def ReadOthers(dir_):
"""
Read the given Analyze, NIfTI, Compressed NIfTI or PAR/REC file,
remove singleton image dimensions and convert image orientation to
RAS+ canonical coordinate system. Analyze header does not support
affine transformation matrix, though cannot be converted automatically
to canonical orientation.
:param dir_: file path
:return: imagedata object
"""
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
try:
imagedata = nib.squeeze_image(nib.load(dir_))
imagedata = nib.as_closest_canonical(imagedata)
imagedata.update_header()
except (nib.filebasedimages.ImageFileError):
return False
return imagedata
def _load(self, in_file, mask_file=None):
stem, ext = split_ext(in_file)
self.stem, self.ext = stem, ext
if mask_file is None:
mask_file = self.inputs.mask
self.mask = None
if ext in [".nii", ".nii.gz"]:
in_img = nib.load(in_file)
self.in_img = in_img
ndim = np.asanyarray(in_img.dataobj).ndim
if ndim == 3:
volumes = [in_img]
elif ndim == 4:
volumes = nib.four_to_three(in_img)
else:
raise ValueError(
f'Unexpect number of dimensions {ndim:d} in "{in_file}"')
volume_shape = volumes[0].shape
n_voxels = np.prod(volume_shape)
if (isdefined(mask_file) and isinstance(mask_file, str)
and Path(mask_file).is_file()):
mask_img = nib.squeeze_image(nib.load(mask_file))
assert nvol(mask_img) == 1
assert np.allclose(mask_img.affine, in_img.affine)
mask_fdata = mask_img.get_fdata(dtype=np.float64)
mask_bin = np.logical_not(
np.logical_or(mask_fdata <= 0,
np.isclose(mask_fdata, 0, atol=1e-2)))
self.mask = mask_bin
n_voxels = np.count_nonzero(mask_bin)
n_volumes = len(volumes)
array = np.zeros((n_volumes, n_voxels))
for i, volume in enumerate(volumes):
volume_data = volume.get_fdata()
if self.mask is not None:
array[i, :] = volume_data[self.mask]
else:
array[i, :] = np.ravel(volume_data)
else: # a text file
in_df = read_spreadsheet(in_file)
self.in_df = in_df
array = in_df.to_numpy().astype(np.float64)
return array
def ReadOthers(dir_):
"""
Read the given Analyze, NIfTI, Compressed NIfTI or PAR/REC file,
remove singleton image dimensions and convert image orientation to
RAS+ canonical coordinate system. Analyze header does not support
affine transformation matrix, though cannot be converted automatically
to canonical orientation.
:param dir_: file path
:return: imagedata object
"""
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
try:
imagedata = nib.squeeze_image(nib.load(dir_))
imagedata = nib.as_closest_canonical(imagedata)
imagedata.update_header()
except(nib.filebasedimages.ImageFileError):
return False
return imagedata
def sanitize(input_fname):
im = nb.as_closest_canonical(nb.squeeze_image(nb.load(str(input_fname))))
hdr = im.header.copy()
dtype = 'int16'
data = None
if str(input_fname).endswith('_mask.nii.gz'):
dtype = 'uint8'
data = im.get_fdata() > 0
if str(input_fname).endswith('_probseg.nii.gz'):
dtype = 'float32'
hdr['cal_max'] = 1.0
hdr['cal_min'] = 0.0
data = im.get_fdata()
data[data < 0] = 0
if input_fname.name.split('_')[-1].split('.')[0] in ('T1w', 'T2w', 'PD'):
data = im.get_fdata()
data[data < 0] = 0
hdr.set_data_dtype(dtype)
nii = nb.Nifti1Image(
data if data is not None else im.get_fdata().astype(dtype), im.affine,
hdr)
sform = nii.header.get_sform()
nii.header.set_sform(sform, 4)
nii.header.set_qform(sform, 4)
nii.header.set_xyzt_units(xyz='mm')
nii.to_filename(str(input_fname))
def _run_interface(self, runtime):
ref_name = self.inputs.in_file
ref_nii = nb.load(ref_name)
n_volumes_to_discard = _get_vols_to_discard(ref_nii)
self._results["n_volumes_to_discard"] = n_volumes_to_discard
out_ref_fname = os.path.join(runtime.cwd, "ref_bold.nii.gz")
if isdefined(self.inputs.sbref_file):
out_ref_fname = os.path.join(runtime.cwd, "ref_sbref.nii.gz")
ref_name = self.inputs.sbref_file
ref_nii = nb.squeeze_image(nb.load(ref_name))
# If reference is only 1 volume, return it directly
if len(ref_nii.shape) == 3:
ref_nii.header.extensions.clear()
ref_nii.to_filename(out_ref_fname)
self._results['ref_image'] = out_ref_fname
return runtime
else:
# Reset this variable as it no longer applies
# and value for the output is stored in self._results
n_volumes_to_discard = 0
# Slicing may induce inconsistencies with shape-dependent values in extensions.
# For now, remove all. If this turns out to be a mistake, we can select extensions
# that don't break pipeline stages.
ref_nii.header.extensions.clear()
if n_volumes_to_discard == 0:
if ref_nii.shape[-1] > 40:
ref_name = os.path.join(runtime.cwd, "slice.nii.gz")
nb.Nifti1Image(ref_nii.dataobj[:, :, :, 20:40], ref_nii.affine,
ref_nii.header).to_filename(ref_name)
if self.inputs.mc_method == "AFNI":
res = afni.Volreg(in_file=ref_name,
args='-Fourier -twopass',
zpad=4,
outputtype='NIFTI_GZ').run()
elif self.inputs.mc_method == "FSL":
res = fsl.MCFLIRT(in_file=ref_name,
ref_vol=0,
interpolation='sinc').run()
mc_slice_nii = nb.load(res.outputs.out_file)
median_image_data = np.median(mc_slice_nii.get_fdata(), axis=3)
else:
median_image_data = np.median(
ref_nii.dataobj[:, :, :, :n_volumes_to_discard], axis=3)
nb.Nifti1Image(median_image_data, ref_nii.affine,
ref_nii.header).to_filename(out_ref_fname)
self._results["ref_image"] = out_ref_fname
return runtime
def _run_interface(self, runtime):
in_files = self.inputs.in_files
if not isinstance(in_files, list):
in_files = [self.inputs.in_files]
# Generate output average name early
self._results['out_avg'] = fname_presuffix(self.inputs.in_files[0],
suffix='_avg',
newpath=runtime.cwd)
if self.inputs.to_ras:
in_files = [reorient(inf, newpath=runtime.cwd) for inf in in_files]
if len(in_files) == 1:
filenii = nb.load(in_files[0])
# magnitude files can have an extra dimension empty
if len(filenii.shape) == 5:
filenii = nb.squeeze_image(filenii)
if len(filenii.shape) == 5:
raise RuntimeError('Input image (%s) is 5D' % in_files[0])
in_files = [
fname_presuffix(in_files[0],
suffix='_squeezed',
newpath=runtime.cwd)
]
filenii.to_filename(in_files[0])
if filenii.dataobj.ndim < 4:
self._results['out_file'] = in_files[0]
self._results['out_avg'] = in_files[0]
# TODO: generate identity out_mats and zero-filled out_movpar
return runtime
in_files = in_files[0]
else:
magmrg = fsl.Merge(dimension='t', in_files=self.inputs.in_files)
in_files = magmrg.run().outputs.merged_file
mcflirt = fsl.MCFLIRT(cost='normcorr',
save_mats=True,
save_plots=True,
ref_vol=0,
in_file=in_files)
mcres = mcflirt.run()
self._results['out_mats'] = mcres.outputs.mat_file
self._results['out_movpar'] = mcres.outputs.par_file
self._results['out_file'] = mcres.outputs.out_file
hmcnii = nb.load(mcres.outputs.out_file)
hmcdat = hmcnii.get_fdata().mean(axis=3)
if self.inputs.zero_based_avg:
hmcdat -= hmcdat.min()
nb.Nifti1Image(hmcdat, hmcnii.affine,
hmcnii.header).to_filename(self._results['out_avg'])
return runtime
def median(in_file):
"""Average a 4D dataset across the last dimension using median."""
out_file = fname_presuffix(in_file, suffix="_mean.nii.gz", use_ext=False)
img = nib.load(in_file)
if img.dataobj.ndim == 3:
return in_file
if img.shape[-1] == 1:
nib.squeeze_image(img).to_filename(out_file)
return out_file
median_data = np.median(img.get_fdata(dtype="float32"), axis=-1)
hdr = img.header.copy()
hdr.set_xyzt_units("mm")
hdr.set_data_dtype(np.float32)
nib.Nifti1Image(median_data, img.affine, hdr).to_filename(out_file)
return out_file
def median(in_file, newpath=None):
"""Average a 4D dataset across the last dimension using median."""
out_file = fname_presuffix(in_file, suffix='_b0ref', newpath=newpath)
img = nb.load(in_file)
if img.dataobj.ndim == 3:
return in_file
if img.shape[-1] == 1:
nb.squeeze_image(img).to_filename(out_file)
return out_file
median_data = np.median(img.get_fdata(dtype='float32'), axis=-1)
hdr = img.header.copy()
hdr.set_xyzt_units('mm')
hdr.set_data_dtype(np.float32)
nb.Nifti1Image(median_data, img.affine, hdr).to_filename(out_file)
return out_file
def median(in_file, out_path=None):
"""Average a 4D dataset across the last dimension using median."""
if out_path is None:
out_path = fname_presuffix(in_file, suffix='_b0ref', use_ext=True)
img = nb.load(in_file)
if img.dataobj.ndim == 3:
return in_file
if img.shape[-1] == 1:
nb.squeeze_image(img).to_filename(out_path)
return out_path
dtype = img.get_data_dtype()
median_data = np.median(img.get_fdata(), axis=-1)
nb.Nifti1Image(median_data.astype(dtype), img.affine,
img.header).to_filename(out_path)
return out_path
def _run_interface(self, runtime):
ref_name = self.inputs.in_file
ref_nii = nb.load(ref_name)
n_volumes_to_discard = _get_vols_to_discard(ref_nii)
self._results["n_volumes_to_discard"] = n_volumes_to_discard
out_ref_fname = os.path.join(runtime.cwd, "ref_bold.nii.gz")
if isdefined(self.inputs.sbref_file):
out_ref_fname = os.path.join(runtime.cwd, "ref_sbref.nii.gz")
ref_name = self.inputs.sbref_file
ref_nii = nb.squeeze_image(nb.load(ref_name))
# If reference is only 1 volume, return it directly
if len(ref_nii.shape) == 3:
ref_nii.header.extensions.clear()
ref_nii.to_filename(out_ref_fname)
self._results['ref_image'] = out_ref_fname
return runtime
else:
