def get_data_unregistered(petmr_path, trio_path, scans_list, input_scanner):
# This function simply uploads the training scans that are specified in the list "scans_list"
# The scans that are uploaded are not registered between the scanners (hence unregistered)
train_val_test_inp = []
train_val_test_out = []
if input_scanner == "PETMR":
input_path = petmr_path
output_path = trio_path
else:
input_path = trio_path
output_path = petmr_path
for subj_scan in scans_list:
input_scan_image = nib.load(
str(input_path) + "/Subj" + str(subj_scan[0]) + "Scan" +
str(subj_scan[1]) + "/Brain_Matched.nii.gz")
input_scan_data = input_scan_image.get_data()
# Upload the corresponding output scan (unregistered)
output_scan_image1 = nib.load(
str(output_path) + "/Subj" + str(subj_scan[0]) + "Scan1" +
"/Brain_Matched.nii.gz")
output_scan_data1 = output_scan_image1.get_data()
input_bvals_scan, input_bvecs_scan = read_bvals_bvecs(str(input_path) + "/Subj" + str(subj_scan[0]) + "Scan" + str(subj_scan[1]) + "/NODDI.bval",\
str(input_path) + "/Subj" + str(subj_scan[0]) + "Scan" + str(subj_scan[1]) + "/NODDI.bvec")
output_bvals_scan1, output_bvecs_scan1 = read_bvals_bvecs(str(output_path) + "/Subj" + str(subj_scan[0]) + "Scan1/NODDI.bval",\
str(output_path) + "/Subj" + str(subj_scan[0]) + "Scan1/NODDI.bvec")
#set a threshold value for b=0 values (due to TRIO dataset)
input_gtab_scan = gradient_table(input_bvals_scan,
input_bvecs_scan,
b0_threshold=5)
input_s0s_scan = input_scan_data[:, :, :, input_gtab_scan.b0s_mask]
output_gtab_scan1 = gradient_table(output_bvals_scan1,
output_bvecs_scan1,
b0_threshold=5)
output_s0s_scan1 = output_scan_data1[:, :, :,
output_gtab_scan1.b0s_mask]
print("Uploading unregistered Subject %s Scan %s" %
(str(subj_scan[0]), str(subj_scan[1])))
# Append the data to the lists containing the training inputs and outputs
# upload the first volume of each slice only
train_val_test_inp.append(input_s0s_scan[:, :, :, [0]])
train_val_test_out.append(output_s0s_scan1[:, :, :, [0]])
return (train_val_test_inp, train_val_test_out)
def single_shell_extraction(dir_src, dir_out, verbose=False):
fbval = pjoin(dir_src, 'bvals')
fbvec = pjoin(dir_src, 'bvecs')
fmask = pjoin(dir_src, 'nodif_brain_mask.nii.gz')
fdwi = pjoin(dir_src, 'data.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
data, affine = load_nifti(fdwi, verbose)
if par_b_shell == 1000:
sind = (bvals < 10) | ((bvals < 1100) & (bvals > 900))
elif par_b_shell == 2000:
sind = (bvals < 10) | ((bvals < 2100) & (bvals > 1900))
elif par_b_shell == 3000:
sind = (bvals < 10) | ((bvals < 3100) & (bvals > 2900))
shell_data = data[..., sind]
shell_gtab = gradient_table(bvals[sind], bvecs[sind, :],
b0_threshold=par_b0_threshold)
fname = 'data_' + par_b_tag + '.nii.gz'
save_nifti(pjoin(dir_out, fname), shell_data, affine)
np.savetxt(pjoin(dir_out, 'bvals_' + par_b_tag), shell_gtab.bvals)
np.savetxt(pjoin(dir_out, 'bvecs_' + par_b_tag), shell_gtab.bvecs.T)
def load_bval_bvec_dti(self, fbval, fbvec, dti_file, dti_file_out):
"""
Takes bval and bvec files and produces a structure in dipy format
**Positional Arguments:**
"""
# Load Data
img = nb.load(dti_file)
data = img.get_data()
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
# Get rid of spurrious scans
idx = np.where((bvecs[:, 0] == 100) & (bvecs[:, 1] == 100)
& (bvecs[:, 2] == 100))
bvecs = np.delete(bvecs, idx, axis=0)
bvals = np.delete(bvals, idx, axis=0)
data = np.delete(data, idx, axis=3)
# Save corrected DTI volume
dti_new = nb.Nifti1Image(data,
affine=img.get_affine(),
header=img.get_header())
dti_new.update_header()
nb.save(dti_new, dti_file_out)
gtab = gradient_table(bvals, bvecs, atol=0.01)
print(gtab.info)
return gtab
def load_diff_files(subj_folder, file_names):
from dipy.io import read_bvals_bvecs
# Load diff nii file:
diff_file = nib.load(os.path.join(subj_folder,file_names['data']))
diff_img = diff_file.get_fdata() # i1
info_nii = diff_file.header
data = np.asarray(diff_img, dtype='float64')
data[data < 0] = 0
affine = diff_file.affine
# Load bval/bvec:
bval, bvec = read_bvals_bvecs(os.path.join(subj_folder,file_names['bval']), os.path.join(subj_folder,file_names['bvec']))
bvec = np.reshape(bvec, [len(bval), -1]);
# Round bval to closest 50 and divide by 1000:
bval2 = 2 * np.asarray(bval)
bval2 = bval2.round(-2)
bval = bval2 / 2000
# Remove bval<1000 from calc:
blow_locs = np.intersect1d(np.where(bval > 0)[0], np.where(bval < 1)[0])
bval = np.delete(bval, blow_locs)
bvec = np.delete(bvec, blow_locs, 0)
data = np.delete(data, blow_locs, 3)
# Load mask:
mask = nib.load(os.path.join(subj_folder,file_names['mask'])).get_fdata()
return data, affine, info_nii, bval, bvec, mask
def gtabs(path_dicts):
gtabs = []
for patient, path_dict in path_dicts.items():
bvals, bvecs = read_bvals_bvecs(path_dict["bval"], path_dict["bvec"])
gtab = gradient_table(bvals, bvecs)
gtabs.append(gtab)
