Source code for fmriprep.workflows.bold.hmc

# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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Head-Motion Estimation and Correction (HMC) of BOLD images

.. autofunction:: init_bold_hmc_wf


from niworkflows.nipype.pipeline import engine as pe
from niworkflows.nipype.interfaces import utility as niu, fsl
from niworkflows.interfaces import NormalizeMotionParams
from ...interfaces import MCFLIRT2ITK


# pylint: disable=R0914
[docs]def init_bold_hmc_wf(mem_gb, omp_nthreads, name='bold_hmc_wf'): """ This workflow estimates the motion parameters to perform :abbr:`HMC (head motion correction)` over the input :abbr:`BOLD (blood-oxygen-level dependent)` image. .. workflow:: :graph2use: orig :simple_form: yes from fmriprep.workflows.bold import init_bold_hmc_wf wf = init_bold_hmc_wf( mem_gb=3, omp_nthreads=1) **Parameters** mem_gb : float Size of BOLD file in GB omp_nthreads : int Maximum number of threads an individual process may use name : str Name of workflow (default: ``bold_hmc_wf``) **Inputs** bold_file BOLD series NIfTI file raw_ref_image Reference image to which BOLD series is motion corrected **Outputs** xforms ITKTransform file aligning each volume to ``ref_image`` movpar_file MCFLIRT motion parameters, normalized to SPM format (X, Y, Z, Rx, Ry, Rz) """ workflow = pe.Workflow(name=name) inputnode = pe.Node(niu.IdentityInterface(fields=['bold_file', 'raw_ref_image']), name='inputnode') outputnode = pe.Node( niu.IdentityInterface(fields=['xforms', 'movpar_file']), name='outputnode') # Head motion correction (hmc) mcflirt = pe.Node(fsl.MCFLIRT(save_mats=True, save_plots=True), name='mcflirt', mem_gb=mem_gb * 3) fsl2itk = pe.Node(MCFLIRT2ITK(), name='fsl2itk', mem_gb=0.05, n_procs=omp_nthreads) normalize_motion = pe.Node(NormalizeMotionParams(format='FSL'), name="normalize_motion", mem_gb=DEFAULT_MEMORY_MIN_GB) workflow.connect([ (inputnode, mcflirt, [('raw_ref_image', 'ref_file'), ('bold_file', 'in_file')]), (inputnode, fsl2itk, [('raw_ref_image', 'in_source'), ('raw_ref_image', 'in_reference')]), (mcflirt, fsl2itk, [('mat_file', 'in_files')]), (mcflirt, normalize_motion, [('par_file', 'in_file')]), (fsl2itk, outputnode, [('out_file', 'xforms')]), (normalize_motion, outputnode, [('out_file', 'movpar_file')]), ]) return workflow