# Reset this variable as it no longer applies
# and value for the output is stored in self._results
n_volumes_to_discard = 0
# Slicing may induce inconsistencies with shape-dependent values in extensions.
# For now, remove all. If this turns out to be a mistake, we can select extensions
# that don't break pipeline stages.
ref_nii.header.extensions.clear()
if n_volumes_to_discard == 0:
if ref_nii.shape[-1] > 40:
ref_name = os.path.join(runtime.cwd, "slice.nii.gz")
nb.Nifti1Image(ref_nii.dataobj[:, :, :, 20:40], ref_nii.affine,
ref_nii.header).to_filename(ref_name)
if self.inputs.mc_method == "AFNI":
res = afni.Volreg(in_file=ref_name, args='-Fourier -twopass',
zpad=4, outputtype='NIFTI_GZ').run()
elif self.inputs.mc_method == "FSL":
res = fsl.MCFLIRT(in_file=ref_name,
ref_vol=0, interpolation='sinc').run()
mc_slice_nii = nb.load(res.outputs.out_file)
median_image_data = np.median(mc_slice_nii.get_data(), axis=3)
else:
median_image_data = np.median(
ref_nii.dataobj[:, :, :, :n_volumes_to_discard], axis=3)
nb.Nifti1Image(median_image_data, ref_nii.affine,
ref_nii.header).to_filename(out_ref_fname)
self._results["ref_image"] = out_ref_fname
return runtime
def fit(
cope_files: List[Path],
var_cope_files: Optional[List[Path]],
mask_files: List[Path],
regressors: Dict[str, List[float]],
contrasts: List[Tuple],
algorithms_to_run: List[str],
num_threads: int,
) -> Dict:
voxel_data, cmatdict = load_data(
cope_files,
var_cope_files,
mask_files,
regressors,
contrasts,
algorithms_to_run,
)
# setup run
if num_threads < 2:
pool: Optional[Pool] = None
it: Iterator = map(voxel_calc, voxel_data)
cm: ContextManager = nullcontext()
else:
pool = Pool(processes=num_threads)
it = pool.imap_unordered(voxel_calc, voxel_data)
cm = pool
# run
voxel_results: Dict = defaultdict(lambda: defaultdict(dict))
with cm:
for x in tqdm(it, unit="voxels"):
if x is None:
continue
for a, d in x.items(): # transpose
if d is None:
continue
for k, v in d.items():
if v is None:
continue
voxel_results[a][k].update(v)
ref_image = nib.squeeze_image(nib.load(cope_files[0]))
output_files = dict()
for a, v in voxel_results.items():
output_files.update(algorithms[a].write_outputs(
ref_image, cmatdict, v))
return output_files
def _run_interface(self, runtime):
# Squeeze 4th dimension if possible (#660)
nii = nb.squeeze_image(nb.load(self.inputs.in_file))
hdr = nii.header.copy()
if self.inputs.check_ras:
nii = nb.as_closest_canonical(nii)
if self.inputs.check_dtype:
changed = True
datatype = int(hdr["datatype"])
if datatype == 1:
config.loggers.interface.warning(
'Input image %s has a suspicious data type "%s"',
self.inputs.in_file,
hdr.get_data_dtype(),
)
# signed char and bool to uint8
if datatype == 1 or datatype == 2 or datatype == 256:
dtype = np.uint8
# int16 to uint16
elif datatype == 4:
dtype = np.uint16
# Signed long, long long, etc to uint32
elif datatype == 8 or datatype == 1024 or datatype == 1280:
dtype = np.uint32
# Floats over 32 bits
elif datatype == 64 or datatype == 1536:
dtype = np.float32
else:
changed = False
if changed:
hdr.set_data_dtype(dtype)
nii = nb.Nifti1Image(nii.get_data().astype(dtype), nii.affine,
hdr)
# Generate name
out_file, ext = op.splitext(op.basename(self.inputs.in_file))
if ext == ".gz":
out_file, ext2 = op.splitext(out_file)
ext = ext2 + ext
self._results["out_file"] = op.abspath("{}_conformed{}".format(
out_file, ext))
nii.to_filename(self._results["out_file"])
return runtime
def _merge(in_file):
import nibabel as nb
import numpy as np
img = nb.squeeze_image(nb.load(in_file))
data = np.asanyarray(img.dataobj)
if data.ndim == 3:
return in_file
from pathlib import Path
data = data.mean(-1)
out_file = (Path() / "merged.nii.gz").absolute()
img.__class__(data, img.affine, img.header).to_filename(out_file)
return str(out_file)
def _run_interface(self, runtime):
# Squeeze 4th dimension if possible (#660)
nii = nb.squeeze_image(nb.load(self.inputs.in_file))
hdr = nii.get_header().copy()
if self.inputs.check_ras:
nii = nb.as_closest_canonical(nii)
if self.inputs.check_dtype:
changed = True
datatype = int(hdr['datatype'])
if datatype == 1:
IFLOGGER.warn('Input image %s has a suspicious data type "%s"',
self.inputs.in_file, hdr.get_data_dtype())
# signed char and bool to uint8
if datatype == 1 or datatype == 2 or datatype == 256:
dtype = np.uint8
# int16 to uint16
elif datatype == 4:
dtype = np.uint16
# Signed long, long long, etc to uint32
elif datatype == 8 or datatype == 1024 or datatype == 1280:
dtype = np.uint32
# Floats over 32 bits
elif datatype == 64 or datatype == 1536:
dtype = np.float32
else:
changed = False
if changed:
hdr.set_data_dtype(dtype)
nii = nb.Nifti1Image(nii.get_data().astype(dtype),
nii.get_affine(), hdr)
# Generate name
out_file, ext = op.splitext(op.basename(self.inputs.in_file))
if ext == '.gz':
out_file, ext2 = op.splitext(out_file)
ext = ext2 + ext
self._results['out_file'] = op.abspath('{}_conformed{}'.format(out_file, ext))
nii.to_filename(self._results['out_file'])
return runtime
def _flatten_split_merge(in_files):
if isinstance(in_files, str):
in_files = [in_files]
nfiles = len(in_files)
all_nii = []
for fname in in_files:
nii = nb.squeeze_image(nb.load(fname))
if nii.get_data().ndim > 3:
all_nii += nb.four_to_three(nii)
else:
all_nii.append(nii)
if len(all_nii) == 1:
LOGGER.warning('File %s cannot be split', all_nii[0])
return in_files[0], in_files
if len(all_nii) == nfiles:
flat_split = in_files
else:
splitname = fname_presuffix(in_files[0],
suffix='_split%04d',
newpath=os.getcwd())
flat_split = []
for i, nii in enumerate(all_nii):
flat_split.append(splitname % i)
nii.to_filename(flat_split[-1])
# Only one 4D file was supplied
if nfiles == 1:
merged = in_files[0]
else:
# More that one in_files - need merge
merged = fname_presuffix(in_files[0],
suffix='_merged',
newpath=os.getcwd())
nb.concat_images(all_nii).to_filename(merged)
return merged, flat_split
def rescale_b0(in_file, mask_file, out_path=None):
"""Rescale the input volumes using the median signal intensity."""
if out_path is None:
out_path = fname_presuffix(in_file, suffix='_rescaled', use_ext=True)
img = nb.squeeze_image(nb.load(in_file))
if img.dataobj.ndim == 3:
return in_file, [1.0]
mask_data = nb.load(mask_file).get_fdata() > 0
dtype = img.get_data_dtype()
data = img.get_fdata()
median_signal = np.median(data[mask_data, ...], axis=0)
# Normalize to the first volume
signal_drift = median_signal[0] / median_signal
data /= signal_drift
nb.Nifti1Image(data.astype(dtype), img.affine,
img.header).to_filename(out_path)
return out_path, signal_drift.tolist()
def _flatten_split_merge(in_files):
from builtins import bytes, str
if isinstance(in_files, (bytes, str)):
in_files = [in_files]
nfiles = len(in_files)
all_nii = []
for fname in in_files:
nii = nb.squeeze_image(nb.load(fname))
if nii.get_data().ndim > 3:
all_nii += nb.four_to_three(nii)
else:
all_nii.append(nii)
if len(all_nii) == 1:
LOGGER.warn('File %s cannot be split', all_nii[0])
return in_files[0], in_files
if len(all_nii) == nfiles:
flat_split = in_files
else:
splitname = genfname(in_files[0], suffix='split%04d')
flat_split = []
for i, nii in enumerate(all_nii):
flat_split.append(splitname % i)
nii.to_filename(flat_split[-1])
# Only one 4D file was supplied
if nfiles == 1:
merged = in_files[0]
else:
# More that one in_files - need merge
merged = genfname(in_files[0], suffix='merged')
nb.concat_images(all_nii).to_filename(merged)
return merged, flat_split
def _run_interface(self, runtime):
"""
Execute this interface with the provided runtime.
TODO: Is the *runtime* argument required? It doesn't seem to be used
anywhere.
Parameters
----------
runtime : Any
Execution runtime ?
Returns
-------
Any
Execution runtime ?
"""
# Squeeze 4th dimension if possible (#660)
nii = nib.squeeze_image(nib.load(self.inputs.in_file))
if self.inputs.check_ras:
nii = nib.as_closest_canonical(nii)
if self.inputs.check_dtype:
nii = self._check_dtype(nii)
# Generate name
out_file, ext = op.splitext(op.basename(self.inputs.in_file))
if ext == ".gz":
out_file, ext2 = op.splitext(out_file)
ext = ext2 + ext
out_file_name = OUT_FILE.format(prefix=out_file, ext=ext)
self._results["out_file"] = op.abspath(out_file_name)
nii.to_filename(self._results["out_file"])
return runtime
def _run_interface(self, runtime):
nii_list = []
for f in self.inputs.in_files:
filenii = nb.squeeze_image(nb.load(f))
ndim = filenii.dataobj.ndim
if ndim == 3:
nii_list.append(filenii)
continue
elif self.inputs.allow_4D and ndim == 4:
nii_list += nb.four_to_three(filenii)
continue
else:
raise ValueError(
"Input image has an incorrect number of dimensions"
f" ({ndim}).")
img_4d = nb.concat_images(nii_list)
out_file = fname_presuffix(self.inputs.in_files[0],
suffix="_merged",
newpath=runtime.cwd)
img_4d.to_filename(out_file)
self._results["out_file"] = out_file
return runtime
def main():
"""
Visualize Freesurfer, SimNIBS headreco, and Nexstim coil locations in the scanner coordinate system.
"""
SHOW_AXES = True
SHOW_SCENE_AXES = True
SHOW_COIL_AXES = True
SHOW_SKIN = True
SHOW_BRAIN = True
SHOW_FREESURFER = True
SHOW_COIL = True
SHOW_MARKERS = True
TRANSF_COIL = True
SHOW_PLANE = False
SELECT_LANDMARKS = 'scalp' # 'all', 'mri' 'scalp'
SAVE_ID = False
AFFINE_IMG = True
NO_SCALE = True
SCREENSHOT = False
reorder = [0, 2, 1]
flipx = [True, False, False]
# reorder = [0, 1, 2]
# flipx = [False, False, False]
# default folder and subject
# subj = 's03'
subj = 'S5'
id_extra = False # 8, 9, 10, 12, False
data_dir = os.environ['OneDrive'] + r'\data\nexstim_coord'
# data_dir = 'P:\\tms_eeg\\mTMS\\projects\\lateral ppTMS M1\\E-fields\\'
# data_subj = data_dir + subj + '\\'
simnibs_dir = data_dir + r'\simnibs\m2m_ppM1_{}_nc'.format(subj)
fs_dir = data_dir + r'\freesurfer\ppM1_{}'.format(subj)
if id_extra:
nav_dir = data_dir + r'\nav_coordinates\ppM1_{}_{}'.format(
subj, id_extra)
else:
nav_dir = data_dir + r'\nav_coordinates\ppM1_{}'.format(subj)
# filenames
# coil_file = data_dir + 'magstim_fig8_coil.stl'
coil_file = os.environ[
'OneDrive'] + r'\data\nexstim_coord\magstim_fig8_coil.stl'
if id_extra:
coord_file = nav_dir + r'\ppM1_eximia_{}_{}.txt'.format(subj, id_extra)
else:
coord_file = nav_dir + r'\ppM1_eximia_{}.txt'.format(subj)
# img_file = data_subj + subj + '.nii'
img_file = data_dir + r'\mri\ppM1_{}\ppM1_{}.nii'.format(subj, subj)
brain_file = simnibs_dir + r'\wm.stl'
skin_file = simnibs_dir + r'\skin.stl'
fs_file = fs_dir + r'\lh.pial.stl'
fs_t1 = fs_dir + r'\mri\T1.mgz'
if id_extra:
output_file = nav_dir + r'\transf_mat_{}_{}'.format(subj, id_extra)
else:
output_file = nav_dir + r'\transf_mat_{}'.format(subj)
coords = lc.load_nexstim(coord_file)
# red, green, blue, maroon (dark red),
# olive (shitty green), teal (petrol blue), yellow, orange
col = [[1., 0., 0.], [0., 1., 0.], [0., 0., 1.], [1., .0, 1.],
[.5, .5, 0.], [0., .5, .5], [1., 1., 0.], [1., .4, .0]]
# extract image header shape and affine transformation from original nifti file
imagedata = nb.squeeze_image(nb.load(img_file))
imagedata = nb.as_closest_canonical(imagedata)
imagedata.update_header()
pix_dim = imagedata.header.get_zooms()
img_shape = imagedata.header.get_data_shape()
print("Pixel size: \n")
print(pix_dim)
print("\nImage shape: \n")
print(img_shape)
if AFFINE_IMG:
affine = imagedata.affine
if NO_SCALE:
scale, shear, angs, trans, persp = tf.decompose_matrix(
imagedata.affine)
affine = tf.compose_matrix(scale=None,
shear=shear,
angles=angs,
translate=trans,
perspective=persp)
print("\nAffine: \n")
print(affine)
else:
affine = np.identity(4)
# affine_I = np.identity(4)
# create a camera, render window and renderer
camera = vtk.vtkCamera()
camera.SetPosition(0, 1000, 0)
camera.SetFocalPoint(0, 0, 0)
camera.SetViewUp(0, 0, 1)
camera.ComputeViewPlaneNormal()
camera.Azimuth(90.0)
camera.Elevation(10.0)
ren = vtk.vtkRenderer()
ren.SetActiveCamera(camera)
ren.ResetCamera()
camera.Dolly(1.5)
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetSize(800, 800)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
if SELECT_LANDMARKS == 'mri':
# MRI landmarks
coord_mri = [['Nose/Nasion'], ['Left ear'], ['Right ear'],
['Coil Loc'], ['EF max']]
pts_ref = [1, 2, 3, 7, 10]
elif SELECT_LANDMARKS == 'all':
# all coords
coord_mri = [['Nose/Nasion'], ['Left ear'], ['Right ear'],
['Nose/Nasion'], ['Left ear'], ['Right ear'],
['Coil Loc'], ['EF max']]
pts_ref = [1, 2, 3, 5, 4, 6, 7, 10]
elif SELECT_LANDMARKS == 'scalp':
# scalp landmarks
coord_mri = [['Nose/Nasion'], ['Left ear'], ['Right ear'],
['Coil Loc'], ['EF max']]
hdr_mri = [
'Nose/Nasion', 'Left ear', 'Right ear', 'Coil Loc', 'EF max'
]
pts_ref = [5, 4, 6, 7, 10]
coords_np = np.zeros([len(pts_ref), 3])
for n, pts_id in enumerate(pts_ref):
# to keep in the MRI space use the identity as the affine
# coord_aux = n2m.coord_change(coords[pts_id][1:], img_shape, affine_I, flipx, reorder)
# affine_trans = affine_I.copy()
# affine_trans = affine.copy()
# affine_trans[:3, -1] = affine[:3, -1]
coord_aux = n2m.coord_change(coords[pts_id][1:], img_shape, affine,
flipx, reorder)
coords_np[n, :] = coord_aux
[coord_mri[n].append(s) for s in coord_aux]
if SHOW_MARKERS:
marker_actor = add_marker(coord_aux, ren, col[n])
print('\nOriginal coordinates from Nexstim: \n')
[print(s) for s in coords]
print('\nTransformed coordinates to MRI space: \n')
[print(s) for s in coord_mri]
# coil location, normal vector and direction vector
coil_loc = coord_mri[-2][1:]
coil_norm = coords[8][1:]
coil_dir = coords[9][1:]
# creating the coil coordinate system by adding a point in the direction of each given coil vector
# the additional vector is just the cross product from coil direction and coil normal vectors
# origin of the coordinate system is the coil location given by Nexstim
# the vec_length is to allow line creation with visible length in VTK scene
vec_length = 75
p1 = coords[7][1:]
p2 = [x + vec_length * y for x, y in zip(p1, coil_norm)]
p2_norm = n2m.coord_change(p2, img_shape, affine, flipx, reorder)
p2 = [x + vec_length * y for x, y in zip(p1, coil_dir)]
p2_dir = n2m.coord_change(p2, img_shape, affine, flipx, reorder)
coil_face = np.cross(coil_norm, coil_dir)
p2 = [x - vec_length * y for x, y in zip(p1, coil_face.tolist())]
p2_face = n2m.coord_change(p2, img_shape, affine, flipx, reorder)
# Coil face unit vector (X)
u1 = np.asarray(p2_face) - np.asarray(coil_loc)
u1_n = u1 / np.linalg.norm(u1)
# Coil direction unit vector (Y)
u2 = np.asarray(p2_dir) - np.asarray(coil_loc)
u2_n = u2 / np.linalg.norm(u2)
# Coil normal unit vector (Z)
u3 = np.asarray(p2_norm) - np.asarray(coil_loc)
u3_n = u3 / np.linalg.norm(u3)
transf_matrix = np.identity(4)
if TRANSF_COIL:
transf_matrix[:3, 0] = u1_n
transf_matrix[:3, 1] = u2_n
transf_matrix[:3, 2] = u3_n
transf_matrix[:3, 3] = coil_loc[:]
# the absolute value of the determinant indicates the scaling factor
# the sign of the determinant indicates how it affects the orientation: if positive maintain the
# original orientation and if negative inverts all the orientations (flip the object inside-out)'
# the negative determinant is what makes objects in VTK scene to become
# black
print('Transformation matrix: \n', transf_matrix, '\n')
print('Determinant: ', np.linalg.det(transf_matrix))
if SAVE_ID:
coord_dict = {
'm_affine': transf_matrix,
'coords_labels': hdr_mri,
'coords': coords_np
}
io.savemat(output_file + '.mat', coord_dict)
hdr_names = ';'.join(
['m' + str(i) + str(j) for i in range(1, 5) for j in range(1, 5)])
np.savetxt(output_file + '.txt',
transf_matrix.reshape([1, 16]),
delimiter=';',
header=hdr_names)
if SHOW_BRAIN:
# brain_actor = load_stl(brain_file, ren, colour=[0., 1., 1.], opacity=0.7, user_matrix=np.linalg.inv(affine))
brain_actor = load_stl(brain_file,
ren,
colour=[0., 1., 1.],
opacity=1.)