return gtabs
def load_bval_bvec_dwi(fbval, fbvec, dwi_file, dwi_file_out):
"""
Takes bval and bvec files and produces a structure in dipy format
**Positional Arguments:**
"""
# Load Data
img = nb.load(dwi_file)
data = img.get_data()
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
# Get rid of spurrious scans
idx = np.where((bvecs[:, 0] == 100) & (bvecs[:, 1] == 100) &
(bvecs[:, 2] == 100))
bvecs = np.delete(bvecs, idx, axis=0)
bvals = np.delete(bvals, idx, axis=0)
data = np.delete(data, idx, axis=3)
# Save corrected DTI volume
dwi_new = nb.Nifti1Image(data, affine=img.get_affine(),
header=img.get_header())
dwi_new.update_header()
nb.save(dwi_new, dwi_file_out)
gtab = gradient_table(bvals, bvecs, atol=0.01)
print(gtab.info)
return gtab
def shell_extraction(src_dwi,
src_bvec,
src_bval,
out_b0,
delta=100,
verbose=False):
shell = [0]
bvals, bvecs = read_bvals_bvecs(src_bval, src_bvec)
img = nib.load(src_dwi)
data = img.get_data()
affine = img.get_affine()
header = img.header
sind = np.zeros((bvals.size), dtype=bool)
for b in shell:
tind = (bvals < b + delta) & (bvals > b - delta)
sind = sind | tind
shell_data = data[..., sind].mean(axis=3)
shell_img = nib.Nifti1Image(shell_data, affine, header)
shell_img.update_header()
nib.save(shell_img, out_b0)
return sind.sum()
def main(dti_file, bvals_file, bvecs_file, b_ss=1000):
# Load the image data
nii = nib.load(dti_file)
img_data = nii.get_data()
# Read in the b-shell values and gradient directions
bvals, bvecs = read_bvals_bvecs(bvals_file, bvecs_file)
# Boolean array to identify entries with either b = 0 or b = b_ss
bvals_eq_0_b_ss = (bvals == 0) | (bvals == b_ss)
# Extract info needed to run single-compartment dti model
dti_bvals = bvals[bvals_eq_0_b_ss].copy()
dti_bvecs = bvecs[bvals_eq_0_b_ss].copy()
dti_img_data = img_data[:, :, :, bvals_eq_0_b_ss].copy()
# Compute gradient table
grad_table = gradient_table(dti_bvals, dti_bvecs)
# Extract brain so we don't fit the background
brain_img_data, brain_mask = median_otsu(dti_img_data, 2, 1)
# Run the dti model and fit it to the brain extracted image data
ten_model = dti.TensorModel(grad_table)
ten_fit = ten_model.fit(brain_img_data)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.INFO)
assert_inputs_exist(parser, [args.dwi, args.bvals, args.bvecs])
assert_outputs_exist(
parser, args, [args.output_dwi, args.output_bvals, args.output_bvecs])
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
# Find the volume indices that correspond to the shells to extract.
tol = args.tolerance
img = nib.load(args.dwi)
outputs = extract_dwi_shell(img, bvals, bvecs, args.bvals_to_extract, tol,
args.block_size)
indices, shell_data, new_bvals, new_bvecs = outputs
logging.info("Selected indices: {}".format(indices))
np.savetxt(args.output_bvals, new_bvals, '%d')
np.savetxt(args.output_bvecs, new_bvecs.T, '%0.15f')
nib.save(nib.Nifti1Image(shell_data, img.affine, img.header),
args.output_dwi)
def main(args = None):
if not args:
args = sys.argv[1:]
# Get parser info
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
fname_in = arguments['-i']
if '-o' in arguments:
fname_out = arguments['-o']
else:
fname_out = ''
verbose = int(arguments['-v'])
# get bvecs in proper orientation
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(None, fname_in)
# # Transpose bvecs
# printv('Transpose bvecs...', verbose)
# # from numpy import transpose
# bvecs = bvecs.transpose()
# Write new file
if fname_out == '':
path_in, file_in, ext_in = extract_fname(fname_in)
fname_out = path_in+file_in+ext_in
fid = open(fname_out, 'w')
for iLine in range(bvecs.shape[0]):
fid.write(' '.join(str(i) for i in bvecs[iLine, :])+'\n')
fid.close()
# display message
printv('Created file:\n--> '+fname_out+'\n', verbose, 'info')
def prepare_q4half_257vol(fimg, fbtext, fbval, fbvec, fmask, flipy):
img = nib.load(fimg)
data = img.get_data()
affine = img.get_affine()
zooms = img.get_header().get_zooms()[:3]
# Read b-values from bval file
bvals, temp = read_bvals_bvecs(fbval, fbvec)
bvals = bvals[0:257]
# Read Wedeen file grad514.txt (fbtxt)
bmat = np.loadtxt(fbtext)
bvecs = bmat[0:257, 1:]
# Normalize diffusion directions
bvecs = bvecs / np.sqrt(np.sum(bvecs ** 2, axis=1))[:, None]
bvecs[np.isnan(bvecs)] = 0
if flipy:
bvecs[:,1] = -bvecs[:,1]
# Delete empty DSI volumes
data = data[:,:,:, 0:257]
# Read mask
img_mask = nib.load(fmask)
mask = img_mask.get_data()
return data, affine, zooms, bvals, bvecs, mask
def execution( self, context):
bvals, bvecs = read_bvals_bvecs(self.bvals.fullPath(), self.bvecs.fullPath())
if self.round_bvals:
context.write("Rouding bvalues to : useful for shell based models")
bvals = np.round(bvals,-2)
try:
minf = self.diffusion_data.minf()
t = minf['storage_to_memory']
except KeyError:
context.write("No storage_to_memory field in the minf file associated to the volume, using the one of the header of the volume")
