def _run_interface(self, runtime):
dx, dy, dz = get_data_dims(self.inputs.image_file)
vx, vy, vz = get_vox_dims(self.inputs.image_file)
image_file = nb.load(self.inputs.image_file)
affine = image_file.get_affine()
out_filename = op.abspath(self.inputs.out_filename)
# Reads MRTrix tracks
header, streamlines = read_mrtrix_tracks(self.inputs.in_file, as_generator=True)
iflogger.info("MRTrix Header:")
iflogger.info(header)
# Writes to Trackvis
trk_header = nb.trackvis.empty_header()
trk_header["dim"] = [dx, dy, dz]
trk_header["voxel_size"] = [vx, vy, vz]
trk_header["n_count"] = header["count"]
if isdefined(self.inputs.matrix_file) and isdefined(self.inputs.registration_image_file):
iflogger.info("Applying transformation from matrix file {m}".format(m=self.inputs.matrix_file))
xfm = np.genfromtxt(self.inputs.matrix_file)
iflogger.info(xfm)
registration_image_file = nb.load(self.inputs.registration_image_file)
reg_affine = registration_image_file.get_affine()
r_dx, r_dy, r_dz = get_data_dims(self.inputs.registration_image_file)
r_vx, r_vy, r_vz = get_vox_dims(self.inputs.registration_image_file)
iflogger.info("Using affine from registration image file {r}".format(r=self.inputs.registration_image_file))
iflogger.info(reg_affine)
trk_header["vox_to_ras"] = reg_affine
trk_header["dim"] = [r_dx, r_dy, r_dz]
trk_header["voxel_size"] = [r_vx, r_vy, r_vz]
affine = np.dot(affine, np.diag(1.0 / np.array([vx, vy, vz, 1])))
transformed_streamlines = transform_to_affine(streamlines, trk_header, affine)
aff = affine_from_fsl_mat_file(xfm, [vx, vy, vz], [r_vx, r_vy, r_vz])
iflogger.info(aff)
axcode = aff2axcodes(reg_affine)
trk_header["voxel_order"] = axcode[0] + axcode[1] + axcode[2]
final_streamlines = move_streamlines(transformed_streamlines, aff)
trk_tracks = ((ii, None, None) for ii in final_streamlines)
trk.write(out_filename, trk_tracks, trk_header)
iflogger.info("Saving transformed Trackvis file as {out}".format(out=out_filename))
iflogger.info("New TrackVis Header:")
iflogger.info(trk_header)
else:
iflogger.info(
"Applying transformation from scanner coordinates to {img}".format(img=self.inputs.image_file)
)
axcode = aff2axcodes(affine)
trk_header["voxel_order"] = axcode[0] + axcode[1] + axcode[2]
trk_header["vox_to_ras"] = affine
transformed_streamlines = transform_to_affine(streamlines, trk_header, affine)
trk_tracks = ((ii, None, None) for ii in transformed_streamlines)
trk.write(out_filename, trk_tracks, trk_header)
iflogger.info("Saving Trackvis file as {out}".format(out=out_filename))
iflogger.info("TrackVis Header:")
iflogger.info(trk_header)
return runtime
def _run_interface(self, runtime):
dx, dy, dz = get_data_dims(self.inputs.image_file)
vx, vy, vz = get_vox_dims(self.inputs.image_file)
image_file = nb.load(self.inputs.image_file)
affine = image_file.get_affine()
out_filename = op.abspath(self.inputs.out_filename)
#Reads MRTrix tracks
header, streamlines = read_mrtrix_tracks(self.inputs.in_file, as_generator=True)
iflogger.info('MRTrix Header:')
iflogger.info(header)
# Writes to Trackvis
trk_header = nb.trackvis.empty_header()
trk_header['dim'] = [dx,dy,dz]
trk_header['voxel_size'] = [vx,vy,vz]
trk_header['n_count'] = header['count']
if isdefined(self.inputs.matrix_file) and isdefined(self.inputs.registration_image_file):
iflogger.info('Applying transformation from matrix file {m}'.format(m=self.inputs.matrix_file))
xfm = np.genfromtxt(self.inputs.matrix_file)
iflogger.info(xfm)