if SHOW_SKIN:
# skin_actor = load_stl(skin_file, ren, opacity=0.5, user_matrix=np.linalg.inv(affine))
skin_actor = load_stl(skin_file, ren, colour="SkinColor", opacity=.4)
if SHOW_FREESURFER:
img = fsio.MGHImage.load(fs_t1)
#print("MGH Header: ", img)
#print("MGH data: ", img.header['Pxyz_c'])
# skin_actor = load_stl(skin_file, ren, opacity=0.5, user_matrix=np.linalg.inv(affine))
trans_fs = np.identity(4)
trans_fs[:3, -1] = img.header['Pxyz_c']
fs_actor = load_stl(fs_file,
ren,
colour=[1., 0., 1.],
opacity=0.5,
user_matrix=trans_fs)
if SHOW_COIL:
# reposition STL object prior to transformation matrix
# [translation_x, translation_y, translation_z, rotation_x, rotation_y, rotation_z]
# old translation when using Y as normal vector
# repos = [0., -6., 0., 0., -90., 90.]
# Translate coil loc coordinate to coil bottom
# repos = [0., 0., 5.5, 0., 0., 180.]
repos = [0., 0., 0., 0., 0., 180.]
act_coil = load_stl(coil_file,
ren,
replace=repos,
user_matrix=transf_matrix,
opacity=.3)
if SHOW_PLANE:
act_plane = add_plane(ren, user_matrix=transf_matrix)
# Add axes to scene origin
if SHOW_AXES:
add_line(ren, [0, 0, 0], [150, 0, 0], color=[1.0, 0.0, 0.0])
add_line(ren, [0, 0, 0], [0, 150, 0], color=[0.0, 1.0, 0.0])
add_line(ren, [0, 0, 0], [0, 0, 150], color=[0.0, 0.0, 1.0])
# Add axes to object origin
if SHOW_COIL_AXES:
add_line(ren, coil_loc, p2_norm, color=[.0, .0, 1.0])
add_line(ren, coil_loc, p2_dir, color=[.0, 1.0, .0])
add_line(ren, coil_loc, p2_face, color=[1.0, .0, .0])
# Add interactive axes to scene
if SHOW_SCENE_AXES:
axes = vtk.vtkAxesActor()
widget = vtk.vtkOrientationMarkerWidget()
widget.SetOutlineColor(0.9300, 0.5700, 0.1300)
widget.SetOrientationMarker(axes)
widget.SetInteractor(iren)
# widget.SetViewport(0.0, 0.0, 0.4, 0.4)
widget.SetEnabled(1)
widget.InteractiveOn()
if SCREENSHOT:
# screenshot of VTK scene
w2if = vtk.vtkWindowToImageFilter()
w2if.SetInput(ren_win)
w2if.Update()
writer = vtk.vtkPNGWriter()
writer.SetFileName("screenshot.png")
writer.SetInput(w2if.GetOutput())
writer.Write()
# Enable user interface interactor
# ren_win.Render()
ren.ResetCameraClippingRange()
iren.Initialize()
iren.Start()
def main():
SHOW_AXES = True
SHOW_SCENE_AXES = True
SHOW_COIL_AXES = True
SHOW_SKIN = True
SHOW_BRAIN = True
SHOW_COIL = True
SHOW_MARKERS = True
TRANSF_COIL = True
SHOW_PLANE = False
SELECT_LANDMARKS = 'scalp' # 'all', 'mri' 'scalp'
SAVE_ID = True
AFFINE_IMG = True
NO_SCALE = True
SCREENSHOT = False
SHOW_OTHER = False
reorder = [0, 2, 1]
flipx = [True, False, False]
# reorder = [0, 1, 2]
# flipx = [False, False, False]
# default folder and subject
# for Bert image use the translation in the base_affine (fall-back)
subj_list = ['VictorSouza', 'JaakkoNieminen', 'AinoTervo',
'JuusoKorhonen', 'BaranAydogan', 'AR', 'Bert']
subj = 0
data_dir = os.environ.get('OneDrive') + r'\vh\eventos\sf 2019\mri_science_factory\{}'.format(subj_list[subj])
# filenames
img_file = data_dir + r'\{}.nii'.format(subj_list[subj])
brain_file = data_dir + r'\gm.stl'
skin_file = data_dir + r'\gm_sn.stl'
if subj == 3:
other_file = data_dir + r'\gm.ply'
elif subj == 4:
other_file = data_dir + r'\tracks.vtp'
elif subj == 6:
other_file = data_dir + r'\gm.ply'
else:
other_file = data_dir + r'\gm.stl'
# coords = lc.load_nexstim(coord_file)
# red, green, blue, maroon (dark red),
# olive (shitty green), teal (petrol blue), yellow, orange
col = [[1., 0., 0.], [0., 1., 0.], [0., 0., 1.], [1., .0, 1.],
[.5, .5, 0.], [0., .5, .5], [1., 1., 0.], [1., .4, .0]]
# extract image header shape and affine transformation from original nifti file
imagedata = nb.squeeze_image(nb.load(img_file))
imagedata = nb.as_closest_canonical(imagedata)
imagedata.update_header()
pix_dim = imagedata.header.get_zooms()
img_shape = imagedata.header.get_data_shape()
print("Pixel size: \n")
print(pix_dim)
print("\nImage shape: \n")
print(img_shape)
print("\nSform: \n")
print(imagedata.get_qform(coded=True))
print("\nQform: \n")
print(imagedata.get_sform(coded=True))
print("\nFall-back: \n")
print(imagedata.header.get_base_affine())
scale_back, shear_back, angs_back, trans_back, persp_back = tf.decompose_matrix(imagedata.header.get_base_affine())
if AFFINE_IMG:
affine = imagedata.affine
# affine = imagedata.header.get_base_affine()
if NO_SCALE:
scale, shear, angs, trans, persp = tf.decompose_matrix(affine)
affine = tf.compose_matrix(scale=None, shear=shear, angles=angs, translate=trans, perspective=persp)
else:
affine = np.identity(4)
# affine_I = np.identity(4)
# create a camera, render window and renderer
camera = vtk.vtkCamera()
camera.SetPosition(0, 1000, 0)
camera.SetFocalPoint(0, 0, 0)
camera.SetViewUp(0, 0, 1)
camera.ComputeViewPlaneNormal()
camera.Azimuth(90.0)
camera.Elevation(10.0)
ren = vtk.vtkRenderer()
ren.SetActiveCamera(camera)
ren.ResetCamera()
ren.SetUseDepthPeeling(1)
ren.SetOcclusionRatio(0.1)
ren.SetMaximumNumberOfPeels(100)
camera.Dolly(1.5)
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetSize(800, 800)
ren_win.SetMultiSamples(0)
ren_win.SetAlphaBitPlanes(1)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
# if SELECT_LANDMARKS == 'mri':
# # MRI landmarks
# coord_mri = [['Nose/Nasion'], ['Left ear'], ['Right ear'], ['Coil Loc'], ['EF max']]
# pts_ref = [1, 2, 3, 7, 10]
# elif SELECT_LANDMARKS == 'all':
# # all coords
# coord_mri = [['Nose/Nasion'], ['Left ear'], ['Right ear'], ['Nose/Nasion'], ['Left ear'], ['Right ear'],
# ['Coil Loc'], ['EF max']]
# pts_ref = [1, 2, 3, 5, 4, 6, 7, 10]
# elif SELECT_LANDMARKS == 'scalp':
# # scalp landmarks
# coord_mri = [['Nose/Nasion'], ['Left ear'], ['Right ear'], ['Coil Loc'], ['EF max']]
# hdr_mri = ['Nose/Nasion', 'Left ear', 'Right ear', 'Coil Loc', 'EF max']
# pts_ref = [5, 4, 6, 7, 10]
#
# coords_np = np.zeros([len(pts_ref), 3])
# for n, pts_id in enumerate(pts_ref):
# # to keep in the MRI space use the identity as the affine
# # coord_aux = n2m.coord_change(coords[pts_id][1:], img_shape, affine_I, flipx, reorder)
# # affine_trans = affine_I.copy()
# # affine_trans = affine.copy()
# # affine_trans[:3, -1] = affine[:3, -1]
# coord_aux = n2m.coord_change(coords[pts_id][1:], img_shape, affine, flipx, reorder)
# coords_np[n, :] = coord_aux
# [coord_mri[n].append(s) for s in coord_aux]
# if SHOW_MARKERS:
# marker_actor = add_marker(coord_aux, ren, col[n])
#
# print('\nOriginal coordinates from Nexstim: \n')
# [print(s) for s in coords]
# print('\nTransformed coordinates to MRI space: \n')
# [print(s) for s in coord_mri]
#
# # coil location, normal vector and direction vector
# coil_loc = coord_mri[-2][1:]
# coil_norm = coords[8][1:]
# coil_dir = coords[9][1:]
#
# # creating the coil coordinate system by adding a point in the direction of each given coil vector
# # the additional vector is just the cross product from coil direction and coil normal vectors
# # origin of the coordinate system is the coil location given by Nexstim
# # the vec_length is to allow line creation with visible length in VTK scene
# vec_length = 75
# p1 = coords[7][1:]
# p2 = [x + vec_length * y for x, y in zip(p1, coil_norm)]
# p2_norm = n2m.coord_change(p2, img_shape, affine, flipx, reorder)
#
# p2 = [x + vec_length * y for x, y in zip(p1, coil_dir)]
# p2_dir = n2m.coord_change(p2, img_shape, affine, flipx, reorder)
#
# coil_face = np.cross(coil_norm, coil_dir)
# p2 = [x - vec_length * y for x, y in zip(p1, coil_face.tolist())]
# p2_face = n2m.coord_change(p2, img_shape, affine, flipx, reorder)
# Coil face unit vector (X)
# u1 = np.asarray(p2_face) - np.asarray(coil_loc)
# u1_n = u1 / np.linalg.norm(u1)
# # Coil direction unit vector (Y)
# u2 = np.asarray(p2_dir) - np.asarray(coil_loc)
# u2_n = u2 / np.linalg.norm(u2)
# # Coil normal unit vector (Z)
# u3 = np.asarray(p2_norm) - np.asarray(coil_loc)
# u3_n = u3 / np.linalg.norm(u3)
#
# transf_matrix = np.identity(4)
# if TRANSF_COIL:
# transf_matrix[:3, 0] = u1_n
# transf_matrix[:3, 1] = u2_n
# transf_matrix[:3, 2] = u3_n
# transf_matrix[:3, 3] = coil_loc[:]
# the absolute value of the determinant indicates the scaling factor
# the sign of the determinant indicates how it affects the orientation: if positive maintain the
# original orientation and if negative inverts all the orientations (flip the object inside-out)'
# the negative determinant is what makes objects in VTK scene to become black
# print('Transformation matrix: \n', transf_matrix, '\n')
# print('Determinant: ', np.linalg.det(transf_matrix))
# if SAVE_ID:
# coord_dict = {'m_affine': transf_matrix, 'coords_labels': hdr_mri, 'coords': coords_np}
# io.savemat(output_file + '.mat', coord_dict)
# hdr_names = ';'.join(['m' + str(i) + str(j) for i in range(1, 5) for j in range(1, 5)])
# np.savetxt(output_file + '.txt', transf_matrix.reshape([1, 16]), delimiter=';', header=hdr_names)
if SHOW_BRAIN:
# brain_actor = load_stl(brain_file, ren, colour=[0., 1., 1.], opacity=0.7, user_matrix=np.linalg.inv(affine))
affine_orig = np.identity(4)
# affine_orig = affine.copy()
# affine_orig[0, 3] = affine_orig[0, 3] + pix_dim[0]*img_shape[0]
# affine_orig[1, 3] = affine_orig[1, 3] + pix_dim[1]*img_shape[1]
# affine_orig[0, 3] = affine_orig[0, 3] + pix_dim[0]*img_shape[0]
# affine_orig[0, 3] = affine_orig[0, 3] - 5
# this partially works for DTI Baran
# modified close to correct [-75.99139404 123.88291931 - 148.19839478]
# fall-back [87.50042766 - 127.5 - 127.5]
# affine_orig[0, 3] = -trans_back[0]
# affine_orig[1, 3] = -trans_back[1]
# this works for the bert image
# affine_orig[0, 3] = -127
# affine_orig[1, 3] = 127
# affine_orig[2, 3] = -127
# affine_orig[:3, :3] = affine[:3, :3]
# affine_orig[1, 3] = -affine_orig[1, 3]+27.5 # victorsouza
# affine_orig[1, 3] = -affine_orig[1, 3]+97.5
# affine_orig[1, 3] = -affine_orig[1, 3]
print('Affine original: \n', affine)
scale, shear, angs, trans, persp = tf.decompose_matrix(affine)
print('Angles: \n', np.rad2deg(angs))
print('Translation: \n', trans)
print('Affine modified: \n', affine_orig)
scale, shear, angs, trans, persp = tf.decompose_matrix(affine_orig)
print('Angles: \n', np.rad2deg(angs))
print('Translation: \n', trans)
# colour=[0., 1., 1.],
brain_actor, brain_mesh = load_stl(brain_file, ren, replace=True, colour=[1., 0., 0.],
opacity=.3, user_matrix=affine_orig)
# print('Actor origin: \n', brain_actor.GetPosition())
if SHOW_SKIN:
# skin_actor = load_stl(skin_file, ren, opacity=0.5, user_matrix=np.linalg.inv(affine))
# affine[0, 3] = affine[0, 3] + pix_dim[0] * img_shape[0]
# this is working
# affine[0, 3] = affine[0, 3] + 8.
affine[1, 3] = affine[1, 3] + pix_dim[1] * img_shape[1]
# affine[2, 3] = affine[2, 3] + pix_dim[2] * img_shape[2]
affine_inv = np.linalg.inv(affine)
# affine_inv[:3, 3] = -affine[:3, 3]
# affine_inv[2, 3] = -affine_inv[2, 3]
skin_actor, skin_mesh = load_stl(skin_file, ren, colour="SkinColor", opacity=1., user_matrix=affine_inv)
# skin_actor, skin_mesh = load_stl(skin_file, ren, colour="SkinColor", opacity=1.)
skino_actor, skino_mesh = load_stl(skin_file, ren, colour=[1., 0., 0.], opacity=1.)
if SHOW_OTHER:
# skin_actor = load_stl(skin_file, ren, opacity=0.5, user_matrix=np.linalg.inv(affine))
affine[1, 3] = affine[1, 3] + pix_dim[1] * img_shape[1]
affine_inv = np.linalg.inv(affine)
# affine_inv[:3, 3] = -affine[:3, 3]
affine_inv[1, 3] = affine_inv[1, 3]
# other_actor, other_mesh = load_stl(other_file, ren, opacity=1., user_matrix=affine_inv)
# other_actor, other_mesh = load_stl(other_file, ren, opacity=1.)
# if SHOW_COIL:
# # reposition STL object prior to transformation matrix
# # [translation_x, translation_y, translation_z, rotation_x, rotation_y, rotation_z]
# # old translation when using Y as normal vector
# # repos = [0., -6., 0., 0., -90., 90.]
# # Translate coil loc coordinate to coil bottom
# # repos = [0., 0., 5.5, 0., 0., 180.]
# repos = [0., 0., 0., 0., 0., 180.]
# act_coil = load_stl(coil_file, ren, replace=repos, user_matrix=transf_matrix, opacity=.3)
#
# if SHOW_PLANE:
# act_plane = add_plane(ren, user_matrix=transf_matrix)
# Add axes to scene origin
if SHOW_AXES:
add_line(ren, [0, 0, 0], [150, 0, 0], color=[1.0, 0.0, 0.0])
add_line(ren, [0, 0, 0], [0, 150, 0], color=[0.0, 1.0, 0.0])
add_line(ren, [0, 0, 0], [0, 0, 150], color=[0.0, 0.0, 1.0])
# Add axes to object origin
# if SHOW_COIL_AXES:
# add_line(ren, coil_loc, p2_norm, color=[.0, .0, 1.0])
# add_line(ren, coil_loc, p2_dir, color=[.0, 1.0, .0])
# add_line(ren, coil_loc, p2_face, color=[1.0, .0, .0])
# Add interactive axes to scene
if SHOW_SCENE_AXES:
axes = vtk.vtkAxesActor()
widget = vtk.vtkOrientationMarkerWidget()
widget.SetOutlineColor(0.9300, 0.5700, 0.1300)
widget.SetOrientationMarker(axes)
widget.SetInteractor(iren)
# widget.SetViewport(0.0, 0.0, 0.4, 0.4)
widget.SetEnabled(1)
widget.InteractiveOn()
#
# if SCREENSHOT:
# # screenshot of VTK scene
# w2if = vtk.vtkWindowToImageFilter()
# w2if.SetInput(ren_win)
# w2if.Update()
#
# writer = vtk.vtkPNGWriter()
# writer.SetFileName("screenshot.png")
# writer.SetInput(w2if.GetOutput())
# writer.Write()
# Enable user interface interactor
# ren_win.Render()
ren.ResetCameraClippingRange()
iren.Initialize()
iren.Start()
def main():
SHOW_AXES = True
AFFINE_IMG = True
NO_SCALE = True
n_tracts = 240
n_threads = 2 * psutil.cpu_count()
data_dir = os.environ.get(
'OneDrive') + r'\data\dti_navigation\baran\pilot_20200131'
data_dir = data_dir.encode('utf-8')
# FOD_path = 'Baran_FOD.nii'
# trk_path = os.path.join(data_dir, FOD_path)
# data_dir = b'C:\Users\deoliv1\OneDrive\data\dti'
stl_path = b'wm_orig_smooth_world.stl'
brain_path = os.path.join(data_dir, stl_path)
# data_dir = b'C:\Users\deoliv1\OneDrive\data\dti'
stl_path = b'gm.stl'
brain_inv_path = os.path.join(data_dir, stl_path)
nii_path = b'Baran_FOD.nii'
trk_path = os.path.join(data_dir, nii_path)
nii_path = b'Baran_T1_inFODspace.nii'
img_path = os.path.join(data_dir, nii_path)
imagedata = nb.squeeze_image(nb.load(img_path.decode('utf-8')))
imagedata = nb.as_closest_canonical(imagedata)
imagedata.update_header()
pix_dim = imagedata.header.get_zooms()
img_shape = imagedata.header.get_data_shape()
# print(imagedata.header)
print("pix_dim: {}, img_shape: {}".format(pix_dim, img_shape))
if AFFINE_IMG:
affine = imagedata.affine
if NO_SCALE:
scale, shear, angs, trans, persp = tf.decompose_matrix(
imagedata.affine)
affine = tf.compose_matrix(scale=None,
shear=shear,
angles=angs,
translate=trans,
perspective=persp)
else:
affine = np.identity(4)
print("affine: {0}\n".format(affine))
# Create a rendering window and renderer
ren = vtk.vtkRenderer()
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetSize(800, 800)
# Create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
start_time = time.time()
tracker = Trekker.initialize(trk_path)
tracker.seed_maxTrials(1)
tracker.minFODamp(0.1)
tracker.writeInterval(50)
tracker.maxLength(200)
tracker.minLength(20)
tracker.maxSamplingPerStep(100)
tracker.numberOfThreads(n_threads)
duration = time.time() - start_time
print("Initialize Trekker: {:.2f} ms".format(1e3 * duration))
repos = [0., 0., 0., 0., 0., 0.]
brain_actor = load_stl(brain_inv_path,
ren,
opacity=.1,
colour=[1.0, 1.0, 1.0],
replace=repos,
user_matrix=np.identity(4))
bds = brain_actor.GetBounds()
print("Y length: {} --- Bounds: {}".format(bds[3] - bds[2], bds))
# repos = [0., 0., 0., 0., 0., 0.]
# brain_actor_mri = load_stl(brain_path, ren, opacity=.1, colour=[0.0, 1.0, 0.0], replace=repos, user_matrix=np.linalg.inv(affine))
# bds = brain_actor_mri.GetBounds()
# print("Y length: {} --- Bounds: {}".format(bds[3] - bds[2], bds))
repos = [0., 256., 0., 0., 0., 0.]
# brain_inv_actor = load_stl(brain_inv_path, ren, colour="SkinColor", opacity=0.5, replace=repos, user_matrix=np.linalg.inv(affine))
brain_inv_actor = load_stl(brain_inv_path,
ren,
colour="SkinColor",
opacity=.1,
replace=repos)
# Add axes to scene origin
if SHOW_AXES:
add_line(ren, [0, 0, 0], [150, 0, 0], color=[1.0, 0.0, 0.0])
add_line(ren, [0, 0, 0], [0, 150, 0], color=[0.0, 1.0, 0.0])
add_line(ren, [0, 0, 0], [0, 0, 150], color=[0.0, 0.0, 1.0])
# Show tracks
repos_trk = [0., -256., 0., 0., 0., 0.]
matrix_vtk = vtk.vtkMatrix4x4()
trans = np.identity(4)
trans[1, -1] = repos_trk[1]
final_matrix = np.linalg.inv(affine) @ trans
print("final_matrix: {}".format(final_matrix))
for row in range(0, 4):
for col in range(0, 4):
matrix_vtk.SetElement(row, col, final_matrix[row, col])
root = vtk.vtkMultiBlockDataSet()
# for i in range(10):
# seed = np.array([[-8.49, -8.39, 2.5]])
seed = np.array([[27.53, -77.37, 46.42]])
tracts_actor = dti.single_block(tracker, seed, n_tracts, root, matrix_vtk)
# out_list = []
count_tracts = 0
start_time_all = time.time()
for n in range(round(n_tracts / n_threads)):
branch = dti.multi_block(tracker, seed, n_threads)
count_tracts += branch.GetNumberOfBlocks()
# start_time = time.time()
# root = dti.tracts_root(out_list, root, n)
root.SetBlock(n, branch)
# duration = time.time() - start_time
# print("Compute root {}: {:.2f} ms".format(n, 1e3*duration))
duration = time.time() - start_time_all
print("Compute multi {}: {:.2f} ms".format(n, 1e3 * duration))
print("Number computed tracts {}".format(count_tracts))
print("Number computed branches {}".format(root.GetNumberOfBlocks()))
start_time = time.time()
tracts_actor = dti.compute_actor(root, matrix_vtk)
duration = time.time() - start_time
print("Compute actor: {:.2f} ms".format(1e3 * duration))
# Assign actor to the renderer
ren.AddActor(brain_actor)
ren.AddActor(brain_inv_actor)
start_time = time.time()
ren.AddActor(tracts_actor)
duration = time.time() - start_time
print("Add actor: {:.2f} ms".format(1e3 * duration))
# ren.AddActor(brain_actor_mri)
# Enable user interface interactor
iren.Initialize()
ren_win.Render()
iren.Start()
def _run_interface(self, runtime):
is_sbref = isdefined(self.inputs.sbref_file)
ref_input = self.inputs.sbref_file if is_sbref else self.inputs.in_file
if self.inputs.multiecho:
if len(ref_input) < 2:
input_name = "sbref_file" if is_sbref else "in_file"
raise ValueError("Argument 'multiecho' is True but "
f"'{input_name}' has only one element.")
else:
# Select only the first echo (see LIMITATION above for SBRefs)
ref_input = ref_input[:1]
elif not is_sbref and len(ref_input) > 1:
raise ValueError(
"Input 'in_file' cannot point to more than one file "
"for single-echo BOLD datasets.")
# Build the nibabel spatial image we will work with
ref_im = []
for im_i in ref_input:
nib_i = nb.squeeze_image(nb.load(im_i))
if nib_i.dataobj.ndim == 3:
ref_im.append(nib_i)
elif nib_i.dataobj.ndim == 4:
ref_im += nb.four_to_three(nib_i)
ref_im = nb.squeeze_image(nb.concat_images(ref_im))
# Volumes to discard only makes sense with BOLD inputs.
if not is_sbref:
n_volumes_to_discard = _get_vols_to_discard(ref_im)
out_ref_fname = os.path.join(runtime.cwd, "ref_bold.nii.gz")
else:
n_volumes_to_discard = 0
out_ref_fname = os.path.join(runtime.cwd, "ref_sbref.nii.gz")
# Set interface outputs
self._results["n_volumes_to_discard"] = n_volumes_to_discard
self._results["ref_image"] = out_ref_fname
# Slicing may induce inconsistencies with shape-dependent values in extensions.
# For now, remove all. If this turns out to be a mistake, we can select extensions
# that don't break pipeline stages.
ref_im.header.extensions.clear()
# If reference is only 1 volume, return it directly
if ref_im.dataobj.ndim == 3:
ref_im.to_filename(out_ref_fname)
return runtime
if n_volumes_to_discard == 0:
if ref_im.shape[-1] > 40:
ref_im = nb.Nifti1Image(ref_im.dataobj[:, :, :, 20:40],
ref_im.affine, ref_im.header)
ref_name = os.path.join(runtime.cwd, "slice.nii.gz")
ref_im.to_filename(ref_name)
if self.inputs.mc_method == "AFNI":
res = afni.Volreg(
in_file=ref_name,
args="-Fourier -twopass",
zpad=4,
outputtype="NIFTI_GZ",
).run()
elif self.inputs.mc_method == "FSL":
res = fsl.MCFLIRT(in_file=ref_name,
ref_vol=0,
interpolation="sinc").run()
mc_slice_nii = nb.load(res.outputs.out_file)
median_image_data = np.median(mc_slice_nii.get_fdata(), axis=3)
else:
median_image_data = np.median(
ref_im.dataobj[:, :, :, :n_volumes_to_discard], axis=3)
nb.Nifti1Image(median_image_data, ref_im.affine,
ref_im.header).to_filename(out_ref_fname)
return runtime
def conform_data(in_file,
out_file=None,
out_size=(256, 256, 256),
out_zooms=(1.0, 1.0, 1.0),
order=3):
"""Conform the input dataset to the canonical orientation.