dwi = aims.read(self.diffusion_data.fullPath())
header = dwi.header()
t = header['storage_to_memory']
finally:
try :
t1 = aims.AffineTransformation3d(t).toMatrix()
aff = np.diag(t1)[:-1]
affine = np.diag(aff)
except:
context.write("Warning!: there is no storage to memory matrix, I assume bvecs have an RAS (Nifti convention) orientation")
affine = -1.0*np.eye(3)
context.write("The following transformation is going to be applied:", affine)
bvecs = np.dot(bvecs, np.transpose(affine))
context.write("Transforming bvecs coordinate from storage to Aims referential")
gtab = gradient_table(bvals, bvecs,b0_threshold=self.b0_threshold)
dump(gtab, self.gradient_table.fullPath(), compress=9)
#Handling metadata
self.gradient_table.setMinf('rounded_bvals', self.round_bvals)
self.gradient_table.setMinf('bvalues_uuid', self.bvals.uuid())
self.gradient_table.setMinf('bvectors_uuid',self.bvecs.uuid())
def main(args=None):
if not args:
args = sys.argv[1:]
# Get parser info
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
fname_in = arguments['-bvec']
if '-o' in arguments:
fname_out = arguments['-o']
else:
fname_out = ''
verbose = int(arguments['-v'])
# get bvecs in proper orientation
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(None, fname_in)
# # Transpose bvecs
# printv('Transpose bvecs...', verbose)
# # from numpy import transpose
# bvecs = bvecs.transpose()
# Write new file
if fname_out == '':
path_in, file_in, ext_in = extract_fname(fname_in)
fname_out = path_in+file_in+ext_in
fid = open(fname_out, 'w')
for iLine in range(bvecs.shape[0]):
fid.write(' '.join(str(i) for i in bvecs[iLine, :])+'\n')
fid.close()
# display message
printv('Created file:\n--> '+fname_out+'\n', verbose, 'info')
def bvecs(self):
if self._bvecs is None:
bvals, bvecs = read_bvals_bvecs(self.filename_bval,
self.filename_bvecs)
self._bvals = bvals
self._bvecs = bvecs
return self._bvecs
def main(args=None):
parser = get_parser()
if args:
arguments = parser.parse_args(args)
else:
arguments = parser.parse_args(
args=None if sys.argv[1:] else ['--help'])
fname_in = arguments.bvec
fname_out = arguments.o
verbose = int(arguments.v)
init_sct(log_level=verbose, update=True) # Update log level
# get bvecs in proper orientation
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(None, fname_in)
# # Transpose bvecs
# printv('Transpose bvecs...', verbose)
# # from numpy import transpose
# bvecs = bvecs.transpose()
# Write new file
if fname_out == '':
path_in, file_in, ext_in = extract_fname(fname_in)
fname_out = path_in + file_in + ext_in
fid = open(fname_out, 'w')
for iLine in range(bvecs.shape[0]):
fid.write(' '.join(str(i) for i in bvecs[iLine, :]) + '\n')
fid.close()
# display message
printv('Created file:\n--> ' + fname_out + '\n', verbose, 'info')
def load_dwi(nifti_path,
bval_path,
bvec_path,
mask_path=None,
b0_threshold=250):
"""Load the data needed to process a diffusion-weighted image.
Parameters
----------
nifti_path : string
Path to the nifti DWI
bval_path : string
Path to the .bval file
bvec_path : string
Path to the .bvec file
mask_path : string, optional
Path to the nifti mask, if one exists
b0_threshold
Threshold below which a b-value is considered zero
Returns
-------
img : DiffusionWeightedImage
The DWI data with a mask, if applicable.
"""
img = nib.load(nifti_path)
bvals, bvecs = read_bvals_bvecs(bval_path, bvec_path)
gtab = gradient_table(bvals, bvecs, b0_threshold=b0_threshold)
if mask_path is not None:
mask = nib.load(mask_path)
return MaskedDiffusionWeightedImage(img, gtab, mask.get_data())
else:
return DiffusionWeightedImage(img, gtab)
def compute_tensor_model(dir_src, dir_out, verbose=False):
fbval = pjoin(dir_src, 'bvals_' + par_b_tag)
fbvec = pjoin(dir_src, 'bvecs_' + par_b_tag)
fdwi = pjoin(dir_src, 'data_' + par_b_tag + '_' + par_dim_tag + '.nii.gz')
fmask = pjoin(dir_src, 'nodif_brain_mask_' + par_dim_tag + '.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=par_b0_threshold)
data, affine = load_nifti(fdwi, verbose)
mask, _ = load_nifti(fmask, verbose)
ten_model = TensorModel(gtab)
ten_fit = ten_model.fit(data, mask)
FA = ten_fit.fa
MD = ten_fit.md
EV = ten_fit.evecs.astype(np.float32)
fa_name = 'data_' + par_b_tag + '_' + par_dim_tag + '_FA.nii.gz'
save_nifti(pjoin(dir_out, fa_name), FA, affine)
md_name = 'data_' + par_b_tag + '_' + par_dim_tag + '_MD.nii.gz'
save_nifti(pjoin(dir_out, md_name), MD, affine)
ev_name = 'data_' + par_b_tag + '_' + par_dim_tag + '_EV.nii.gz'
save_nifti(pjoin(dir_out, ev_name), EV, affine)
def load_fibercup_tractography_derivatives_2D():
niftipath = 'data\\fibercup\\R3.nii.gz'
bvalspath = 'data\\fibercup\\R3.bvals'
bvecspath = 'data\\fibercup\\R3.bvecs'
print("Fetching data")
data, affine = load_nifti(niftipath)
bvals, bvecs = read_bvals_bvecs(bvalspath, bvecspath)
gtab = gradient_table(bvals, bvecs)
print("Fitting tensor model...")
tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data)
quadratic_form = tenfit.quadratic_form
evals, evecs = np.linalg.eig(quadratic_form)
max_directions = np.argmax(evals, axis=2)
directions = np.array([[[
evals[i, j, k][max_directions[i, j, k]] *
evecs[i, j, k][max_directions[i, j, k]]
for k in range(len(max_directions[0, 0]))
] for j in range(len(max_directions[0]))]
for i in range(len(max_directions))])
return np.real(directions[:, :, 1, :2])
def to_estimate_dti(file_in, file_inMask, outPath, fbval, fbvec):
print(d.separador + 'building DTI Model...')
ref_name = utils.to_extract_filename(file_in)
if (
not (os.path.exists(outPath + ref_name + d.id_evecs + d.extension))
) | (not (os.path.exists(outPath + ref_name + d.id_evals + d.extension))):
try:
os.remove(outPath + ref_name + d.id_evecs + d.extension)
os.remove(outPath + ref_name + d.id_evals + d.extension)
except:
print("Unexpected error:", sys.exc_info()[0])
img = nib.load(file_in)
data = img.get_data()
mask = nib.load(file_inMask)
mask = mask.get_data()
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs)
tensor_model = dti.TensorModel(gtab)
tensor_fitted = tensor_model.fit(data, mask)
nib.save(
nib.Nifti1Image(tensor_fitted.evecs.astype(np.float32),
img.affine),
outPath + ref_name + d.id_evecs + d.extension)
nib.save(
nib.Nifti1Image(tensor_fitted.evals.astype(np.float32),
img.affine),
outPath + ref_name + d.id_evals + d.extension)
return outPath + ref_name + d.id_evecs + d.extension, outPath + ref_name + d.id_evals + d.extension
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.INFO)
assert_inputs_exist(parser, args.in_bval)
assert_outputs_exist(parser, args, args.out_bval)
bvals, bvecs = read_bvals_bvecs(args.in_bval, None)
# Find the volume indices that correspond to the shells to extract.
tol = args.tolerance
sorted_centroids, sorted_indices = identify_shells(bvals, tol, sort=True)
bvals_to_extract = np.sort(args.bvals_to_extract)
n_shells = np.shape(bvals_to_extract)[0]
logging.info("number of shells: {}".format(n_shells))
logging.info("bvals to extract: {}".format(bvals_to_extract))
logging.info("estimated centroids: {}".format(sorted_centroids))
logging.info("original bvals: {}".format(bvals))
logging.info("selected indices: {}".format(sorted_indices))
new_bvals = bvals
for i in range(n_shells):
if np.abs(sorted_centroids[i] - bvals_to_extract[i]) <= tol:
new_bvals[np.where(sorted_indices == i)] = bvals_to_extract[i]
else:
parser.error("No bvals to resample: tolerance is too low.")
logging.info("new bvals: {}".format(new_bvals))
new_bvals.shape = (1, len(new_bvals))
np.savetxt(args.out_bval, new_bvals, '%d')
def test_bvalMap(self):
inPath= pjoin(FILEDIR, 'connectom_prisma/connectom/A/')
inPrefix= pjoin(inPath, 'dwi_A_connectom_st_b1200')
lowResImgPath= inPrefix+'.nii.gz'
bvalPath= inPrefix+'.bval'
lowResMaskPath= inPrefix+'_mask.nii.gz'
# load signal attributes for pre-processing ----------------------------------------------------------------
imgPath = nrrd2nifti(lowResImgPath)
dwi = load(imgPath)
maskPath = nrrd2nifti(lowResMaskPath)
mask = load(maskPath)
bvals, _ = read_bvals_bvecs(bvalPath, None)
bNew= 1000.
