_UnwarpDWIs -> hmc_sdc_ecc_UnwarpArtifacts_ModulateDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_ModulateDWIs -> hmc_sdc_ecc_UnwarpArtifacts_RemoveNegative;

    hmc_sdc_ecc_UnwarpArtifacts_RemoveNegative -> hmc_sdc_ecc_UnwarpArtifacts_MergeDWIs;

    hmc_sdc_ecc_UnwarpArtifacts_MergeDWIs -> hmc_sdc_ecc_UnwarpArtifacts_outputnode;

  }

  hmc_sdc_ecc_UnwarpArtifacts_outputnode -> hmc_sdc_ecc_outputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_UnwarpArtifacts_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_eddy_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_eddy_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_motion_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_motion_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_motion_correct_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_peb_correction_inputnode;

  hmc_sdc_ecc_inputnode -> hmc_sdc_ecc_peb_correction_inputnode;

  hmc_sdc_ecc_eddy_correct_outputnode -> hmc_sdc_ecc_UnwarpArtifacts_inputnode;

  hmc_sdc_ecc_eddy_correct_outputnode -> hmc_sdc_ecc_b0_avg_post;

  hmc_sdc_ecc_motion_correct_outputnode -> hmc_sdc_ecc_UnwarpArtifacts_inputnode;

  hmc_sdc_ecc_motion_correct_outputnode -> hmc_sdc_ecc_outputnode;

  hmc_sdc_ecc_motion_correct_outputnode -> hmc_sdc_ecc_peb_correction_inputnode;

  hmc_sdc_ecc_motion_correct_outputnode -> hmc_sdc_ecc_eddy_correct_inputnode;

  hmc_sdc_ecc_peb_correction_outputnode -> hmc_sdc_ecc_UnwarpArtifacts_inputnode;

  hmc_sdc_ecc_bet_dwi_pre -> hmc_sdc_ecc_motion_correct_inputnode;

  hmc_sdc_ecc_bet_dwi_pre -> hmc_sdc_ecc_peb_correction_inputnode;

  hmc_sdc_ecc_bet_dwi_pre -> hmc_sdc_ecc_eddy_correct_inputnode;

}

ecc_pipeline()

Link to code

ECC stands for Eddy currents correction.

Creates a pipeline that corrects for artifacts induced by Eddy currents in dMRI sequences. It takes a series of diffusion weighted images and linearly co-registers them to one reference image (the average of all b0s in the dataset).

DWIs are also modulated by the determinant of the Jacobian as indicated by [Jones10] and [Rohde04].

A list of rigid transformation matrices can be provided, sourcing from a hmc_pipeline() workflow, to initialize registrations in a motion free framework.

A list of affine transformation matrices is available as output, so that transforms can be chained (discussion here).

Example

>>> from nipype.workflows.dmri.fsl.artifacts import ecc_pipeline
>>> ecc = ecc_pipeline()
>>> ecc.inputs.inputnode.in_file = 'diffusion.nii'
>>> ecc.inputs.inputnode.in_bval = 'diffusion.bval'
>>> ecc.inputs.inputnode.in_mask = 'mask.nii'
>>> ecc.run() 

Inputs:

inputnode.in_file - input dwi file
inputnode.in_mask - weights mask of reference image (a file with data range sin [0.0, 1.0], indicating the weight of each voxel when computing the metric.
inputnode.in_bval - b-values table
inputnode.in_xfms - list of matrices to initialize registration (from head-motion correction)

Outputs:

outputnode.out_file - corrected dwi file
outputnode.out_xfms - list of transformation matrices

Graph

digraph eddy_correct{

  label="eddy_correct";

  eddy_correct_inputnode[label="inputnode (utility)"];

  eddy_correct_b0_avg[label="b0_avg (utility)"];

  eddy_correct_ExtractDWI[label="ExtractDWI (utility)"];

  eddy_correct_GatherMatrices[label="GatherMatrices (utility)"];

  eddy_correct_SplitDWIs[label="SplitDWIs (fsl)"];

  eddy_correct_ModulateDWIs[label="ModulateDWIs (fsl)"];

  eddy_correct_RemoveNegative[label="RemoveNegative (fsl)"];

  eddy_correct_MergeDWIs[label="MergeDWIs (utility)"];