Parameters
----------
in_file: str - Path
Path to the input MRI volume to conform.
out_file: str - Path, default=None
Path to save the conformed volume. By default the
volume is saved as /tmp/conformed.nii.gz
out_size: tuple of size 3, optional, default=(256, 256, 256)
The shape to conform the 3D volume to.
out_zooms: tuple of size 3, optional, default=(1.0, 1.0, 1.0)
Factors to normalize voxel size to.
order: int, optional, default=3
Order of the spline interpolation. The order has to be in
the range 0-5.
Returns
-------
str - Path
The path to where the conformed volume is saved.
"""
if isinstance(in_file, (str, Path)):
in_file = nb.load(in_file)
# Drop axes with just 1 sample (typically, a 3D file stored as 4D)
in_file = nb.squeeze_image(in_file)
dtype = in_file.header.get_data_dtype()
# Reorient to closest canonical
in_file = nb.as_closest_canonical(in_file)
data = np.asanyarray(in_file.dataobj)
# Calculate the factors to normalize voxel size to out_zooms
normed = np.array(out_zooms) / np.array(in_file.header.get_zooms()[:3])
# Calculate the new indexes, sampling at 1mm^3 with out_size sizes.
# center_ijk = 0.5 * (np.array(in_file.shape) - 1)
new_ijk = normed[:, np.newaxis] * np.array(
np.meshgrid(
np.arange(out_size[0]),
np.arange(out_size[1]),
np.arange(out_size[2]),
indexing="ij",
)).reshape((3, -1))
offset = 0.5 * (np.max(new_ijk, axis=1) - np.array(in_file.shape))
# Align the centers of the two sampling extents
new_ijk -= offset[:, np.newaxis]
# Resample data in the new grid
resampled = map_coordinates(
data,
new_ijk,
output=dtype,
order=order,
mode="constant",
cval=0,
prefilter=True,
).reshape(out_size)
resampled[resampled < 0] = 0
# Create a new x-form affine, aligned with cardinal axes, 1mm3 and centered.
newaffine = np.eye(4)
newaffine[:3, 3] = -0.5 * (np.array(out_size) - 1)
nii = nb.Nifti1Image(resampled, newaffine, None)
if out_file is None:
out_file = Path(mkdtemp()) / "conformed.nii.gz"
out_file = Path(out_file).absolute()
nii.to_filename(out_file)
return out_file
def ReadAnalyze(filename):
anlz = squeeze_image(AnalyzeImage.from_filename(filename))
return anlz
def ReadNifti(filename):
nft = squeeze_image(Nifti1Image.from_filename(filename))
return nft
def main():
SHOW_AXES = True
SHOW_SCENE_AXES = True
SHOW_COIL_AXES = True
SHOW_SKIN = True
SHOW_BRAIN = True
SHOW_COIL = True
SHOW_MARKERS = True
TRANSF_COIL = True
SHOW_PLANE = False
SELECT_LANDMARKS = 'scalp' # 'all', 'mri' 'scalp'
SAVE_ID = False
AFFINE_IMG = True
NO_SCALE = True
SCREENSHOT = False
reorder = [0, 2, 1]
flipx = [True, False, False]
# reorder = [0, 1, 2]
# flipx = [False, False, False]
# default folder and subject
# subj = 's03'
subj = 'EEGTA04'
id_extra = False # 8, 9, 10, 12, False
# data_dir = os.environ['OneDriveConsumer'] + '\\data\\nexstim_coord\\'
data_dir = r'P:\tms_eeg\mTMS\projects\2019 EEG-based target automatization\Analysis\EEG electrode transformation'
# filenames
# coil_file = data_dir + 'magstim_fig8_coil.stl'
coil_file = os.environ[
'OneDrive'] + '\\data\\nexstim_coord\\magstim_fig8_coil.stl'
if id_extra:
coord_file = data_dir + 'ppM1_eximia_%s_%d.txt' % (subj, id_extra)
else:
coord_file = nav_dir + 'ppM1_eximia_%s.txt' % subj
# img_file = data_subj + subj + '.nii'
img_file = data_dir + 'mri\\ppM1_%s\\ppM1_%s.nii' % (subj, subj)
brain_file = simnibs_dir + "wm.stl"
skin_file = simnibs_dir + "skin.stl"
if id_extra:
output_file = nav_dir + 'transf_mat_%s_%d' % (subj, id_extra)
else:
output_file = nav_dir + 'transf_mat_%s' % subj
coords = lc.load_nexstim(coord_file)
# red, green, blue, maroon (dark red),
# olive (shitty green), teal (petrol blue), yellow, orange
col = [[1., 0., 0.], [0., 1., 0.], [0., 0., 1.], [1., .0, 1.],
[.5, .5, 0.], [0., .5, .5], [1., 1., 0.], [1., .4, .0]]
# extract image header shape and affine transformation from original nifti file
imagedata = nb.squeeze_image(nb.load(img_file))
imagedata = nb.as_closest_canonical(imagedata)
imagedata.update_header()
pix_dim = imagedata.header.get_zooms()
img_shape = imagedata.header.get_data_shape()
print("Pixel size: \n")
print(pix_dim)
print("\nImage shape: \n")
print(img_shape)
affine_aux = imagedata.affine.copy()
if NO_SCALE:
scale, shear, angs, trans, persp = tf.decompose_matrix(
imagedata.affine)
affine_aux = tf.compose_matrix(scale=None,
shear=shear,
angles=angs,
translate=trans,
perspective=persp)
if AFFINE_IMG:
affine = affine_aux
# if NO_SCALE:
# scale, shear, angs, trans, persp = tf.decompose_matrix(imagedata.affine)
# affine = tf.compose_matrix(scale=None, shear=shear, angles=angs, translate=trans, perspective=persp)
else:
affine = np.identity(4)
# affine_I = np.identity(4)
# create a camera, render window and renderer
camera = vtk.vtkCamera()
camera.SetPosition(0, 1000, 0)
camera.SetFocalPoint(0, 0, 0)
camera.SetViewUp(0, 0, 1)
camera.ComputeViewPlaneNormal()
camera.Azimuth(90.0)
camera.Elevation(10.0)
ren = vtk.vtkRenderer()
ren.SetActiveCamera(camera)
ren.ResetCamera()
camera.Dolly(1.5)
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetSize(800, 800)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
if SELECT_LANDMARKS == 'mri':
# MRI landmarks
coord_mri = [['Nose/Nasion'], ['Left ear'], ['Right ear'],
['Coil Loc'], ['EF max']]
pts_ref = [1, 2, 3, 7, 10]
elif SELECT_LANDMARKS == 'all':
# all coords
coord_mri = [['Nose/Nasion'], ['Left ear'], ['Right ear'],
['Nose/Nasion'], ['Left ear'], ['Right ear'],
['Coil Loc'], ['EF max']]
pts_ref = [1, 2, 3, 5, 4, 6, 7, 10]
elif SELECT_LANDMARKS == 'scalp':
# scalp landmarks
coord_mri = [['Nose/Nasion'], ['Left ear'], ['Right ear'],
['Coil Loc'], ['EF max']]
hdr_mri = [
'Nose/Nasion', 'Left ear', 'Right ear', 'Coil Loc', 'EF max'
]
pts_ref = [5, 4, 6, 7, 10]
coords_np = np.zeros([len(pts_ref), 3])
for n, pts_id in enumerate(pts_ref):
# to keep in the MRI space use the identity as the affine
# coord_aux = n2m.coord_change(coords[pts_id][1:], img_shape, affine_I, flipx, reorder)
# affine_trans = affine_I.copy()
# affine_trans = affine.copy()
# affine_trans[:3, -1] = affine[:3, -1]
coord_aux = n2m.coord_change(coords[pts_id][1:], img_shape, affine,
flipx, reorder)
coords_np[n, :] = coord_aux
[coord_mri[n].append(s) for s in coord_aux]
if SHOW_MARKERS:
marker_actor = add_marker(coord_aux, ren, col[n])
if id_extra:
# compare coil locations in experiments with 8, 9, 10 and 12 mm shifts
# MRI Nexstim space: 8, 9, 10, 12 mm coil locations
# coord_others = [[122.2, 198.8, 99.7],
# [121.1, 200.4, 100.1],
# [120.5, 200.7, 98.2],
# [117.7, 202.9, 96.6]]
if AFFINE_IMG:
# World space: 8, 9, 10, 12 mm coil locations
coord_others = [
[-42.60270233154297, 28.266497802734378, 81.02450256347657],
[-41.50270233154296, 28.66649780273437, 82.62450256347657],
[-40.90270233154297, 26.766497802734378, 82.92450256347655],
[-38.10270233154297, 25.16649780273437, 85.12450256347657]
]
else:
# MRI space reordered and flipped: 8, 9, 10, 12 mm coil locations
coord_others = [[27.8, 99.7, 198.8], [28.9, 100.1, 200.4],
[29.5, 98.2, 200.7], [32.3, 96.6, 202.9]]
col_others = [[1., 0., 0.], [0., 1., 0.], [0., 0., 1.], [0., 0., 0.]]
for n, c in enumerate(coord_others):
marker_actor = add_marker(c, ren, col_others[n])
print('\nOriginal coordinates from Nexstim: \n')
[print(s) for s in coords]
print('\nMRI coordinates flipped and reordered: \n')
[print(s) for s in coords_np]
print('\nTransformed coordinates to MRI space: \n')
[print(s) for s in coord_mri]
# coil location, normal vector and direction vector
coil_loc = coord_mri[-2][1:]
coil_norm = coords[8][1:]
coil_dir = coords[9][1:]
# creating the coil coordinate system by adding a point in the direction of each given coil vector
# the additional vector is just the cross product from coil direction and coil normal vectors
# origin of the coordinate system is the coil location given by Nexstim
# the vec_length is to allow line creation with visible length in VTK scene
vec_length = 75
p1 = coords[7][1:]
p2 = [x + vec_length * y for x, y in zip(p1, coil_norm)]
p2_norm = n2m.coord_change(p2, img_shape, affine, flipx, reorder)
p2 = [x + vec_length * y for x, y in zip(p1, coil_dir)]
p2_dir = n2m.coord_change(p2, img_shape, affine, flipx, reorder)
coil_face = np.cross(coil_norm, coil_dir)
p2 = [x - vec_length * y for x, y in zip(p1, coil_face.tolist())]
p2_face = n2m.coord_change(p2, img_shape, affine, flipx, reorder)
# Coil face unit vector (X)
u1 = np.asarray(p2_face) - np.asarray(coil_loc)
u1_n = u1 / np.linalg.norm(u1)
# Coil direction unit vector (Y)
u2 = np.asarray(p2_dir) - np.asarray(coil_loc)
u2_n = u2 / np.linalg.norm(u2)
# Coil normal unit vector (Z)
u3 = np.asarray(p2_norm) - np.asarray(coil_loc)
u3_n = u3 / np.linalg.norm(u3)
transf_matrix = np.identity(4)
if TRANSF_COIL:
transf_matrix[:3, 0] = u1_n
transf_matrix[:3, 1] = u2_n
transf_matrix[:3, 2] = u3_n
transf_matrix[:3, 3] = coil_loc[:]
# the absolute value of the determinant indicates the scaling factor
# the sign of the determinant indicates how it affects the orientation: if positive maintain the
# original orientation and if negative inverts all the orientations (flip the object inside-out)'
# the negative determinant is what makes objects in VTK scene to become black
print('Transformation matrix: \n', transf_matrix, '\n')
print('Determinant: ', np.linalg.det(transf_matrix))
if SAVE_ID:
coord_dict = {
'm_affine': transf_matrix,
'coords_labels': hdr_mri,
'coords': coords_np
}
io.savemat(output_file + '.mat', coord_dict)
hdr_names = ';'.join(
['m' + str(i) + str(j) for i in range(1, 5) for j in range(1, 5)])
np.savetxt(output_file + '.txt',
transf_matrix.reshape([1, 16]),
delimiter=';',
header=hdr_names)
if SHOW_BRAIN:
if AFFINE_IMG:
brain_actor = load_stl(brain_file,
ren,
colour=[0., 1., 1.],
opacity=1.)
else:
# to visualize brain in MRI space
brain_actor = load_stl(brain_file,
ren,
colour=[0., 1., 1.],
opacity=1.,
user_matrix=np.linalg.inv(affine_aux))
if SHOW_SKIN:
if AFFINE_IMG:
skin_actor = load_stl(skin_file,
ren,
colour="SkinColor",
opacity=.4)
else:
# to visualize skin in MRI space
skin_actor = load_stl(skin_file,
ren,
colour="SkinColor",
opacity=.4,
user_matrix=np.linalg.inv(affine_aux))
if SHOW_COIL:
# reposition STL object prior to transformation matrix
# [translation_x, translation_y, translation_z, rotation_x, rotation_y, rotation_z]
# old translation when using Y as normal vector
# repos = [0., -6., 0., 0., -90., 90.]
# Translate coil loc coordinate to coil bottom
# repos = [0., 0., 5.5, 0., 0., 180.]
repos = [0., 0., 0., 0., 0., 180.]