registration_image_file = nb.load(self.inputs.registration_image_file)
reg_affine = registration_image_file.get_affine()
r_dx, r_dy, r_dz = get_data_dims(self.inputs.registration_image_file)
r_vx, r_vy, r_vz = get_vox_dims(self.inputs.registration_image_file)
iflogger.info('Using affine from registration image file {r}'.format(r=self.inputs.registration_image_file))
iflogger.info(reg_affine)
trk_header['vox_to_ras'] = reg_affine
trk_header['dim'] = [r_dx,r_dy,r_dz]
trk_header['voxel_size'] = [r_vx,r_vy,r_vz]
affine = np.dot(affine,np.diag(1./np.array([vx, vy, vz, 1])))
transformed_streamlines = transform_to_affine(streamlines, trk_header, affine)
aff = affine_from_fsl_mat_file(xfm, [vx,vy,vz], [r_vx,r_vy,r_vz])
iflogger.info(aff)
axcode = aff2axcodes(reg_affine)
trk_header['voxel_order'] = axcode[0]+axcode[1]+axcode[2]
final_streamlines = move_streamlines(transformed_streamlines, aff)
trk_tracks = ((ii,None,None) for ii in final_streamlines)
trk.write(out_filename, trk_tracks, trk_header)
iflogger.info('Saving transformed Trackvis file as {out}'.format(out=out_filename))
iflogger.info('New TrackVis Header:')
iflogger.info(trk_header)
else:
iflogger.info('Applying transformation from scanner coordinates to {img}'.format(img=self.inputs.image_file))
axcode = aff2axcodes(affine)
trk_header['voxel_order'] = axcode[0]+axcode[1]+axcode[2]
trk_header['vox_to_ras'] = affine
transformed_streamlines = transform_to_affine(streamlines, trk_header, affine)
trk_tracks = ((ii,None,None) for ii in transformed_streamlines)
trk.write(out_filename, trk_tracks, trk_header)
iflogger.info('Saving Trackvis file as {out}'.format(out=out_filename))
iflogger.info('TrackVis Header:')
iflogger.info(trk_header)
return runtime
def _run_interface(self, runtime):
from dipy.tracking.utils import move_streamlines, \
affine_from_fsl_mat_file
dx, dy, dz = get_data_dims(self.inputs.image_file)
vx, vy, vz = get_vox_dims(self.inputs.image_file)
image_file = nb.load(self.inputs.image_file)
affine = image_file.affine
out_filename = op.abspath(self.inputs.out_filename)
# Reads MRTrix tracks
header, streamlines = read_mrtrix_tracks(
self.inputs.in_file, as_generator=True)
iflogger.info('MRTrix Header:')
iflogger.info(header)
# Writes to Trackvis
trk_header = nb.trackvis.empty_header()
trk_header['dim'] = [dx, dy, dz]
trk_header['voxel_size'] = [vx, vy, vz]
trk_header['n_count'] = header['count']
if isdefined(self.inputs.matrix_file) and isdefined(
self.inputs.registration_image_file):
iflogger.info('Applying transformation from matrix file %s',
self.inputs.matrix_file)
xfm = np.genfromtxt(self.inputs.matrix_file)
iflogger.info(xfm)
registration_image_file = nb.load(
self.inputs.registration_image_file)
reg_affine = registration_image_file.affine
r_dx, r_dy, r_dz = get_data_dims(
self.inputs.registration_image_file)
r_vx, r_vy, r_vz = get_vox_dims(
self.inputs.registration_image_file)
iflogger.info('Using affine from registration image file %s',
self.inputs.registration_image_file)
iflogger.info(reg_affine)
trk_header['vox_to_ras'] = reg_affine
trk_header['dim'] = [r_dx, r_dy, r_dz]
trk_header['voxel_size'] = [r_vx, r_vy, r_vz]
affine = np.dot(affine, np.diag(1. / np.array([vx, vy, vz, 1])))
transformed_streamlines = transform_to_affine(
streamlines, trk_header, affine)
aff = affine_from_fsl_mat_file(xfm, [vx, vy, vz],
[r_vx, r_vy, r_vz])
iflogger.info(aff)
axcode = aff2axcodes(reg_affine)
trk_header['voxel_order'] = axcode[0] + axcode[1] + axcode[2]