  eddy_correct_outputnode[label="outputnode (utility)"];

  eddy_correct_inputnode -> eddy_correct_ExtractDWI;

  eddy_correct_inputnode -> eddy_correct_ExtractDWI;

  eddy_correct_inputnode -> eddy_correct_GatherMatrices;

  eddy_correct_inputnode -> eddy_correct_MergeDWIs;

  eddy_correct_inputnode -> eddy_correct_MergeDWIs;

  eddy_correct_inputnode -> eddy_correct_b0_avg;

  eddy_correct_inputnode -> eddy_correct_b0_avg;

  subgraph cluster_eddy_correct_DWICoregistration {

      label="DWICoregistration";

    eddy_correct_DWICoregistration_inputnode[label="inputnode (utility)"];

    eddy_correct_DWICoregistration_MskDilate[label="MskDilate (fsl)"];

    eddy_correct_DWICoregistration_SplitDWIs[label="SplitDWIs (fsl)"];

    eddy_correct_DWICoregistration_DWEqualize[label="DWEqualize (utility)"];

    eddy_correct_DWICoregistration_InitXforms[label="InitXforms (utility)"];

    eddy_correct_DWICoregistration_Bias[label="Bias (ants)"];

    eddy_correct_DWICoregistration_B0Equalize[label="B0Equalize (utility)"];

    eddy_correct_DWICoregistration_CoRegistration[label="CoRegistration (fsl)"];

    eddy_correct_DWICoregistration_RemoveNegative[label="RemoveNegative (fsl)"];

    eddy_correct_DWICoregistration_MergeDWIs[label="MergeDWIs (fsl)"];

    eddy_correct_DWICoregistration_outputnode[label="outputnode (utility)"];

    eddy_correct_DWICoregistration_inputnode -> eddy_correct_DWICoregistration_Bias;

    eddy_correct_DWICoregistration_inputnode -> eddy_correct_DWICoregistration_Bias;

    eddy_correct_DWICoregistration_inputnode -> eddy_correct_DWICoregistration_InitXforms;

    eddy_correct_DWICoregistration_inputnode -> eddy_correct_DWICoregistration_InitXforms;

    eddy_correct_DWICoregistration_inputnode -> eddy_correct_DWICoregistration_SplitDWIs;

    eddy_correct_DWICoregistration_inputnode -> eddy_correct_DWICoregistration_B0Equalize;

    eddy_correct_DWICoregistration_inputnode -> eddy_correct_DWICoregistration_MskDilate;

    eddy_correct_DWICoregistration_MskDilate -> eddy_correct_DWICoregistration_CoRegistration;

    eddy_correct_DWICoregistration_MskDilate -> eddy_correct_DWICoregistration_CoRegistration;

    eddy_correct_DWICoregistration_MskDilate -> eddy_correct_DWICoregistration_DWEqualize;

    eddy_correct_DWICoregistration_SplitDWIs -> eddy_correct_DWICoregistration_DWEqualize;

    eddy_correct_DWICoregistration_DWEqualize -> eddy_correct_DWICoregistration_CoRegistration;

    eddy_correct_DWICoregistration_InitXforms -> eddy_correct_DWICoregistration_CoRegistration;

    eddy_correct_DWICoregistration_Bias -> eddy_correct_DWICoregistration_B0Equalize;

    eddy_correct_DWICoregistration_B0Equalize -> eddy_correct_DWICoregistration_CoRegistration;

    eddy_correct_DWICoregistration_CoRegistration -> eddy_correct_DWICoregistration_outputnode;

    eddy_correct_DWICoregistration_CoRegistration -> eddy_correct_DWICoregistration_RemoveNegative;

    eddy_correct_DWICoregistration_RemoveNegative -> eddy_correct_DWICoregistration_MergeDWIs;

    eddy_correct_DWICoregistration_MergeDWIs -> eddy_correct_DWICoregistration_outputnode;