print('B value mapping ', imgPath)
dwiNew, bvalsNew= remapBval(dwi.get_fdata(), mask.get_fdata(), bvals, bNew)
outPrefix = imgPath.split('.nii')[0] + '_bmapped'
save_nifti(outPrefix + '.nii.gz', dwiNew, dwi.affine, dwi.header)
copyfile(inPrefix + '.bvec', outPrefix + '.bvec')
write_bvals(outPrefix + '.bval', bvals)
def _get_from_file_mapping(self, path, file_mapping: dict, b0_threshold: float = 10.0):
path_mapping = {key: os.path.join(path, file_mapping[key]) for key in file_mapping}
bvals, bvecs = read_bvals_bvecs(path_mapping['bvals'],
path_mapping['bvecs'])
# img, t1, gradient table, affine and dwi
img = nb.load(path_mapping['img'])
t1 = nb.load(path_mapping['t1']).get_data()
dwi = img.get_data().astype("float32")
aff = img.affine
# binary mask
if 'mask' in path_mapping:
binary_mask = nb.load(path_mapping['mask']).get_data()
else:
_, binary_mask = median_otsu(dwi[..., 0], 2, 1)
# calculating b0
b0 = dwi[..., bvals < b0_threshold].mean(axis=-1)
# Do not generate fa yet
fa = None
gtab = gradient_table(bvals, bvecs)
data_container = DataContainer(bvals, bvecs, gtab, t1, dwi, aff, binary_mask, b0, fa)
return self._preprocess(data_container)
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
fname_in = arguments.bvec
fname_out = arguments.o
# get bvecs in proper orientation
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(None, fname_in)
# # Transpose bvecs
# printv('Transpose bvecs...', verbose)
# # from numpy import transpose
# bvecs = bvecs.transpose()
# Write new file
if fname_out == '':
path_in, file_in, ext_in = extract_fname(fname_in)
fname_out = path_in + file_in + ext_in
fid = open(fname_out, 'w')
for iLine in range(bvecs.shape[0]):
fid.write(' '.join(str(i) for i in bvecs[iLine, :]) + '\n')
fid.close()
# display message
printv('Created file:\n--> ' + fname_out + '\n', verbose, 'info')
def constrained_spherical_deconvolution(dir_src, dir_out, verbose=False):
# Load data
fbval = pjoin(dir_src, 'bvals_' + par_b_tag)
fbvec = pjoin(dir_src, 'bvecs_' + par_b_tag)
fdwi = pjoin(dir_src, 'data_' + par_b_tag + '_' + par_dim_tag + '.nii.gz')
#fmask = pjoin(dir_src, 'nodif_brain_mask_' + par_dim_tag + '.nii.gz')
fmask = pjoin(dir_src, 'wm_mask_' + par_b_tag + '_' + par_dim_tag + '.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=par_b0_threshold)
data, affine = load_nifti(fdwi, verbose)
mask, _ = load_nifti(fmask, verbose)
sphere = get_sphere('symmetric724')
response, ratio = auto_response(gtab, data, roi_radius=par_ar_radius,
fa_thr=par_ar_fa_th)
# print('Response function', response)
# Model fitting
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd_model.fit(data, mask=mask)
# Saving Spherical Harmonic Coefficient
out_peaks = 'sh_' + par_b_tag + '_' + par_dim_tag + '.nii.gz'
save_nifti(pjoin(dir_out, out_peaks), csd_fit.shm_coeff, affine)
def compute_tensor_model(dir_src, dir_out, verbose=False):
fbval = pjoin(dir_src, 'bvals_' + par_b_tag)
fbvec = pjoin(dir_src, 'bvecs_' + par_b_tag)
fdwi = pjoin(dir_src, 'data_' + par_b_tag + '_' + par_dim_tag + '.nii.gz')
fmask = pjoin(dir_src, 'nodif_brain_mask_' + par_dim_tag + '.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=par_b0_threshold)
data, affine = load_nifti(fdwi, verbose)
mask, _ = load_nifti(fmask, verbose)
ten_model = TensorModel(gtab)
ten_fit = ten_model.fit(data, mask)
FA = ten_fit.fa
MD = ten_fit.md
EV = ten_fit.evecs.astype(np.float32)
fa_name = 'data_' + par_b_tag + '_' + par_dim_tag + '_FA.nii.gz'
save_nifti(pjoin(dir_out, fa_name), FA, affine)
md_name = 'data_' + par_b_tag + '_' + par_dim_tag + '_MD.nii.gz'
save_nifti(pjoin(dir_out, md_name), MD, affine)
ev_name = 'data_' + par_b_tag + '_' + par_dim_tag + '_EV.nii.gz'
save_nifti(pjoin(dir_out, ev_name), EV, affine)
def single_shell_extraction(dir_src, dir_out, verbose=False):
fbval = pjoin(dir_src, 'bvals')
fbvec = pjoin(dir_src, 'bvecs')
fmask = pjoin(dir_src, 'nodif_brain_mask.nii.gz')
fdwi = pjoin(dir_src, 'data.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
data, affine = load_nifti(fdwi, verbose)
if par_b_shell == 1000:
sind = (bvals < 10) | ((bvals < 1100) & (bvals > 900))
elif par_b_shell == 2000:
sind = (bvals < 10) | ((bvals < 2100) & (bvals > 1900))
elif par_b_shell == 3000:
sind = (bvals < 10) | ((bvals < 3100) & (bvals > 2900))
shell_data = data[..., sind]
shell_gtab = gradient_table(bvals[sind],
bvecs[sind, :],
b0_threshold=par_b0_threshold)
fname = 'data_' + par_b_tag + '.nii.gz'
save_nifti(pjoin(dir_out, fname), shell_data, affine)
np.savetxt(pjoin(dir_out, 'bvals_' + par_b_tag), shell_gtab.bvals)
np.savetxt(pjoin(dir_out, 'bvecs_' + par_b_tag), shell_gtab.bvecs.T)
def constrained_spherical_deconvolution(dir_src, dir_out, verbose=False):
# Load data
fbval = pjoin(dir_src, 'bvals_' + par_b_tag)
fbvec = pjoin(dir_src, 'bvecs_' + par_b_tag)
fdwi = pjoin(dir_src, 'data_' + par_b_tag + '_' + par_dim_tag + '.nii.gz')
#fmask = pjoin(dir_src, 'nodif_brain_mask_' + par_dim_tag + '.nii.gz')
fmask = pjoin(dir_src,
'wm_mask_' + par_b_tag + '_' + par_dim_tag + '.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=par_b0_threshold)
data, affine = load_nifti(fdwi, verbose)
mask, _ = load_nifti(fmask, verbose)
sphere = get_sphere('symmetric724')
response, ratio = auto_response(gtab,
data,
roi_radius=par_ar_radius,
fa_thr=par_ar_fa_th)
# print('Response function', response)
# Model fitting
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
csd_fit = csd_model.fit(data, mask=mask)
# Saving Spherical Harmonic Coefficient
out_peaks = 'sh_' + par_b_tag + '_' + par_dim_tag + '.nii.gz'
save_nifti(pjoin(dir_out, out_peaks), csd_fit.shm_coeff, affine)
def nifti_read_gtab(filename, meta):
fsbvals, fsbvecs = nifti_get_specific_bvals_bvecs_filenames(filename)
fgbvals, fgbvecs = nifti_get_global_bvals_bvecs_filenames(filename)