act_coil = load_stl(coil_file,
ren,
replace=repos,
user_matrix=transf_matrix,
opacity=.3)
if SHOW_PLANE:
act_plane = add_plane(ren, user_matrix=transf_matrix)
# Add axes to scene origin
if SHOW_AXES:
add_line(ren, [0, 0, 0], [150, 0, 0], color=[1.0, 0.0, 0.0])
add_line(ren, [0, 0, 0], [0, 150, 0], color=[0.0, 1.0, 0.0])
add_line(ren, [0, 0, 0], [0, 0, 150], color=[0.0, 0.0, 1.0])
# Add axes to object origin
if SHOW_COIL_AXES:
add_line(ren, coil_loc, p2_norm, color=[.0, .0, 1.0])
add_line(ren, coil_loc, p2_dir, color=[.0, 1.0, .0])
add_line(ren, coil_loc, p2_face, color=[1.0, .0, .0])
# Add interactive axes to scene
if SHOW_SCENE_AXES:
axes = vtk.vtkAxesActor()
widget = vtk.vtkOrientationMarkerWidget()
widget.SetOutlineColor(0.9300, 0.5700, 0.1300)
widget.SetOrientationMarker(axes)
widget.SetInteractor(iren)
# widget.SetViewport(0.0, 0.0, 0.4, 0.4)
widget.SetEnabled(1)
widget.InteractiveOn()
if SCREENSHOT:
# screenshot of VTK scene
w2if = vtk.vtkWindowToImageFilter()
w2if.SetInput(ren_win)
w2if.Update()
writer = vtk.vtkPNGWriter()
writer.SetFileName("screenshot.png")
writer.SetInput(w2if.GetOutput())
writer.Write()
# Enable user interface interactor
# ren_win.Render()
ren.ResetCameraClippingRange()
iren.Initialize()
iren.Start()
def main():
SHOW_AXES = True
AFFINE_IMG = True
NO_SCALE = True
n_tracts = 240
# n_tracts = 24
# n_threads = 2*psutil.cpu_count()
img_shift = 256 # 255
data_dir = os.environ.get('OneDrive') + r'\data\dti_navigation\baran\anat_reg_improve_20200609'
data_dir = data_dir.encode('utf-8')
# FOD_path = 'Baran_FOD.nii'
# trk_path = os.path.join(data_dir, FOD_path)
# data_dir = b'C:\Users\deoliv1\OneDrive\data\dti'
stl_path = b'wm_orig_smooth_world.stl'
brain_path = os.path.join(data_dir, stl_path)
# data_dir = b'C:\Users\deoliv1\OneDrive\data\dti'
stl_path = b'wm_2.stl'
brain_simnibs_path = os.path.join(data_dir, stl_path)
stl_path = b'wm.stl'
brain_inv_path = os.path.join(data_dir, stl_path)
nii_path = b'Baran_FOD.nii'
trk_path = os.path.join(data_dir, nii_path)
nii_path = b'Baran_T1_inFODspace.nii'
img_path = os.path.join(data_dir, nii_path)
nii_path = b'Baran_trekkerACTlabels_inFODspace.nii'
act_path = os.path.join(data_dir, nii_path)
stl_path = b'magstim_fig8_coil.stl'
coil_path = os.path.join(data_dir, stl_path)
imagedata = nb.squeeze_image(nb.load(img_path.decode('utf-8')))
imagedata = nb.as_closest_canonical(imagedata)
imagedata.update_header()
pix_dim = imagedata.header.get_zooms()
img_shape = imagedata.header.get_data_shape()
act_data = nb.squeeze_image(nb.load(act_path.decode('utf-8')))
act_data = nb.as_closest_canonical(act_data)
act_data.update_header()
act_data_arr = act_data.get_fdata()
# print(imagedata.header)
print("pix_dim: {}, img_shape: {}".format(pix_dim, img_shape))
if AFFINE_IMG:
affine = imagedata.affine
if NO_SCALE:
scale, shear, angs, trans, persp = tf.decompose_matrix(imagedata.affine)
affine = tf.compose_matrix(scale=None, shear=shear, angles=angs, translate=trans, perspective=persp)
else:
affine = np.identity(4)
print("affine: {0}\n".format(affine))
# Create a rendering window and renderer
ren = vtk.vtkRenderer()
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetSize(800, 800)
# Create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
minFODamp = np.arange(0.01, 0.11, 0.01)
dataSupportExponent = np.arange(0.1, 1.1, 0.1)
# COMBINATION 1
# tracker = minFODamp(0.01)
# tracker = dataSupportExponent(0.1)
# COMBINATION "n"
# tracker = minFODamp(0.01 * n)
# tracker = dataSupportExponent(0.1 * n)
start_time = time.time()
trekker_cfg = {'seed_max': 1, 'step_size': 0.1, 'min_fod': 0.1, 'probe_quality': 3,
'max_interval': 1, 'min_radius_curv': 0.8, 'probe_length': 0.4,
'write_interval': 50, 'numb_threads': '', 'max_lenth': 200,
'min_lenth': 20, 'max_sampling_step': 100}
tracker = Trekker.initialize(trk_path)
tracker, n_threads = dti.set_trekker_parameters(tracker, trekker_cfg)
duration = time.time() - start_time
print("Initialize Trekker: {:.2f} ms".format(1e3*duration))
repos = [0., -img_shift, 0., 0., 0., 0.]
# brain_actor = load_stl(brain_inv_path, ren, opacity=1., colour=[1.0, 1.0, 1.0], replace=repos, user_matrix=np.identity(4))
# the one always been used
brain_actor = load_stl(brain_simnibs_path, ren, opacity=1., colour=[1.0, 1.0, 1.0], replace=repos, user_matrix=np.linalg.inv(affine))
# bds = brain_actor.GetBounds()
# print("Y length: {} --- Bounds: {}".format(bds[3] - bds[2], bds))
# invesalius surface
# repos = [0., 0., 0., 0., 0., 0.]
# brain_actor = load_stl(brain_inv_path, ren, opacity=.5, colour=[1.0, .5, .5], replace=repos, user_matrix=np.identity(4))
# repos = [0., 0., 0., 0., 0., 0.]
# brain_actor_mri = load_stl(brain_path, ren, opacity=.1, colour=[0.0, 1.0, 0.0], replace=repos, user_matrix=np.linalg.inv(affine))
# bds = brain_actor_mri.GetBounds()
# print("Y length: {} --- Bounds: {}".format(bds[3] - bds[2], bds))
# repos = [0., 256., 0., 0., 0., 0.]
# brain_inv_actor = load_stl(brain_inv_path, ren, colour="SkinColor", opacity=0.5, replace=repos, user_matrix=np.linalg.inv(affine))
# brain_inv_actor = load_stl(brain_inv_path, ren, colour="SkinColor", opacity=.6, replace=repos)
# bds = brain_inv_actor.GetBounds()
# print("Reposed: Y length: {} --- Bounds: {}".format(bds[3] - bds[2], bds))
# Add axes to scene origin
if SHOW_AXES:
add_line(ren, [0, 0, 0], [150, 0, 0], color=[1.0, 0.0, 0.0])
add_line(ren, [0, 0, 0], [0, 150, 0], color=[0.0, 1.0, 0.0])
add_line(ren, [0, 0, 0], [0, 0, 150], color=[0.0, 0.0, 1.0])
# Show tracks
repos_trk = [0., -img_shift, 0., 0., 0., 0.]
# repos_trk = [0., 0., 0., 0., 0., 0.]
matrix_vtk = vtk.vtkMatrix4x4()
trans = np.identity(4)
trans[1, -1] = repos_trk[1]
final_matrix = np.linalg.inv(affine) @ trans
print("final_matrix: {}".format(final_matrix))
for row in range(0, 4):
for col in range(0, 4):
matrix_vtk.SetElement(row, col, final_matrix[row, col])
root = vtk.vtkMultiBlockDataSet()
# for i in range(10):
# seed = np.array([[-8.49, -8.39, 2.5]])
# seed = np.array([[27.53, -77.37, 46.42]])
# from the invesalius exported fiducial markers you have to multiply the Y coordinate by -1 to
# transform to the regular 3D invesalius space where coil location is saved
fids_inv = np.array([[168.300, -126.600, 97.000],
[9.000, -120.300, 93.700],
[90.100, -33.500, 150.000]])
for n in range(3):
fids_actor = add_marker(fids_inv[n, :], ren, [1., 0., 0.], radius=2)
seed = np.array([[-25.66, -30.07, 54.91]])
coil_pos = [40.17, 152.28, 235.78, -18.22, -25.27, 64.99]
m_coil = coil_transform_pos(coil_pos)
repos = [0., 0., 0., 0., 0., 90.]
coil_actor = load_stl(coil_path, ren, opacity=.6, replace=repos, colour=[1., 1., 1.], user_matrix=m_coil)
# coil_actor = load_stl(coil_path, ren, opacity=.6, replace=repos, colour=[1., 1., 1.])
# create coil vectors
vec_length = 75
print(m_coil.shape)
p1 = m_coil[:-1, -1]
print(p1)
coil_dir = m_coil[:-1, 0]
coil_face = m_coil[:-1, 1]
p2_face = p1 + vec_length * coil_face
p2_dir = p1 + vec_length * coil_dir
coil_norm = np.cross(coil_dir, coil_face)
p2_norm = p1 - vec_length * coil_norm
add_line(ren, p1, p2_dir, color=[1.0, .0, .0])
add_line(ren, p1, p2_face, color=[.0, 1.0, .0])
add_line(ren, p1, p2_norm, color=[.0, .0, 1.0])
colours = [[1., 0., 0.], [0., 1., 0.], [0., 0., 1.], [1., .0, 1.],
[.5, .5, 0.], [0., .5, .5], [1., 1., 0.], [1., .4, .0]]
marker_actor = add_marker(p1, ren, colours[0], radius=1)
# p1_change = n2m.coord_change(p1)
p1_change = p1.copy()
p1_change[1] = -p1_change[1]
# p1_change[1] += img_shift
marker_actor2 = add_marker(p1_change, ren, colours[1], radius=1)
offset = 40
coil_norm = coil_norm/np.linalg.norm(coil_norm)
coord_offset_nav = p1 - offset * coil_norm
marker_actor_seed_nav = add_marker(coord_offset_nav, ren, colours[3], radius=1)
coord_offset_mri = coord_offset_nav.copy()
coord_offset_mri[1] += img_shift
marker_actor_seed_nav = add_marker(coord_offset_mri, ren, colours[3], radius=1)
coord_mri_label = [int(s) for s in coord_offset_mri]
print("offset MRI: {}, and label: {}".format(coord_mri_label,
act_data_arr[tuple(coord_mri_label)]))
offset_list = 10 + np.arange(0, 31, 3)
coord_offset_list = p1 - np.outer(offset_list, coil_norm)
coord_offset_list += [0, img_shift, 0]
coord_offset_list = coord_offset_list.astype(int).tolist()
# for pt in coord_offset_list:
# print(pt)
# if act_data_arr[tuple(pt)] == 2:
# cl = colours[5]
# else:
# cl = colours[4]
# _ = add_marker(pt, ren, cl)
x = np.arange(-4, 5, 2)
y = np.arange(-4, 5, 2)
z = 10 + np.arange(0, 31, 3)
xv, yv, zv = np.meshgrid(x, y, - z)
coord_grid = np.array([xv, yv, zv])
start_time = time.time()
for p in range(coord_grid.shape[1]):
for n in range(coord_grid.shape[2]):
for m in range(coord_grid.shape[3]):
pt = coord_grid[:, p, n, m]
pt = np.append(pt, 1)
pt_tr = m_coil @ pt[:, np.newaxis]
pt_tr = np.squeeze(pt_tr[:3]).astype(int) + [0, img_shift, 0]
pt_tr = tuple(pt_tr.tolist())
if act_data_arr[pt_tr] == 2:
cl = colours[6]
elif act_data_arr[pt_tr] == 1:
cl = colours[7]
else:
cl = [1., 1., 1.]
# print(act_data_arr[pt_tr])
_ = add_marker(pt_tr, ren, cl, radius=1)
duration = time.time() - start_time
print("Compute coil grid: {:.2f} ms".format(1e3*duration))
start_time = time.time()
# create grid of points
grid_number = x.shape[0]*y.shape[0]*z.shape[0]
coord_grid = coord_grid.reshape([3, grid_number]).T
# sort grid from distance to the origin/coil center
coord_list = coord_grid[np.argsort(np.linalg.norm(coord_grid, axis=1)), :]
# make the coordinates homogeneous
coord_list_w = np.append(coord_list.T, np.ones([1, grid_number]), axis=0)
# apply the coil transformation matrix
coord_list_w_tr = m_coil @ coord_list_w
# convert to int so coordinates can be used as indices in the MRI image space
coord_list_w_tr = coord_list_w_tr[:3, :].T.astype(int) + np.array([[0, img_shift, 0]])
# extract the first occurrence of a specific label from the MRI image
labs = act_data_arr[coord_list_w_tr[..., 0], coord_list_w_tr[..., 1], coord_list_w_tr[..., 2]]
lab_first = np.argmax(labs == 1)
if labs[lab_first] == 1:
pt_found = coord_list_w_tr[lab_first, :]
_ = add_marker(pt_found, ren, [0., 0., 1.], radius=1)
# convert coordinate back to invesalius 3D space
pt_found_inv = pt_found - np.array([0., img_shift, 0.])