  }

  eddy_correct_GatherMatrices -> eddy_correct_outputnode;

  eddy_correct_SplitDWIs -> eddy_correct_ModulateDWIs;

  eddy_correct_ModulateDWIs -> eddy_correct_RemoveNegative;

  eddy_correct_RemoveNegative -> eddy_correct_MergeDWIs;

  eddy_correct_MergeDWIs -> eddy_correct_outputnode;

  eddy_correct_ExtractDWI -> eddy_correct_DWICoregistration_inputnode;

  eddy_correct_b0_avg -> eddy_correct_DWICoregistration_inputnode;

  eddy_correct_DWICoregistration_outputnode -> eddy_correct_ModulateDWIs;

  eddy_correct_DWICoregistration_outputnode -> eddy_correct_SplitDWIs;

  eddy_correct_DWICoregistration_outputnode -> eddy_correct_GatherMatrices;

  eddy_correct_inputnode -> eddy_correct_DWICoregistration_inputnode;

  eddy_correct_inputnode -> eddy_correct_DWICoregistration_inputnode;

  eddy_correct_inputnode -> eddy_correct_DWICoregistration_inputnode;

}

hmc_pipeline()

Link to code

HMC stands for head-motion correction.

Creates a pipeline that corrects for head motion artifacts in dMRI sequences. It takes a series of diffusion weighted images and rigidly co-registers them to one reference image. Finally, the b-matrix is rotated accordingly [Leemans09] making use of the rotation matrix obtained by FLIRT.

Search angles have been limited to 4 degrees, based on results in [Yendiki13].

A list of rigid transformation matrices is provided, so that transforms can be chained. This is useful to correct for artifacts with only one interpolation process (as previously discussed here), and also to compute nuisance regressors as proposed by [Yendiki13].

Warning

This workflow rotates the b-vectors, so please be advised that not all the dicom converters ensure the consistency between the resulting nifti orientation and the gradients table (e.g. dcm2nii checks it).

References

[Leemans09](1, 2, 3, 4) Leemans A, and Jones DK, The B-matrix must be rotated when correcting for subject motion in DTI data, Magn Reson Med. 61(6):1336-49. 2009. doi: 10.1002/mrm.21890.
[Yendiki13](1, 2) Yendiki A et al., Spurious group differences due to head motion in a diffusion MRI study. Neuroimage. 21(88C):79-90. 2013. doi: 10.1016/j.neuroimage.2013.11.027

Example

>>> from nipype.workflows.dmri.fsl.artifacts import hmc_pipeline
>>> hmc = hmc_pipeline()
>>> hmc.inputs.inputnode.in_file = 'diffusion.nii'
>>> hmc.inputs.inputnode.in_bvec = 'diffusion.bvec'
>>> hmc.inputs.inputnode.in_bval = 'diffusion.bval'
>>> hmc.inputs.inputnode.in_mask = 'mask.nii'
>>> hmc.run() 

Inputs:

inputnode.in_file - input dwi file
inputnode.in_mask - weights mask of reference image (a file with data range in [0.0, 1.0], indicating the weight of each voxel when computing the metric.
inputnode.in_bval - b-values file
inputnode.in_bvec - gradients file (b-vectors)
inputnode.ref_num (optional, default=0) index of the b0 volume that should be taken as reference

Outputs:

outputnode.out_file - corrected dwi file
outputnode.out_bvec - rotated gradient vectors table
outputnode.out_xfms - list of transformation matrices

Graph

digraph motion_correct{

  label="motion_correct";

  motion_correct_inputnode[label="inputnode (utility)"];

  motion_correct_SplitDWI[label="SplitDWI (utility)"];

  motion_correct_InsertRefmat[label="InsertRefmat (utility)"];

  motion_correct_Rotate_Bvec[label="Rotate_Bvec (utility)"];

  motion_correct_outputnode[label="outputnode (utility)"];

  motion_correct_inputnode -> motion_correct_Rotate_Bvec;

  motion_correct_inputnode -> motion_correct_SplitDWI;

  motion_correct_inputnode -> motion_correct_SplitDWI;

  motion_correct_inputnode -> motion_correct_SplitDWI;

  motion_correct_SplitDWI -> motion_correct_InsertRefmat;

  subgraph cluster_motion_correct_DWICoregistration {

      label="DWICoregistration";

    motion_correct_DWICoregistration_inputnode[label="inputnode (utility)"];

    motion_correct_DWICoregistration_MskDilate[label="MskDilate (fsl)"];

    motion_correct_DWICoregistration_SplitDWIs[label="SplitDWIs (fsl)"];

    motion_correct_DWICoregistration_DWEqualize[label="DWEqualize (utility)"];