# where to find the files?
if os.path.isfile(fsbvals) and os.path.isfile(fsbvecs):
# specific bvals/bvecs for this nifti file?
bvals, bvecs = read_bvals_bvecs(fsbvals, fsbvecs)
elif os.path.isfile(fgbvals) and os.path.isfile(fgbvecs):
# general bvals/bvecs in the same directory?
bvals, bvecs = read_bvals_bvecs(fgbvals, fgbvecs)
else:
raise Exception('no bvals/bvecs files found for ' + filename)
if fields.auto_convert_world_space:
bvecs = _nifti_bvecs_to_worldspace(bvecs, meta)
return GradientTable(bvals, bvecs)
def bval_vec(bval_file):
from dipy.io import read_bvals_bvecs
bvals = read_bvals_bvecs(bval_file, None)[0]
bvals = np.around(bvals, decimals=-1)
b0i = np.where(bvals == 0)[0]
return bvals, b0i
def load_hcp_data(data_path, bvals_path, bvecs_path):
# load HCP data
img = nib.load(data_path)
data = img.get_data()
# load b-values and vectors
bvals, bvecs = read_bvals_bvecs(bvals_path, bvecs_path)
return data, bvals, bvecs
def _retrieve_data(self, file_names, denoise=False, b0_threshold=10):
"""
Reads data from specific files and returns them as object.
This functions reads the filenames of the DWI image and loads/parses them accordingly.
Also, it denoises them, if specified and generates a b0 image.
The `file_names` param should be a dict with the following keys:
`['bvals', 'bvecs', 'img', 't1', 'mask']`
Parameters
----------
file_names : dict
The filenames, or relative paths from `self.path`.
denoise : bool, optional
A boolean indicating wether the given data should be denoised, by default False
b0_threshold : float, optional
A single value indicating the b0 threshold used for b0 calculation, by default 10.0
Returns
-------
RawData
An object holding all data as attributes, usable for further processing.
Raises
------
DataContainerNotLoadableError
This error is thrown if one or multiple files cannot be found.
"""
data = RawData()
try:
data.bvals, data.bvecs = read_bvals_bvecs(os.path.join(self.path, file_names['bvals']),
os.path.join(self.path, file_names['bvecs']))
data.img = nb.load(os.path.join(self.path, file_names['img']))
data.t1 = nb.load(os.path.join(self.path, file_names['t1'])).get_data()
except FileNotFoundError as error:
raise DataContainerNotLoadableError(self.path, error.filename) from None
data.gtab = gradient_table(bvals=data.bvals, bvecs=data.bvecs)
data.dwi = data.img.get_data().astype("float32")
data.aff = data.img.affine
data.fa = None
if denoise:
sigma = pca_noise_estimate(data.dwi, data.gtab, correct_bias=True,
smooth=Config.get_config().getint("denoise", "smooth",
fallback="3"))
data.dwi = localpca(data.dwi, sigma=sigma,
patch_radius=Config.get_config().getint("denoise", "pathRadius",
fallback="2"))
if 'mask' in file_names:
data.binarymask = nb.load(os.path.join(self.path, file_names['mask'])).get_data()
else:
_, data.binarymask = median_otsu(data.dwi[..., 0], 2, 1)
data.b0 = data.dwi[..., data.bvals < b0_threshold].mean(axis=-1)
return data
def handle(self):
img = nib.load(self.dmri_file)
data = img.get_data()
bvals, bvecs = read_bvals_bvecs(self.fbvals, self.fbvecs)
gtab = gradient_table(bvals, bvecs)
maskdata, mask = median_otsu(data, 3, 1, True,\
vol_idx=range(10, 50), dilate=2)
#print('maskdata.shape (%d, %d, %d, %d)' % maskdata.shape)
tenmodel = dti.TensorModel(gtab)
self.tenfit = tenmodel.fit(maskdata)
def compute_dti(fname_in, fname_bvals, fname_bvecs, prefix):
"""
Compute DTI.
:param fname_in: input 4d file.
:param bvals: bvals txt file
:param bvecs: bvecs txt file
:param prefix: output prefix. Example: "dti_"
:return: True/False
"""
# Open file.
from msct_image import Image
nii = Image(fname_in)
data = nii.data
print('data.shape (%d, %d, %d, %d)' % data.shape)
# open bvecs/bvals
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fname_bvals, fname_bvecs)
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs)
