Exemple #1
0
def surf_convert(fsdir, t1files, surffiles, output_directory=None,
                 rm_orig=False,
                 fsconfig="/i2bm/local/freesurfer/SetUpFreeSurfer.sh"):
    """ Export FreeSurfer surfaces to the native space.

    Note that all the vetices are given in the index coordinate system.
    The subjecy id in the t1 and surf files must appear in the -3 position:
        xxx/subject_id/convert/t1.nii.gz

    <unit>
        <input name="fsdir" type="Directory" description="The
            freesurfer working directory with all the subjects."/>
        <input name="output_directory" type="Directory" description="The
            conversion destination folder."/>
        <input name="t1files" type="List_File" description="The t1 nifti
            files."/>
        <input name="surffiles" type="List_File" description="The surface
            to be converted."/>
        <input name="rm_orig" type="Bool" description="If true remove
            the input surfaces."/>
        <input name="fsconfig" type="File" description="The freesurfer
            configuration batch."/>
        <output name="csurffiles" type="List_File" description="The converted
            surfaces in the native space."/>
    </unit>
    """
    # Create a t1 subject map
    t1map = {}
    for fname in t1files:
        subject_id = fname.split("/")[-3]
        if subject_id in t1map:
            raise ("Can't map two t1 for subject '{0}'.".format(subject_id))
        t1map[subject_id] = fname

    # Convert all the surfaces
    csurffiles = []
    for fname in surffiles:

        # Get the t1 reference image
        subject_id = fname.split("/")[-3]
        t1file = t1map[subject_id]
        t1_image = nibabel.load(t1file)

        # Compute the conformed space to the native anatomical deformation
        asegfile = os.path.join(fsdir, subject_id, "mri", "aseg.mgz")
        physical_to_index = numpy.linalg.inv(t1_image.get_affine())
        translation = tkregister_translation(asegfile, fsconfig)
        deformation = numpy.dot(physical_to_index, translation)

        # Load and warp the mesh
        # The mesh: a 2-uplet with vertex (x, y, z) coordinates and
        # mesh triangles
        mesh = freesurfer.read_geometry(fname)
        surf = TriSurface(vertices=apply_affine_on_mesh(mesh[0], deformation),
                          triangles=mesh[1])

        # Save the mesh in the native space
        outputfile = fname + ".native"
        surf.save(os.path.dirname(outputfile), os.path.basename(outputfile))
        csurffiles.append(outputfile)

        # Clean input surface if specified
        if rm_orig:
            os.remove(fname)

    return csurffiles
Exemple #2
0
    flirt(nodif_file,
          t1_file,
          omat=trf_file,
          out=reg_file,
          usesqform=False,
          cost="normmi",
          dof=6)
"""
Launch the tractography on the requested point of the cortical surface on the
selected hemisphere
"""
# Load the white mesh in the diffusion space
surface = TriSurface.load(whitefile)
voxel_diff_to_t1 = flirt2aff(trf_file, nodif_file, t1_file)
voxel_t1_to_diff = numpy.linalg.inv(voxel_diff_to_t1)
white_diff_vertices = apply_affine_on_mesh(surface.vertices, voxel_t1_to_diff)

# Select the vertices of interest
if vertices_indices is None:
    vertices_indices = range(len(surface.vertices))

# Go through all the hemisphere vertices
textures = {}
for index in vertices_indices:

    # Select the seeding vertex
    point = white_diff_vertices[index]

    # Create a directory for each seeding vertex in order to avoid collision
    # Raise an exception if the directory has already been created
    vertexdir = os.path.join(connectdir, "{0}_{1}".format(hemi, index))
Exemple #3
0
def surf_convert(fsdir,
                 t1files,
                 surffiles,
                 output_directory=None,
                 rm_orig=False,
                 fsconfig="/i2bm/local/freesurfer/SetUpFreeSurfer.sh"):
    """ Export FreeSurfer surfaces to the native space.

    Note that all the vetices are given in the index coordinate system.
    The subjecy id in the t1 and surf files must appear in the -3 position:
        xxx/subject_id/convert/t1.nii.gz

    <unit>
        <input name="fsdir" type="Directory" description="The
            freesurfer working directory with all the subjects."/>
        <input name="output_directory" type="Directory" description="The
            conversion destination folder."/>
        <input name="t1files" type="List_File" description="The t1 nifti
            files."/>
        <input name="surffiles" type="List_File" description="The surface
            to be converted."/>
        <input name="rm_orig" type="Bool" description="If true remove
            the input surfaces."/>
        <input name="fsconfig" type="File" description="The freesurfer
            configuration batch."/>
        <output name="csurffiles" type="List_File" description="The converted
            surfaces in the native space."/>
    </unit>
    """
    # Create a t1 subject map
    t1map = {}
    for fname in t1files:
        subject_id = fname.split("/")[-3]
        if subject_id in t1map:
            raise ("Can't map two t1 for subject '{0}'.".format(subject_id))
        t1map[subject_id] = fname

    # Convert all the surfaces
    csurffiles = []
    for fname in surffiles:

        # Get the t1 reference image
        subject_id = fname.split("/")[-3]
        t1file = t1map[subject_id]
        t1_image = nibabel.load(t1file)

        # Compute the conformed space to the native anatomical deformation
        asegfile = os.path.join(fsdir, subject_id, "mri", "aseg.mgz")
        physical_to_index = numpy.linalg.inv(t1_image.get_affine())
        translation = tkregister_translation(asegfile, fsconfig)
        deformation = numpy.dot(physical_to_index, translation)

        # Load and warp the mesh
        # The mesh: a 2-uplet with vertex (x, y, z) coordinates and
        # mesh triangles
        mesh = freesurfer.read_geometry(fname)
        surf = TriSurface(vertices=apply_affine_on_mesh(mesh[0], deformation),
                          triangles=mesh[1])

        # Save the mesh in the native space
        outputfile = fname + ".native"
        surf.save(os.path.dirname(outputfile), os.path.basename(outputfile))
        csurffiles.append(outputfile)

        # Clean input surface if specified
        if rm_orig:
            os.remove(fname)

    return csurffiles
if trf_file is None:
    trf_file = os.path.join(connectdir, "dmri_to_t1.trf")
    reg_file = os.path.join(connectdir, "nodif_to_t1.nii.gz")
    flirt(nodif_file, t1_file, omat=trf_file, out=reg_file, usesqform=False,
          cost="normmi", dof=6)


"""
Launch the tractography on the requested point of the cortical surface on the
selected hemisphere
"""
# Load the white mesh in the diffusion space
surface = TriSurface.load(whitefile)
voxel_diff_to_t1 = flirt2aff(trf_file, nodif_file, t1_file)
voxel_t1_to_diff = numpy.linalg.inv(voxel_diff_to_t1)
white_diff_vertices = apply_affine_on_mesh(surface.vertices, voxel_t1_to_diff)

# Select the vertices of interest
if vertices_indices is None:
    vertices_indices = range(len(surface.vertices))

# Go through all the hemisphere vertices
textures = {}
for index in vertices_indices:

    # Select the seeding vertex
    point = white_diff_vertices[index]

    # Create a directory for each seeding vertex in order to avoid collision
    # Raise an exception if the directory has already been created
    vertexdir = os.path.join(connectdir, "{0}_{1}".format(hemi, index))