e0c9d018aca7bf05486c385484d5ed1c37bac423,pynets/diffconnectometry.py,,coreg_mask_to_diff,#Any#Any#,177

Before Change

    args = "-bin"
    maths = fsl.ImageMaths(in_file=out_file, op_string=args, out_file=out_file)
    print("\nBinarizing custom mask...")
    os.system(maths.cmdline)
    return out_file


def build_coord_list(coords, dwi_dir):

After Change

        dwi_infile = "%s%s" % (dwi_dir, "/dwi.nii.gz")

    out_file = "%s%s" % (dwi_dir, "/mask_custom_diff.nii.gz")
    mask_transforms_wf = pe.Workflow(name="wm_transforms")
    inputnode = pe.Node(niu.IdentityInterface(fields=["dwi_infile", "mask", "out_file", "mat_file", "dwi_dir"]),
                        name="inputnode")
    inputnode.inputs.dwi_infile = dwi_infile
    inputnode.inputs.mask = mask
    inputnode.inputs.out_file = out_file
    inputnode.inputs.mat_file = "%s%s" % (dwi_dir, "/xfms/MNI2diff.mat")
    inputnode.inputs.dwi_dir = dwi_dir

    flirt = pe.Node(interface=fsl.FLIRT(cost_func="mutualinfo"), name="coregister_wm")
    flirt.inputs.apply_xfm = True
    flirt.inputs.out_matrix_file = "/tmp/out_flirt.mat"

    def bin_mask(out_file):
        import nipype.interfaces.fsl as fsl
        import os
        args = "-bin"
        maths = fsl.ImageMaths(in_file=out_file, op_string=args, out_file=out_file)
        print("\nBinarizing custom mask...")
        os.system(maths.cmdline)
        return out_file

    bin_mask = pe.Node(niu.Function(input_names=["out_file"], output_names=["out_file"],
                                  function=bin_mask), name="bin_mask_node")

    mask_transforms_wf.connect([(inputnode, flirt, [("dwi_infile", "reference"), ("mask", "in_file"),
                                                    ("out_file", "out_file"), ("mat_file", "in_matrix_file")]),
                                (flirt, bin_mask, [("out_file", "out_file")])
                                ])
    return mask_transforms_wf


def build_coord_list(coords, dwi_dir):
    from nilearn import masking

Instances