    motion_correct_DWICoregistration_Bias[label="Bias (ants)"];

    motion_correct_DWICoregistration_B0Equalize[label="B0Equalize (utility)"];

    motion_correct_DWICoregistration_InitXforms[label="InitXforms (utility)"];

    motion_correct_DWICoregistration_CoRegistration[label="CoRegistration (fsl)"];

    motion_correct_DWICoregistration_RemoveNegative[label="RemoveNegative (fsl)"];

    motion_correct_DWICoregistration_MergeDWIs[label="MergeDWIs (fsl)"];

    motion_correct_DWICoregistration_outputnode[label="outputnode (utility)"];

    motion_correct_DWICoregistration_inputnode -> motion_correct_DWICoregistration_InitXforms;

    motion_correct_DWICoregistration_inputnode -> motion_correct_DWICoregistration_InitXforms;

    motion_correct_DWICoregistration_inputnode -> motion_correct_DWICoregistration_Bias;

    motion_correct_DWICoregistration_inputnode -> motion_correct_DWICoregistration_Bias;

    motion_correct_DWICoregistration_inputnode -> motion_correct_DWICoregistration_SplitDWIs;

    motion_correct_DWICoregistration_inputnode -> motion_correct_DWICoregistration_B0Equalize;

    motion_correct_DWICoregistration_inputnode -> motion_correct_DWICoregistration_MskDilate;

    motion_correct_DWICoregistration_MskDilate -> motion_correct_DWICoregistration_DWEqualize;

    motion_correct_DWICoregistration_MskDilate -> motion_correct_DWICoregistration_CoRegistration;

    motion_correct_DWICoregistration_MskDilate -> motion_correct_DWICoregistration_CoRegistration;

    motion_correct_DWICoregistration_SplitDWIs -> motion_correct_DWICoregistration_DWEqualize;

    motion_correct_DWICoregistration_DWEqualize -> motion_correct_DWICoregistration_CoRegistration;

    motion_correct_DWICoregistration_Bias -> motion_correct_DWICoregistration_B0Equalize;

    motion_correct_DWICoregistration_B0Equalize -> motion_correct_DWICoregistration_CoRegistration;

    motion_correct_DWICoregistration_InitXforms -> motion_correct_DWICoregistration_CoRegistration;

    motion_correct_DWICoregistration_CoRegistration -> motion_correct_DWICoregistration_outputnode;

    motion_correct_DWICoregistration_CoRegistration -> motion_correct_DWICoregistration_RemoveNegative;

    motion_correct_DWICoregistration_RemoveNegative -> motion_correct_DWICoregistration_MergeDWIs;

    motion_correct_DWICoregistration_MergeDWIs -> motion_correct_DWICoregistration_outputnode;

  }

  motion_correct_InsertRefmat -> motion_correct_Rotate_Bvec;

  motion_correct_InsertRefmat -> motion_correct_outputnode;

  motion_correct_Rotate_Bvec -> motion_correct_outputnode;

  motion_correct_SplitDWI -> motion_correct_DWICoregistration_inputnode;

  motion_correct_SplitDWI -> motion_correct_DWICoregistration_inputnode;

  motion_correct_SplitDWI -> motion_correct_DWICoregistration_inputnode;

  motion_correct_DWICoregistration_outputnode -> motion_correct_InsertRefmat;

  motion_correct_DWICoregistration_outputnode -> motion_correct_outputnode;

  motion_correct_inputnode -> motion_correct_DWICoregistration_inputnode;

}

remove_bias()

Link to code

This workflow estimates a single multiplicative bias field from the averaged b0 image, as suggested in [Jeurissen2014].