# convert to world coordinate space to use as seed for fiber tracking
pt_found_tr = np.append(pt_found, 1)[np.newaxis, :].T
pt_found_tr = affine @ pt_found_tr
pt_found_tr = pt_found_tr[:3, 0, np.newaxis].T
duration = time.time() - start_time
print("Compute coil grid fast: {:.2f} ms".format(1e3*duration))
# create tracts
count_tracts = 0
start_time_all = time.time()
# uncertain_params = list(zip(dataSupportExponent, minFODamp))
for n in range(0, round(n_tracts/n_threads)):
# branch = dti.multi_block(tracker, seed, n_threads)
# branch = dti.multi_block(tracker, pt_found_tr, n_threads)
# rescale n so that there is no 0 opacity tracts
n_param = (n % 10) + 1
branch = dti.multi_block_uncertainty(tracker, pt_found_tr, n_threads, n_param)
count_tracts += branch.GetNumberOfBlocks()
# start_time = time.time()
# root = dti.tracts_root(out_list, root, n)
root.SetBlock(n, branch)
# duration = time.time() - start_time
# print("Compute root {}: {:.2f} ms".format(n, 1e3*duration))
duration = time.time() - start_time_all
print("Compute multi {}: {:.2f} ms".format(n, 1e3*duration))
print("Number computed tracts {}".format(count_tracts))
print("Number computed branches {}".format(root.GetNumberOfBlocks()))
start_time = time.time()
tracts_actor = dti.compute_actor(root, matrix_vtk)
duration = time.time() - start_time
print("Compute actor: {:.2f} ms".format(1e3*duration))
# Assign actor to the renderer
# ren.AddActor(brain_actor)
# ren.AddActor(brain_inv_actor)
# ren.AddActor(coil_actor)
start_time = time.time()
ren.AddActor(tracts_actor)
duration = time.time() - start_time
print("Add actor: {:.2f} ms".format(1e3*duration))
# ren.AddActor(brain_actor_mri)
planex, planey, planez = raw_image(act_path, ren)
planex.SetInteractor(iren)
planex.On()
planey.SetInteractor(iren)
planey.On()
planez.SetInteractor(iren)
planez.On()
_ = add_marker(np.squeeze(seed).tolist(), ren, [0., 1., 0.], radius=1)
_ = add_marker(np.squeeze(pt_found_tr).tolist(), ren, [1., 0., 0.], radius=1)
_ = add_marker(pt_found_inv, ren, [1., 1., 0.], radius=1)
# Enable user interface interactor
iren.Initialize()
ren_win.Render()
iren.Start()
def _run_interface(self, runtime):
img = nb.load(self.inputs.in_file)
# If reference is 3D, return it directly
if img.dataobj.ndim == 3:
self._results["out_file"] = self.inputs.in_file
self._results["out_volumes"] = self.inputs.in_file
self._results["out_drift"] = [1.0]
return runtime
fname = partial(fname_presuffix,
self.inputs.in_file,
newpath=runtime.cwd)
# Slicing may induce inconsistencies with shape-dependent values in extensions.
# For now, remove all. If this turns out to be a mistake, we can select extensions
# that don't break pipeline stages.
img.header.extensions.clear()
img = nb.squeeze_image(img)
# If reference was 4D, but single-volume - write out squeezed and return.
if img.dataobj.ndim == 3:
self._results["out_file"] = fname(suffix="_squeezed")
img.to_filename(self._results["out_file"])
self._results["out_volumes"] = self.inputs.in_file
self._results["out_drift"] = [1.0]
return runtime
img_len = img.shape[3]
t_mask = (self.inputs.t_mask
if isdefined(self.inputs.t_mask) else [True] * img_len)
if len(t_mask) != img_len:
raise ValueError(
f"Image length ({img_len} timepoints) unmatched by mask ({len(t_mask)})"
)
n_volumes = sum(t_mask)
if n_volumes < 1:
raise ValueError(
"At least one volume should be selected for slicing")
self._results["out_file"] = fname(suffix="_average")
self._results["out_volumes"] = fname(suffix="_sliced")
sliced = nb.concat_images(
i for i, t in zip(nb.four_to_three(img), t_mask) if t)
data = sliced.get_fdata(dtype="float32")
# Data can come with outliers showing very high numbers - preemptively prune
data = np.clip(
data,
a_min=0.0 if self.inputs.nonnegative else np.percentile(data, 0.2),
a_max=np.percentile(data, 99.8),
)
gs_drift = np.mean(data, axis=(0, 1, 2))
gs_drift /= gs_drift.max()
self._results["out_drift"] = [float(i) for i in gs_drift]
data /= gs_drift
data = np.clip(
data,
a_min=0.0 if self.inputs.nonnegative else data.min(),
a_max=data.max(),
)
sliced.__class__(data, sliced.affine, sliced.header).to_filename(
self._results["out_volumes"])
if n_volumes == 1:
nb.squeeze_image(sliced).to_filename(self._results["out_file"])
self._results["out_drift"] = [1.0]
return runtime
if self.inputs.mc_method == "AFNI":
from nipype.interfaces.afni import Volreg
res = Volreg(
in_file=self._results["out_volumes"],
args="-Fourier -twopass",
zpad=4,
outputtype="NIFTI_GZ",
).run()
# self._results["out_hmc"] = res.outputs.oned_matrix_save
elif self.inputs.mc_method == "FSL":
from nipype.interfaces.fsl import MCFLIRT
res = MCFLIRT(
in_file=self._results["out_volumes"],
ref_vol=0,
interpolation="sinc",
).run()
self._results["out_hmc"] = res.outputs.mat_file
if self.inputs.mc_method:
data = nb.load(res.outputs.out_file).get_fdata(dtype="float32")
data = np.clip(
data,
a_min=0.0 if self.inputs.nonnegative else data.min(),
a_max=data.max(),
)
sliced.__class__(np.median(data, axis=3), sliced.affine,
sliced.header).to_filename(self._results["out_file"])
return runtime
def main():
SHOW_AXES = True
AFFINE_IMG = True
NO_SCALE = True
data_dir = b'C:\Users\deoliv1\OneDrive - Aalto University\data\dti_navigation\juuso'
stl_path = b'wm_orig_smooth_world.stl'
brain_path = os.path.join(data_dir, stl_path)
stl_path = b'wm.stl'
brain_inv_path = os.path.join(data_dir, stl_path)
nii_path = b'sub-P0_dwi_FOD.nii'
trk_path = os.path.join(data_dir, nii_path)
nii_path = b'sub-P0_T1w_biascorrected.nii'
img_path = os.path.join(data_dir, nii_path)
imagedata = nb.squeeze_image(nb.load(img_path.decode('utf-8')))
imagedata = nb.as_closest_canonical(imagedata)
imagedata.update_header()
pix_dim = imagedata.header.get_zooms()
img_shape = imagedata.header.get_data_shape()
# print(imagedata.header)
print("pix_dim: {}, img_shape: {}".format(pix_dim, img_shape))
if AFFINE_IMG:
affine = imagedata.affine
if NO_SCALE:
scale, shear, angs, trans, persp = tf.decompose_matrix(imagedata.affine)
affine = tf.compose_matrix(scale=None, shear=shear, angles=angs, translate=trans, perspective=persp)
else:
affine = np.identity(4)
print("affine: {0}\n".format(affine))
# Create a rendering window and renderer
ren = vtk.vtkRenderer()
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetSize(800, 800)
# Create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
tracker = Trekker.initialize(trk_path)
tracker.seed_maxTrials(1)
tracker.minFODamp(0.1)
tracker.writeInterval(50)
tracker.maxLength(200)
tracker.minLength(20)
tracker.maxSamplingPerStep(100)
repos = [0., 0., 0., 0., 0., 0.]
brain_actor = load_stl(brain_inv_path, ren, opacity=.1, colour=[1.0, 1.0, 1.0], replace=repos, user_matrix=np.identity(4))
bds = brain_actor.GetBounds()
print("Y length: {} --- Bounds: {}".format(bds[3] - bds[2], bds))
repos = [0., 0., 0., 0., 0., 0.]
brain_actor_mri = load_stl(brain_path, ren, opacity=.1, colour=[0.0, 1.0, 0.0], replace=repos, user_matrix=np.linalg.inv(affine))
bds = brain_actor_mri.GetBounds()
print("Y length: {} --- Bounds: {}".format(bds[3] - bds[2], bds))
repos = [0., 256., 0., 0., 0., 0.]
# brain_inv_actor = load_stl(brain_inv_path, ren, colour="SkinColor", opacity=0.5, replace=repos, user_matrix=np.linalg.inv(affine))
brain_inv_actor = load_stl(brain_inv_path, ren, colour="SkinColor", opacity=.1, replace=repos)
# Add axes to scene origin
if SHOW_AXES:
add_line(ren, [0, 0, 0], [150, 0, 0], color=[1.0, 0.0, 0.0])
add_line(ren, [0, 0, 0], [0, 150, 0], color=[0.0, 1.0, 0.0])
add_line(ren, [0, 0, 0], [0, 0, 150], color=[0.0, 0.0, 1.0])
# Show tracks
repos_trk = [0., -256., 0., 0., 0., 0.]
matrix_vtk = vtk.vtkMatrix4x4()
trans = np.identity(4)
trans[1, -1] = repos_trk[1]
final_matrix = np.linalg.inv(affine) @ trans
print("final_matrix: {}".format(final_matrix))
for row in range(0, 4):
for col in range(0, 4):
matrix_vtk.SetElement(row, col, final_matrix[row, col])
for i in range(10):
seed = np.array([[-8.49, -8.39, 2.5]])
visualizeTracks(ren, ren_win, tracker, seed, user_matrix=matrix_vtk)
# Assign actor to the renderer
ren.AddActor(brain_actor)
ren.AddActor(brain_inv_actor)
ren.AddActor(brain_actor_mri)
# Enable user interface interactor
iren.Initialize()
ren_win.Render()
iren.Start()
def ReadAnalyze(filename):
anlz = squeeze_image(AnalyzeImage.from_filename(filename))
return anlz
def _advanced_clip(
in_file,
p_min=35,
p_max=99.98,
nonnegative=True,
dtype="int16",
invert=False,
newpath=None,
):
"""
Remove outliers at both ends of the intensity distribution and fit into a given dtype.
This interface tries to emulate ANTs workflows' massaging that truncate images into
the 0-255 range, and applies percentiles for clipping images.
For image registration, normalizing the intensity into a compact range (e.g., uint8)
is generally advised.
To more robustly determine the clipping thresholds, data are removed of spikes
with a median filter.
Once the thresholds are calculated, the denoised data are thrown away and the thresholds
are applied on the original image.
"""
from pathlib import Path
import nibabel as nb
import numpy as np
from scipy import ndimage
from skimage.morphology import ball
out_file = (Path(newpath or "") / "clipped.nii.gz").absolute()
# Load data
img = nb.squeeze_image(nb.load(in_file))
if len(img.shape) != 3:
raise RuntimeError(f"<{in_file}> is not a 3D file.")