# # mask and crop the data. This is a quick way to avoid calculating Tensors on the background of the image.
# from dipy.segment.mask import median_otsu
# maskdata, mask = median_otsu(data, 3, 1, True, vol_idx=range(10, 50), dilate=2)
# print('maskdata.shape (%d, %d, %d, %d)' % maskdata.shape)
# fit tensor model
import dipy.reconst.dti as dti
tenmodel = dti.TensorModel(gtab)
tenfit = tenmodel.fit(data)
# Compute metrics
printv('Computing metrics...', param.verbose)
# FA
from dipy.reconst.dti import fractional_anisotropy
nii.data = fractional_anisotropy(tenfit.evals)
nii.setFileName(prefix + 'FA.nii.gz')
nii.save('float32')
# MD
from dipy.reconst.dti import mean_diffusivity
nii.data = mean_diffusivity(tenfit.evals)
nii.setFileName(prefix + 'MD.nii.gz')
nii.save('float32')
# RD
from dipy.reconst.dti import radial_diffusivity
nii.data = radial_diffusivity(tenfit.evals)
nii.setFileName(prefix + 'RD.nii.gz')
nii.save('float32')
# AD
from dipy.reconst.dti import axial_diffusivity
nii.data = axial_diffusivity(tenfit.evals)
nii.setFileName(prefix + 'AD.nii.gz')
nii.save('float32')
return True
def compute_dti(fname_in, fname_bvals, fname_bvecs, prefix):
"""
Compute DTI.
:param fname_in: input 4d file.
:param bvals: bvals txt file
:param bvecs: bvecs txt file
:param prefix: output prefix. Example: "dti_"
:return: True/False
"""
# Open file.
from msct_image import Image
nii = Image(fname_in)
data = nii.data
print('data.shape (%d, %d, %d, %d)' % data.shape)
# open bvecs/bvals
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fname_bvals, fname_bvecs)
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs)
# # mask and crop the data. This is a quick way to avoid calculating Tensors on the background of the image.
# from dipy.segment.mask import median_otsu
# maskdata, mask = median_otsu(data, 3, 1, True, vol_idx=range(10, 50), dilate=2)
# print('maskdata.shape (%d, %d, %d, %d)' % maskdata.shape)
# fit tensor model
import dipy.reconst.dti as dti
tenmodel = dti.TensorModel(gtab)
tenfit = tenmodel.fit(data)
# Compute metrics
printv('Computing metrics...', param.verbose)
# FA
from dipy.reconst.dti import fractional_anisotropy
nii.data = fractional_anisotropy(tenfit.evals)
nii.setFileName(prefix+'FA.nii.gz')
nii.save('float32')
# MD
from dipy.reconst.dti import mean_diffusivity
nii.data = mean_diffusivity(tenfit.evals)
nii.setFileName(prefix+'MD.nii.gz')
nii.save('float32')
# RD
from dipy.reconst.dti import radial_diffusivity
nii.data = radial_diffusivity(tenfit.evals)
nii.setFileName(prefix+'RD.nii.gz')
nii.save('float32')
# AD
from dipy.reconst.dti import axial_diffusivity
nii.data = axial_diffusivity(tenfit.evals)
nii.setFileName(prefix+'AD.nii.gz')
nii.save('float32')
return True
def run_to_estimate_dti(path_input,
path_output,
fbval="",
fbvec="",
file_inMask=""):
if fbval == "" or fbvec == "":
folder_sujeto = path_output
for l in os.listdir(folder_sujeto):
if "TENSOR" in l and "bval" in l:
fbval = os.path.join(folder_sujeto, l)
if "TENSOR" in l and "bvec" in l:
fbvec = os.path.join(folder_sujeto, l)
if file_inMask == "":
folder = os.path.dirname(path_input)
for i in os.listdir(folder):
if "masked_mask" in i:
file_inMask = os.path.join(folder, i)
#def to_estimate_dti(file_in, file_inMask, outPath, fbval, fbvec):
print(d.separador + 'building DTI Model...')
ref_name = utils.to_extract_filename(path_input)
file_evecs = os.path.join(path_output, ref_name + d.id_evecs + d.extension)
file_evals = os.path.join(path_output, ref_name + d.id_evals + d.extension)
if (not (os.path.exists(file_evecs))) | (not (os.path.exists(file_evals))):
try:
os.remove(file_evecs)
os.remove(file_evals)
except:
print("Unexpected error:", sys.exc_info()[0])
img = nib.load(path_input)
data = img.get_data()
mask = nib.load(file_inMask)
mask = mask.get_data()
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs)
tensor_model = dti.TensorModel(gtab)
tensor_fitted = tensor_model.fit(data, mask)
nib.save(
nib.Nifti1Image(tensor_fitted.evecs.astype(np.float32),
img.affine), file_evecs)
nib.save(
nib.Nifti1Image(tensor_fitted.evals.astype(np.float32),
img.affine), file_evals)
print(file_evecs)
print(file_evals)
print(path_input)
return path_input
def merge_multiple_phase_encodes(input_dwi_up, input_bvals_up, input_bvecs_up, input_index_up, input_acqparam_up, input_dwi_down, input_bvals_down, input_bvecs_down, input_index_down, input_acqparam_down, output_dwi, output_bvals, output_bvecs, output_index, output_acqparam):
#First, get the size of the images
img_up = nib.load(input_dwi_up)
img_dn = nib.load(input_dwi_down)
bvals_up, bvecs_up = read_bvals_bvecs(input_bvals_up, input_bvecs_up)
bvals_dn, bvecs_dn = read_bvals_bvecs(input_bvals_down, input_bvecs_down)
index_up = np.loadtxt(input_index_up)
index_dn = np.loadtxt(input_index_down)
acqparam_up = np.loadtxt(input_acqparam_up)
acqparam_dn = np.loadtxt(input_acqparam_down)
numImages_up = img_up.header.get_data_shape()[3]
numImages_dn = img_dn.header.get_data_shape()[3]
if bvals_up.shape[0] != numImages_up:
indices_to_remove_up = np.arange(numImages_up, bvals_up.shape[0])
bvals_up = np.delete(bvals_up, indices_to_remove_up)
bvecs_up = np.delete(bvecs_up, indices_to_remove_up, 0)
if bvals_dn.shape[0] != numImages_dn:
indices_to_remove_dn = np.arange(numImages_dn, bvals_dn.shape[0])
bvals_dn = np.delete(bvals_dn, indices_to_remove_dn)
bvecs_dn = np.delete(bvecs_dn, indices_to_remove_dn, 0)
#Read in the DWI ACQPARAMS FILE, DETERMINE WHICH IMAGES CORRESPOND TO UP AND DOWN, AND MERGE INTO SEPARATE FILES
os.system('fslmerge -t ' + output_dwi + ' ' + input_dwi_up + ' ' + input_dwi_down)
bvals = np.concatenate((bvals_up, bvals_dn), axis=0)
bvecs = np.concatenate((bvecs_up, bvecs_dn), axis=0)
index = np.concatenate((index_up, 2*index_dn), axis=0)
acqparam = np.vstack((acqparam_up, acqparam_dn))
np.savetxt(output_bvals, bvals, fmt='%i', newline=' ')
np.savetxt(output_bvecs, bvecs.transpose(), fmt='%.8f')
np.savetxt(output_index, index, fmt='%i', newline=' ')
np.savetxt(output_acqparam, acqparam, fmt='%.5f')
def main():
parser = build_args_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.INFO)
verify_overwrite(args.output_dwi, parser, args.force)
verify_overwrite(args.output_bvals, parser, args.force)
verify_overwrite(args.output_bvecs, parser, args.force)