References

[Jeurissen2014]Jeurissen B. et al., Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. NeuroImage (2014). doi: 10.1016/j.neuroimage.2014.07.061

Example

>>> from nipype.workflows.dmri.fsl.artifacts import remove_bias
>>> bias = remove_bias()
>>> bias.inputs.inputnode.in_file = 'epi.nii'
>>> bias.inputs.inputnode.in_bval = 'diffusion.bval'
>>> bias.inputs.inputnode.in_mask = 'mask.nii'
>>> bias.run() 

Graph

digraph bias_correct{

  label="bias_correct";

  bias_correct_inputnode[label="inputnode (utility)"];

  bias_correct_SplitDWIs[label="SplitDWIs (fsl)"];

  bias_correct_b0_avg[label="b0_avg (utility)"];

  bias_correct_Bias_b0[label="Bias_b0 (ants)"];

  bias_correct_RemoveBiasOfDWIs[label="RemoveBiasOfDWIs (fsl)"];

  bias_correct_RemoveNegative[label="RemoveNegative (fsl)"];

  bias_correct_MergeDWIs[label="MergeDWIs (fsl)"];

  bias_correct_outputnode[label="outputnode (utility)"];

  bias_correct_inputnode -> bias_correct_b0_avg;

  bias_correct_inputnode -> bias_correct_b0_avg;

  bias_correct_inputnode -> bias_correct_Bias_b0;

  bias_correct_inputnode -> bias_correct_SplitDWIs;

  bias_correct_SplitDWIs -> bias_correct_RemoveBiasOfDWIs;

  bias_correct_b0_avg -> bias_correct_Bias_b0;

  bias_correct_Bias_b0 -> bias_correct_RemoveBiasOfDWIs;

  bias_correct_RemoveBiasOfDWIs -> bias_correct_RemoveNegative;

  bias_correct_RemoveNegative -> bias_correct_MergeDWIs;

  bias_correct_MergeDWIs -> bias_correct_outputnode;

}

sdc_fmb()

Link to code

SDC stands for susceptibility distortion correction. FMB stands for fieldmap-based.

The fieldmap based (FMB) method implements SDC by using a mapping of the B0 field as proposed by [Jezzard95]. This workflow uses the implementation of FSL (FUGUE). Phase unwrapping is performed using PRELUDE [Jenkinson03]. Preparation of the fieldmap is performed reproducing the script in FSL fsl_prepare_fieldmap.

Example

>>> from nipype.workflows.dmri.fsl.artifacts import sdc_fmb
>>> fmb = sdc_fmb()
>>> fmb.inputs.inputnode.in_file = 'diffusion.nii'
>>> fmb.inputs.inputnode.in_ref = list(range(0, 30, 6))
>>> fmb.inputs.inputnode.in_mask = 'mask.nii'
>>> fmb.inputs.inputnode.bmap_mag = 'magnitude.nii'
>>> fmb.inputs.inputnode.bmap_pha = 'phase.nii'
>>> fmb.inputs.inputnode.settings = 'epi_param.txt'
>>> fmb.run() 

Warning

Only SIEMENS format fieldmaps are supported.

References

[Jezzard95]Jezzard P, and Balaban RS, Correction for geometric distortion in echo planar images from B0 field variations, MRM 34(1):65-73. (1995). doi: 10.1002/mrm.1910340111.
[Jenkinson03]Jenkinson M., Fast, automated, N-dimensional phase-unwrapping algorithm, MRM 49(1):193-197, 2003, doi: 10.1002/mrm.10354.

Graph

digraph fmb_correction{

  label="fmb_correction";

  fmb_correction_inputnode[label="inputnode (utility)"];

  fmb_correction_SettingsGrabber[label="SettingsGrabber (io)"];

  fmb_correction_EffEcho[label="EffEcho (utility)"];

  fmb_correction_PreparePhase[label="PreparePhase (utility)"];

  fmb_correction_Baseline[label="Baseline (utility)"];

  fmb_correction_GetFirst[label="GetFirst (fsl)"];

  fmb_correction_Bias[label="Bias (ants)"];

  fmb_correction_BrainExtraction[label="BrainExtraction (fsl)"];

  fmb_correction_MskDilate[label="MskDilate (fsl)"];

  fmb_correction_FMm_to_B0[label="FMm_to_B0 (ants)"];

  fmb_correction_PhaseUnwrap[label="PhaseUnwrap (fsl)"];

  fmb_correction_ToRadSec[label="ToRadSec (utility)"];

  fmb_correction_FMp_to_B0[label="FMp_to_B0 (ants)"];

  fmb_correction_PreliminaryFugue[label="PreliminaryFugue (fsl)"];

  fmb_correction_DemeanFmap[label="DemeanFmap (utility)"];

  fmb_correction_AddEmptyVol[label="AddEmptyVol (utility)"];

