e0c9d018aca7bf05486c385484d5ed1c37bac423,pynets/diffconnectometry.py,,create_mni2diff_transforms,#Any#,13

Before Change

    flirt.inputs.in_file = input_MNI
    flirt.inputs.out_matrix_file = "%s%s" % (dwi_dir, "/xfms/MNI2diff.mat")
    flirt.inputs.out_file = "/tmp/out_flirt.nii.gz"
    flirt.run()

    // Apply transform between diff and MNI using FLIRT
    flirt = pe.Node(interface=fsl.FLIRT(cost_func="mutualinfo"), name="coregister")
    flirt.inputs.reference = dwi_infile

After Change

    input_MNI = "%s%s" % (FSLDIR, "/data/standard/MNI152_T1_1mm_brain.nii.gz")
    out_aff = "%s%s" % (dwi_dir, "/xfms/MNI2diff_affine.nii.gz")

    diff_transforms_wf = pe.Workflow(name="diff_transforms")
    inputnode = pe.Node(niu.IdentityInterface(fields=["dwi_infile", "input_MNI",
                                                      "out_aff", "mat_file"]),
                        name="inputnode")
    inputnode.inputs.dwi_infile = dwi_infile
    inputnode.inputs.input_MNI = input_MNI
    inputnode.inputs.out_aff = out_aff
    inputnode.inputs.mat_file = "%s%s" % (dwi_dir, "/xfms/MNI2diff.mat")

    flirt = pe.Node(interface=fsl.FLIRT(cost_func="mutualinfo"), name="coregister")
    flirt.inputs.out_file = "/tmp/out_flirt.nii.gz"
    flirt_apply = pe.Node(interface=fsl.FLIRT(cost_func="mutualinfo"), name="coregister_apply")
    flirt_apply.inputs.out_matrix_file = "/tmp/out_flirt.mat"
    flirt_apply.inputs.apply_xfm = True

    diff_transforms_wf.connect([
        (inputnode, flirt, [("dwi_infile", "reference"),
                            ("input_MNI", "in_file"),
                            ("mat_file", "out_matrix_file")]),
        (inputnode, flirt_apply, [("dwi_infile", "reference"), ("input_MNI", "in_file"),
                                  ("mat_file", "in_matrix_file"), ("out_aff", "out_file")])
    ])

    return diff_transforms_wf

Instances