final_streamlines = move_streamlines(transformed_streamlines, aff)
trk_tracks = ((ii, None, None) for ii in final_streamlines)
trk.write(out_filename, trk_tracks, trk_header)
iflogger.info('Saving transformed Trackvis file as %s',
out_filename)
iflogger.info('New TrackVis Header:')
iflogger.info(trk_header)
else:
iflogger.info(
'Applying transformation from scanner coordinates to %s',
self.inputs.image_file)
axcode = aff2axcodes(affine)
trk_header['voxel_order'] = axcode[0] + axcode[1] + axcode[2]
trk_header['vox_to_ras'] = affine
transformed_streamlines = transform_to_affine(
streamlines, trk_header, affine)
trk_tracks = ((ii, None, None) for ii in transformed_streamlines)
trk.write(out_filename, trk_tracks, trk_header)
iflogger.info('Saving Trackvis file as %s', out_filename)
iflogger.info('TrackVis Header:')
iflogger.info(trk_header)
return runtime
def _run_interface(self, runtime):
from dipy.tracking.utils import move_streamlines, affine_from_fsl_mat_file
dx, dy, dz = get_data_dims(self.inputs.image_file)
vx, vy, vz = get_vox_dims(self.inputs.image_file)
image_file = nb.load(self.inputs.image_file)
affine = image_file.affine
out_filename = op.abspath(self.inputs.out_filename)
# Reads MRTrix tracks
header, streamlines = read_mrtrix_tracks(self.inputs.in_file,
as_generator=True)
iflogger.info("MRTrix Header:")
iflogger.info(header)
# Writes to Trackvis
trk_header = nb.trackvis.empty_header()
trk_header["dim"] = [dx, dy, dz]
trk_header["voxel_size"] = [vx, vy, vz]
trk_header["n_count"] = header["count"]
if isdefined(self.inputs.matrix_file) and isdefined(
self.inputs.registration_image_file):
iflogger.info("Applying transformation from matrix file %s",
self.inputs.matrix_file)
xfm = np.genfromtxt(self.inputs.matrix_file)
iflogger.info(xfm)
registration_image_file = nb.load(
self.inputs.registration_image_file)
reg_affine = registration_image_file.affine
r_dx, r_dy, r_dz = get_data_dims(
self.inputs.registration_image_file)
r_vx, r_vy, r_vz = get_vox_dims(
self.inputs.registration_image_file)
iflogger.info(
"Using affine from registration image file %s",
self.inputs.registration_image_file,
)
iflogger.info(reg_affine)
trk_header["vox_to_ras"] = reg_affine
trk_header["dim"] = [r_dx, r_dy, r_dz]
trk_header["voxel_size"] = [r_vx, r_vy, r_vz]
affine = np.dot(affine, np.diag(1.0 / np.array([vx, vy, vz, 1])))
transformed_streamlines = transform_to_affine(
streamlines, trk_header, affine)
aff = affine_from_fsl_mat_file(xfm, [vx, vy, vz],
[r_vx, r_vy, r_vz])
iflogger.info(aff)
axcode = aff2axcodes(reg_affine)
trk_header["voxel_order"] = axcode[0] + axcode[1] + axcode[2]
final_streamlines = move_streamlines(transformed_streamlines, aff)
trk_tracks = ((ii, None, None) for ii in final_streamlines)
trk.write(out_filename, trk_tracks, trk_header)
iflogger.info("Saving transformed Trackvis file as %s",
out_filename)
iflogger.info("New TrackVis Header:")
iflogger.info(trk_header)
else:
iflogger.info(
"Applying transformation from scanner coordinates to %s",
self.inputs.image_file,
)
axcode = aff2axcodes(affine)
trk_header["voxel_order"] = axcode[0] + axcode[1] + axcode[2]
trk_header["vox_to_ras"] = affine
transformed_streamlines = transform_to_affine(
streamlines, trk_header, affine)
trk_tracks = ((ii, None, None) for ii in transformed_streamlines)
trk.write(out_filename, trk_tracks, trk_header)
iflogger.info("Saving Trackvis file as %s", out_filename)
iflogger.info("TrackVis Header:")
iflogger.info(trk_header)
return runtime