  fmb_correction_ComputeVSM[label="ComputeVSM (fsl)"];

  fmb_correction_SplitDWIs[label="SplitDWIs (fsl)"];

  fmb_correction_UnwarpDWIs[label="UnwarpDWIs (fsl)"];

  fmb_correction_RemoveNegative[label="RemoveNegative (fsl)"];

  fmb_correction_MergeDWIs[label="MergeDWIs (fsl)"];

  fmb_correction_outputnode[label="outputnode (utility)"];

  fmb_correction_inputnode -> fmb_correction_SplitDWIs;

  fmb_correction_inputnode -> fmb_correction_GetFirst;

  fmb_correction_inputnode -> fmb_correction_PreliminaryFugue;

  fmb_correction_inputnode -> fmb_correction_Baseline;

  fmb_correction_inputnode -> fmb_correction_Baseline;

  fmb_correction_inputnode -> fmb_correction_ComputeVSM;

  fmb_correction_inputnode -> fmb_correction_DemeanFmap;

  fmb_correction_inputnode -> fmb_correction_PreparePhase;

  fmb_correction_inputnode -> fmb_correction_SettingsGrabber;

  fmb_correction_inputnode -> fmb_correction_FMm_to_B0;

  fmb_correction_SettingsGrabber -> fmb_correction_ToRadSec;

  fmb_correction_SettingsGrabber -> fmb_correction_ComputeVSM;

  fmb_correction_SettingsGrabber -> fmb_correction_EffEcho;

  fmb_correction_SettingsGrabber -> fmb_correction_EffEcho;

  fmb_correction_SettingsGrabber -> fmb_correction_UnwarpDWIs;

  fmb_correction_EffEcho -> fmb_correction_ComputeVSM;

  fmb_correction_PreparePhase -> fmb_correction_PhaseUnwrap;

  fmb_correction_Baseline -> fmb_correction_FMm_to_B0;

  fmb_correction_Baseline -> fmb_correction_FMp_to_B0;

  fmb_correction_GetFirst -> fmb_correction_Bias;

  fmb_correction_Bias -> fmb_correction_BrainExtraction;

  fmb_correction_Bias -> fmb_correction_PhaseUnwrap;

  fmb_correction_Bias -> fmb_correction_FMm_to_B0;

  fmb_correction_BrainExtraction -> fmb_correction_MskDilate;

  fmb_correction_MskDilate -> fmb_correction_PhaseUnwrap;

  fmb_correction_MskDilate -> fmb_correction_FMm_to_B0;

  fmb_correction_FMm_to_B0 -> fmb_correction_FMp_to_B0;

  fmb_correction_FMm_to_B0 -> fmb_correction_FMp_to_B0;

  fmb_correction_PhaseUnwrap -> fmb_correction_ToRadSec;

  fmb_correction_ToRadSec -> fmb_correction_FMp_to_B0;

  fmb_correction_FMp_to_B0 -> fmb_correction_PreliminaryFugue;

  fmb_correction_PreliminaryFugue -> fmb_correction_DemeanFmap;

  subgraph cluster_fmb_correction_Cleanup {

      label="Cleanup";

    fmb_correction_Cleanup_inputnode[label="inputnode (utility)"];

    fmb_correction_Cleanup_MskErode[label="MskErode (fsl)"];

    fmb_correction_Cleanup_NewMask[label="NewMask (fsl)"];

    fmb_correction_Cleanup_Despike[label="Despike (fsl)"];

    fmb_correction_Cleanup_ApplyMask[label="ApplyMask (fsl)"];

    fmb_correction_Cleanup_Merge[label="Merge (utility)"];

    fmb_correction_Cleanup_AddEdge[label="AddEdge (fsl)"];

    fmb_correction_Cleanup_outputnode[label="outputnode (utility)"];

    fmb_correction_Cleanup_inputnode -> fmb_correction_Cleanup_Despike;

    fmb_correction_Cleanup_inputnode -> fmb_correction_Cleanup_Despike;

    fmb_correction_Cleanup_inputnode -> fmb_correction_Cleanup_AddEdge;

    fmb_correction_Cleanup_inputnode -> fmb_correction_Cleanup_NewMask;

    fmb_correction_Cleanup_inputnode -> fmb_correction_Cleanup_MskErode;