data = img.get_fdata(dtype="float32")
# Calculate stats on denoised version, to preempt outliers from biasing
denoised = ndimage.median_filter(data, footprint=ball(3))
a_min = np.percentile(denoised[denoised > 0] if nonnegative else denoised,
p_min)
a_max = np.percentile(denoised[denoised > 0] if nonnegative else denoised,
p_max)
# Clip and cast
data = np.clip(data, a_min=a_min, a_max=a_max)
data -= data.min()
data /= data.max()
if invert:
data = 1.0 - data
if dtype in ("uint8", "int16"):
data = np.round(255 * data).astype(dtype)
hdr = img.header.copy()
hdr.set_data_dtype(dtype)
img.__class__(data, img.affine, hdr).to_filename(out_file)
return str(out_file)
import numpy as np
import nibabel as nib
filepath_image = "D:\\Programas\\Google Drive\\Lab\\Doutorado\\projetos\\DTI_coord_transf\\nexstim_coordinates\\OriginalImage\\5_mprage_mgh-variant.nii"
#filepath_data = "D:\\Programas\\Google Drive\\Lab\\Doutorado\\projetos\\DTI_coord_transf\\nexstim_coordinates\\nexstim_coords.mks"
filepath_data = "D:\\Programas\\Google Drive\\Lab\\Doutorado\\projetos\\DTI_coord_transf\\nexstim_coordinates\\nexstim_coords.mks"
imagedata = nib.squeeze_image(nib.load(filepath_image))
imagedata = nib.as_closest_canonical(imagedata)
imagedata.update_header()
hdr = imagedata.header
data = np.loadtxt(filepath_data)
data_flip = data[:, 0:3]
i = np.argsort([0, 2, 1])
data_flip = data[:, i]
data_flip[:, 1] = hdr.get_data_shape()[1] - data[:, 1]
data_flip[:, 0] = hdr.get_data_shape()[0] - data[:, 0]
NBS2INV_markers = np.hstack((data_flip, data[:, 3:]))
np.savetxt(
"D:\\Programas\\Google Drive\\Lab\\Doutorado\\projetos\\DTI_coord_transf\\nexstim_coordinates\\NBS2INV_markers.mks",
NBS2INV_markers)
def ReadNifti(filename):
nft = squeeze_image(Nifti1Image.from_filename(filename))
return nft
def _run_interface(self, runtime):
in_files = self.inputs.in_files
if not isinstance(in_files, list):
in_files = [self.inputs.in_files]
if self.inputs.to_ras:
in_files = [reorient(inf, newpath=runtime.cwd) for inf in in_files]
run_hmc = self.inputs.hmc and len(in_files) > 1
nii_list = []
# Remove one-sized extra dimensions
for i, f in enumerate(in_files):
filenii = nb.load(f)
filenii = nb.squeeze_image(filenii)
if len(filenii.shape) == 5:
raise RuntimeError("Input image (%s) is 5D." % f)
if filenii.dataobj.ndim == 4:
nii_list += nb.four_to_three(filenii)
else:
nii_list.append(filenii)
if len(nii_list) > 1:
filenii = nb.concat_images(nii_list)
else:
filenii = nii_list[0]
merged_fname = fname_presuffix(self.inputs.in_files[0],
suffix="_merged",
newpath=runtime.cwd)
filenii.to_filename(merged_fname)
self._results["out_file"] = merged_fname
self._results["out_avg"] = merged_fname
if filenii.dataobj.ndim < 4:
# TODO: generate identity out_mats and zero-filled out_movpar
return runtime
if run_hmc:
mcflirt = fsl.MCFLIRT(
cost="normcorr",
save_mats=True,
save_plots=True,
ref_vol=0,
in_file=merged_fname,
)
mcres = mcflirt.run()
filenii = nb.load(mcres.outputs.out_file)
self._results["out_file"] = mcres.outputs.out_file
self._results["out_mats"] = mcres.outputs.mat_file
self._results["out_movpar"] = mcres.outputs.par_file
hmcdata = filenii.get_fdata(dtype="float32")
if self.inputs.grand_mean_scaling:
if not isdefined(self.inputs.in_mask):
mean = np.median(hmcdata, axis=-1)
thres = np.percentile(mean, 25)
mask = mean > thres
else:
mask = nb.load(
self.inputs.in_mask).get_fdata(dtype="float32") > 0.5
nimgs = hmcdata.shape[-1]
means = np.median(hmcdata[mask[..., np.newaxis]].reshape(
(-1, nimgs)).T,
axis=-1)
max_mean = means.max()
for i in range(nimgs):
hmcdata[..., i] *= max_mean / means[i]
hmcdata = hmcdata.mean(axis=3)
if self.inputs.zero_based_avg:
hmcdata -= hmcdata.min()
self._results["out_avg"] = fname_presuffix(self.inputs.in_files[0],
suffix="_avg",
newpath=runtime.cwd)
nb.Nifti1Image(hmcdata, filenii.affine,
filenii.header).to_filename(self._results["out_avg"])
return runtime
def main():
SHOW_AXES = True
AFFINE_IMG = True
NO_SCALE = True
COMPUTE_TRACTS = True
n_tracts = 240
# n_tracts = 24
n_threads = 2 * psutil.cpu_count()
img_shift = 0 # 255
data_dir = os.environ.get('OneDrive') + r'\data\dti_navigation\joonas'
filenames = {
'T1': 'sub-S1_ses-S8741_T1w',
'FOD': 'FOD_T1_space',
'ACT': 'trekkerACTlabels',
'COIL': 'magstim_fig8_coil',
'HEAD': 'head_inv',
'BRAIN': 'brain_inv',
'BRAINSIM': 'gm',
'WM': 'skin'
}
img_path = os.path.join(data_dir, filenames['T1'] + '.nii')
trk_path = os.path.join(data_dir, filenames['FOD'] + '.nii')
act_path = os.path.join(data_dir, filenames['ACT'] + '.nii')
coil_path = os.path.join(data_dir, filenames['COIL'] + '.stl')
head_inv_path = os.path.join(data_dir, filenames['HEAD'] + '.stl')
brain_inv_path = os.path.join(data_dir, filenames['BRAIN'] + '.stl')
brain_sim_path = os.path.join(data_dir, filenames['BRAINSIM'] + '.stl')
wm_sim_path = os.path.join(data_dir, filenames['WM'] + '.stl')
imagedata = nb.squeeze_image(nb.load(img_path))
imagedata = nb.as_closest_canonical(imagedata)
imagedata.update_header()
pix_dim = imagedata.header.get_zooms()
img_shape = imagedata.header.get_data_shape()
act_data = nb.squeeze_image(nb.load(act_path))
act_data = nb.as_closest_canonical(act_data)
act_data.update_header()
act_data_arr = act_data.get_fdata()
# print(imagedata.header)
# print("pix_dim: {}, img_shape: {}".format(pix_dim, img_shape))
print("Pixel size: \n")
print(pix_dim)
print("\nImage shape: \n")
print(img_shape)
print("\nSform: \n")
print(imagedata.get_qform(coded=True))
print("\nQform: \n")
print(imagedata.get_sform(coded=True))
print("\nFall-back: \n")
print(imagedata.header.get_base_affine())
if AFFINE_IMG:
affine = imagedata.affine
if NO_SCALE:
scale, shear, angs, trans, persp = tf.decompose_matrix(
imagedata.affine)
affine = tf.compose_matrix(scale=None,
shear=shear,
angles=angs,
translate=trans,
perspective=persp)
else:
affine = np.identity(4)
print("affine: {0}\n".format(affine))
# Create a rendering window and renderer
ren = vtk.vtkRenderer()
ren.SetUseDepthPeeling(1)
ren.SetOcclusionRatio(0.1)
ren.SetMaximumNumberOfPeels(100)
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren)
ren_win.SetSize(800, 800)
ren_win.SetMultiSamples(0)
ren_win.SetAlphaBitPlanes(1)
# Create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
repos = [0., 0., 0., 0., 0., 0.]
# brain in invesalius space (STL as exported by invesalius)
_ = load_stl(head_inv_path,
ren,
opacity=.7,
colour=[1.0, 1.0, 1.0],
replace=repos,
user_matrix=np.identity(4))
_ = load_stl(wm_sim_path,
ren,
opacity=.7,
colour=[1.0, 1.0, 1.0],
replace=repos,
user_matrix=np.identity(4))
# simnibs brain in RAS+ space
# _ = load_stl(brain_sim_path, ren, opacity=1., colour=[1.0, 0., 0.], replace=repos, user_matrix=np.identity(4))
# brain in RAS+ space
inv2ras = affine.copy()
inv2ras[1, 3] += pix_dim[1] * img_shape[1]
inv2ras[0, 3] -= 12
# _ = load_stl(brain_inv_path, ren, opacity=.6, colour="SkinColor", replace=repos, user_matrix=inv2ras)
# brain in voxel space
inv2voxel = np.identity(4)
inv2voxel[1, 3] = inv2voxel[1, 3] + pix_dim[1] * img_shape[1]
# _ = load_stl(brain_inv_path, ren, opacity=.6, colour=[0.482, 0.627, 0.698], replace=repos, user_matrix=inv2voxel)
# simnibs brain in RAS+ space
ras2inv = np.linalg.inv(affine.copy())
ras2inv[1, 3] -= pix_dim[1] * img_shape[1]
_ = load_stl(wm_sim_path,
ren,
opacity=.7,
colour=[0.482, 0.627, 0.698],
replace=repos,
user_matrix=ras2inv)
repos_1 = [0., 0., 0., 0., 0., 180.]
# _ = load_stl(wm_sim_path, ren, opacity=.7, colour=[1., 0., 0.], replace=repos_1, user_matrix=np.linalg.inv(affine))
# create fiducial markers
# rowise the coordinates refer to: right ear, left ear, nasion
# fids_inv = np.array([[168.300, 126.600, 97.000],
# [9.000, 120.300, 93.700],
# [90.100, 33.500, 150.000]])
fids_inv = np.array([[167.7, 120.9, 96.0], [8.2, 122.7, 91.0],
[89.0, 18.6, 129.0]])
fids_inv_vtk = np.array([[167.7, 120.9, 96.0], [8.2, 122.7, 91.0],
[89.0, 18.6, 129.0]])
# from the invesalius exported fiducial markers you have to multiply the Y coordinate by -1 to
# transform to the regular 3D invesalius space where coil location is saved
fids_inv_vtk[:, 1] *= -1
# the following code converts from the invesalius 3D space to the MRI scanner coordinate system
fids_inv_vtk_w = fids_inv_vtk.copy()
fids_inv_vtk_w = np.hstack((fids_inv_vtk_w, np.ones((3, 1))))
fids_scan = np.linalg.inv(ras2inv) @ fids_inv_vtk_w.T
fids_vis = fids_scan.T[:3, :3]
# --- fiducial markers
seed = np.array([60.0, 147.0, 204.0])
seed_inv = np.array([60.0, -147.0, 204.0])
coil_pos = [43.00, 155.47, 225.22, -21.00, -37.45, 58.41]
m_coil = coil_transform_pos(coil_pos)
# show coil
repos_coil = [0., 0., 0., 0., 0., 90.]
# _ = load_stl(coil_path, ren, opacity=.6, replace=repos_coil, colour=[1., 1., 1.], user_matrix=m_coil)
# create coil vectors
vec_length = 75
p1 = m_coil[:-1, -1]
coil_dir = m_coil[:-1, 0]
coil_face = m_coil[:-1, 1]
p2_face = p1 + vec_length * coil_face
p2_dir = p1 + vec_length * coil_dir
coil_norm = np.cross(coil_dir, coil_face)
p2_norm = p1 - vec_length * coil_norm
add_line(ren, p1, p2_dir, color=[1.0, .0, .0])
add_line(ren, p1, p2_face, color=[.0, 1.0, .0])
add_line(ren, p1, p2_norm, color=[.0, .0, 1.0])
# --- coil vectors
p1_change = p1.copy()
p1_change[1] = -p1_change[1]
# offset = 40
# coil_norm = coil_norm/np.linalg.norm(coil_norm)
# coord_offset_nav = p1 - offset * coil_norm
# convert to world coordinate space to use as seed for fiber tracking
seed_world = np.append(seed, 1)[np.newaxis, :].T
seed_world = affine @ seed_world
seed_world = seed_world[:3, 0, np.newaxis].T
# convert to world coordinate space to use as seed for fiber tracking
seed_world_true = np.append(seed_inv, 1)[np.newaxis, :].T
seed_world_true = inv2ras @ seed_world_true
seed_world_true = seed_world_true[:3, 0, np.newaxis].T
# convert to voxel coordinate space
seed_mri = np.append(seed_inv, 1)[np.newaxis, :].T
seed_mri = inv2voxel @ seed_mri
seed_mri = seed_mri[:3, 0, np.newaxis].T
# 0: red, 1: green, 2: blue, 3: maroon (dark red),
# 4: purple, 5: teal (petrol blue), 6: yellow, 7: orange
colours = [[1., 0., 0.], [0., 1., 0.], [0., 0., 1.], [1., .0, 1.],
[0.45, 0., 0.5], [0., .5, .5], [1., 1., 0.], [1., .4, .0]]
# for n in range(3):
# _ = add_marker(fids_inv[n, :], ren, colours[n], radius=2)
for n in range(3):
_ = add_marker(fids_inv_vtk[n, :], ren, colours[n], radius=2)
for n in range(3):
_ = add_marker(fids_vis[n, :], ren, colours[n], radius=2)
_ = add_marker(p1, ren, colours[4], radius=2)
_ = add_marker(seed_inv, ren, colours[5], radius=2)
_ = add_marker(np.squeeze(seed_world), ren, colours[6], radius=2)
_ = add_marker(np.squeeze(seed_world_true), ren, colours[3], radius=2)
_ = add_marker(seed, ren, colours[7], radius=2)
_ = add_marker(np.squeeze(seed_mri), ren, colours[1], radius=2)
# create tracts
if COMPUTE_TRACTS:
# Show tracks
repos_trk = [0., -(pix_dim[1] * img_shape[1]), 0., 0., 0., 0.]
matrix_vtk = vtk.vtkMatrix4x4()
trans = np.identity(4)
trans[1, -1] = repos_trk[1]
final_matrix = np.linalg.inv(affine) @ trans
print("final_matrix: {}".format(final_matrix))
for row in range(0, 4):
for col in range(0, 4):
matrix_vtk.SetElement(row, col, final_matrix[row, col])
root = vtk.vtkMultiBlockDataSet()
start_time = time.time()
tracker = Trekker.initialize(bytes(trk_path, 'utf-8'))
tracker.seed_maxTrials(1)
tracker.minFODamp(0.1)
tracker.writeInterval(50)
tracker.maxLength(200)
tracker.minLength(20)
tracker.maxSamplingPerStep(100)
tracker.numberOfThreads(n_threads)
duration = time.time() - start_time
print("Initialize Trekker: {:.2f} ms".format(1e3 * duration))
count_tracts = 0
start_time_all = time.time()
for n in range(round(n_tracts / n_threads)):
# branch = dti.multi_block(tracker, seed, n_threads)
branch = dti.multi_block(tracker, seed_world_true, n_threads)
count_tracts += branch.GetNumberOfBlocks()
# start_time = time.time()
# root = dti.tracts_root(out_list, root, n)
root.SetBlock(n, branch)
# duration = time.time() - start_time
# print("Compute root {}: {:.2f} ms".format(n, 1e3*duration))
duration = time.time() - start_time_all
print("Compute multi {}: {:.2f} ms".format(n, 1e3 * duration))
print("Number computed tracts {}".format(count_tracts))
print("Number computed branches {}".format(root.GetNumberOfBlocks()))
start_time = time.time()
tracts_actor = dti.compute_actor(root, matrix_vtk)
duration = time.time() - start_time
print("Compute actor: {:.2f} ms".format(1e3 * duration))
ren.AddActor(tracts_actor)
# Add axes to scene origin
if SHOW_AXES:
add_line(ren, [0, 0, 0], [150, 0, 0], color=[1.0, 0.0, 0.0])
add_line(ren, [0, 0, 0], [0, 150, 0], color=[0.0, 1.0, 0.0])
add_line(ren, [0, 0, 0], [0, 0, 150], color=[0.0, 0.0, 1.0])
# Enable user interface interactor
iren.Initialize()
ren_win.Render()
iren.Start()