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
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))
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))