    fmb_correction_Cleanup_MskErode -> fmb_correction_Cleanup_Merge;

    fmb_correction_Cleanup_MskErode -> fmb_correction_Cleanup_NewMask;

    fmb_correction_Cleanup_NewMask -> fmb_correction_Cleanup_ApplyMask;

    fmb_correction_Cleanup_Despike -> fmb_correction_Cleanup_ApplyMask;

    fmb_correction_Cleanup_ApplyMask -> fmb_correction_Cleanup_Merge;

    fmb_correction_Cleanup_Merge -> fmb_correction_Cleanup_AddEdge;

    fmb_correction_Cleanup_AddEdge -> fmb_correction_Cleanup_outputnode;

  }

  fmb_correction_AddEmptyVol -> fmb_correction_ComputeVSM;

  fmb_correction_ComputeVSM -> fmb_correction_outputnode;

  fmb_correction_ComputeVSM -> fmb_correction_UnwarpDWIs;

  fmb_correction_SplitDWIs -> fmb_correction_UnwarpDWIs;

  fmb_correction_UnwarpDWIs -> fmb_correction_RemoveNegative;

  fmb_correction_RemoveNegative -> fmb_correction_MergeDWIs;

  fmb_correction_MergeDWIs -> fmb_correction_outputnode;

  subgraph cluster_fmb_correction_Shiftmap2Warping {

      label="Shiftmap2Warping";

    fmb_correction_Shiftmap2Warping_inputnode[label="inputnode (utility)"];

    fmb_correction_Shiftmap2Warping_Fix_hdr[label="Fix_hdr (utility)"];

    fmb_correction_Shiftmap2Warping_ScaleField[label="ScaleField (fsl)"];

    fmb_correction_Shiftmap2Warping_vsm2dfm[label="vsm2dfm (fsl)"];

    fmb_correction_Shiftmap2Warping_outputnode[label="outputnode (utility)"];

    fmb_correction_Shiftmap2Warping_inputnode -> fmb_correction_Shiftmap2Warping_vsm2dfm;

    fmb_correction_Shiftmap2Warping_inputnode -> fmb_correction_Shiftmap2Warping_vsm2dfm;

    fmb_correction_Shiftmap2Warping_inputnode -> fmb_correction_Shiftmap2Warping_Fix_hdr;

    fmb_correction_Shiftmap2Warping_inputnode -> fmb_correction_Shiftmap2Warping_Fix_hdr;

    fmb_correction_Shiftmap2Warping_inputnode -> fmb_correction_Shiftmap2Warping_ScaleField;

    fmb_correction_Shiftmap2Warping_Fix_hdr -> fmb_correction_Shiftmap2Warping_ScaleField;

    fmb_correction_Shiftmap2Warping_ScaleField -> fmb_correction_Shiftmap2Warping_vsm2dfm;

    fmb_correction_Shiftmap2Warping_vsm2dfm -> fmb_correction_Shiftmap2Warping_outputnode;

  }

  fmb_correction_SettingsGrabber -> fmb_correction_Shiftmap2Warping_inputnode;

  fmb_correction_MergeDWIs -> fmb_correction_Shiftmap2Warping_inputnode;

  fmb_correction_ComputeVSM -> fmb_correction_Shiftmap2Warping_inputnode;

  fmb_correction_inputnode -> fmb_correction_Cleanup_inputnode;

  fmb_correction_Shiftmap2Warping_outputnode -> fmb_correction_outputnode;

  fmb_correction_DemeanFmap -> fmb_correction_Cleanup_inputnode;

  fmb_correction_Cleanup_outputnode -> fmb_correction_AddEmptyVol;

}

sdc_peb()

Link to code

SDC stands for susceptibility distortion correction. PEB stands for phase-encoding-based.

The phase-encoding-based (PEB) method implements SDC by acquiring diffusion images with two different enconding directions [Andersson2003]. The most typical case is acquiring with opposed phase-gradient blips (e.g. A>>>P and P>>>A, or equivalently, -y and y) as in [Chiou2000], but it is also possible to use orthogonal configurations [Cordes2000] (e.g. A>>>P and L>>>R, or equivalently -y and x). This workflow uses the implementation of FSL (TOPUP).

Example

>>> from nipype.workflows.dmri.fsl.artifacts import sdc_peb
>>> peb = sdc_peb()
>>> peb.inputs.inputnode.in_file = 'epi.nii'
>>> peb.inputs.inputnode.alt_file = 'epi_rev.nii'
>>> peb.inputs.inputnode.in_bval = 'diffusion.bval'
>>> peb.inputs.inputnode.in_mask = 'mask.nii'
>>> peb.run() 

References

[Andersson2003]Andersson JL et al., How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging. Neuroimage. 2003 Oct;20(2):870-88. doi: 10.1016/S1053-8119(03)00336-7
[Cordes2000]Cordes D et al., Geometric distortion correction in EPI using two images with orthogonal phase-encoding directions, in Proc. ISMRM (8), p.1712, Denver, US, 2000.
[Chiou2000]Chiou JY, and Nalcioglu O, A simple method to correct off-resonance related distortion in echo planar imaging, in Proc. ISMRM (8), p.1712, Denver, US, 2000.

Graph

digraph peb_correction{

  label="peb_correction";

  peb_correction_inputnode[label="inputnode (utility)"];

  peb_correction_b0_alt[label="b0_alt (fsl)"];

  peb_correction_b0_ref[label="b0_ref (fsl)"];

  peb_correction_b0_list[label="b0_list (utility)"];

  peb_correction_b0_merged[label="b0_merged (fsl)"];

  peb_correction_topup[label="topup (fsl)"];

  peb_correction_unwarp[label="unwarp (fsl)"];

  peb_correction_outputnode[label="outputnode (utility)"];

  peb_correction_inputnode -> peb_correction_b0_ref;

  peb_correction_inputnode -> peb_correction_b0_ref;

  peb_correction_inputnode -> peb_correction_unwarp;

  peb_correction_inputnode -> peb_correction_b0_alt;

  peb_correction_inputnode -> peb_correction_b0_alt;

  peb_correction_b0_alt -> peb_correction_b0_list;

  peb_correction_b0_ref -> peb_correction_b0_list;

  peb_correction_b0_list -> peb_correction_b0_merged;

  peb_correction_b0_merged -> peb_correction_topup;

  peb_correction_topup -> peb_correction_unwarp;

  peb_correction_topup -> peb_correction_unwarp;

  peb_correction_topup -> peb_correction_unwarp;

  peb_correction_topup -> peb_correction_outputnode;

  peb_correction_unwarp -> peb_correction_outputnode;

  subgraph cluster_peb_correction_Shiftmap2Warping {

      label="Shiftmap2Warping";

    peb_correction_Shiftmap2Warping_inputnode[label="inputnode (utility)"];

    peb_correction_Shiftmap2Warping_Fix_hdr[label="Fix_hdr (utility)"];

    peb_correction_Shiftmap2Warping_ScaleField[label="ScaleField (fsl)"];

    peb_correction_Shiftmap2Warping_vsm2dfm[label="vsm2dfm (fsl)"];

    peb_correction_Shiftmap2Warping_outputnode[label="outputnode (utility)"];

    peb_correction_Shiftmap2Warping_inputnode -> peb_correction_Shiftmap2Warping_ScaleField;

    peb_correction_Shiftmap2Warping_inputnode -> peb_correction_Shiftmap2Warping_Fix_hdr;

    peb_correction_Shiftmap2Warping_inputnode -> peb_correction_Shiftmap2Warping_Fix_hdr;

    peb_correction_Shiftmap2Warping_inputnode -> peb_correction_Shiftmap2Warping_vsm2dfm;

    peb_correction_Shiftmap2Warping_inputnode -> peb_correction_Shiftmap2Warping_vsm2dfm;

    peb_correction_Shiftmap2Warping_Fix_hdr -> peb_correction_Shiftmap2Warping_ScaleField;

    peb_correction_Shiftmap2Warping_ScaleField -> peb_correction_Shiftmap2Warping_vsm2dfm;

    peb_correction_Shiftmap2Warping_vsm2dfm -> peb_correction_Shiftmap2Warping_outputnode;

  }

  peb_correction_b0_ref -> peb_correction_Shiftmap2Warping_inputnode;

  peb_correction_topup -> peb_correction_Shiftmap2Warping_inputnode;

  peb_correction_Shiftmap2Warping_outputnode -> peb_correction_outputnode;

}