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
# Find the volume indices that correspond to the shells to extract.
tol = args.tolerance
def get_shell_indices(bval):
return np.where(np.logical_and(bvals < bval + tol,
bvals > bval - tol))[0]
indices = [get_shell_indices(b) for b in args.bvals_to_extract]
indices = np.sort(np.hstack(indices))
if len(indices) == 0:
parser.error('There are no volumes that have the supplied b-values.')
logging.info(
'Extracting shells [{}], with number of images per shell [{}], '
'from {} images from {}.'.format(
' '.join([str(b) for b in args.bvals_to_extract]), ' '.join([
str(len(get_shell_indices(b))) for b in args.bvals_to_extract
]), len(bvals), args.dwi))
img = nib.load(args.dwi)
if args.block_size is None:
args.block_size = img.shape[-1]
# Load the shells by iterating through blocks of volumes. This approach
# is slower for small files, but allows very big files to be split
# with less memory usage.
shell_data = np.zeros((img.shape[:-1] + (len(indices), )),
dtype=img.get_data_dtype())
for vi, data in volumes(img, args.block_size):
in_volume = np.array([i in vi for i in indices])
in_data = np.array([i in indices for i in vi])
shell_data[..., in_volume] = data[..., in_data]
bvals = bvals[indices].astype(int)
bvals.shape = (1, len(bvals))
np.savetxt(args.output_bvals, bvals, '%d')
np.savetxt(args.output_bvecs, bvecs[indices, :].T, '%0.15f')
nib.save(nib.Nifti1Image(shell_data, img.affine), args.output_dwi)
def load_bval_bvec(fbval, fbvec):
"""
Takes bval and bvec files and produces a structure in dipy format
**Positional Arguments:**
"""
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, atol=0.01)
print(gtab.info)
return gtab
def to_register_dwi_to_mni(path_in, path_out, path_bvec, path_bval):
ref_name = utils.to_extract_filename(path_in)
# if not os.path.exists(path_out + ref_name + '_normalized' + d.extension):
img_DWI = nib.load(path_in)
data_DWI = img_DWI.get_data()
affine_DWI = img_DWI.affine
bvals, bvecs = read_bvals_bvecs(path_bval, path_bvec)
gtab = gradient_table(bvals, bvecs)
b0 = data_DWI[..., gtab.b0s_mask]
mean_b0 = np.mean(b0, -1)
mni_t2 = nib.load(d.standard_t2)
mni_t2_data = mni_t2.get_data()
MNI_T2_affine = mni_t2.affine
directionWarped = np.zeros((mni_t2_data.shape[0], mni_t2_data.shape[1],
mni_t2_data.shape[2], data_DWI.shape[-1]))
rangos = range(data_DWI.shape[-1])
affine, starting_affine = tools.affine_registration(
mean_b0,
mni_t2_data,
moving_grid2world=affine_DWI,
static_grid2world=MNI_T2_affine)
warped_moving, mapping = tools.syn_registration(
mean_b0,
mni_t2_data,
moving_grid2world=affine_DWI,
static_grid2world=MNI_T2_affine,
# step_length=0.1,
# sigma_diff=2.0,
metric='CC',
dim=3,
level_iters=[10, 10, 5],
# prealign=affine.affine)
prealign=starting_affine)
for gradientDirection in rangos:
# print(gradientDirection)
directionWarped[:, :, :, gradientDirection] = mapping.transform(
data_DWI[:, :, :, gradientDirection].astype(int),
interpolation='nearest')
nib.save(nib.Nifti1Image(directionWarped, MNI_T2_affine),
path_out + ref_name + '_normalized' + d.extension)
return path_out + ref_name + '_normalized' + d.extension, mapping
def tracking_eudx4csd(dir_src, dir_out, verbose=False):
# Load data
fbval = pjoin(dir_src, 'bvals_' + par_b_tag)
fbvec = pjoin(dir_src, 'bvecs_' + par_b_tag)
fdwi = pjoin(dir_src, 'data_' + par_b_tag + '_' + par_dim_tag + '.nii.gz')
#fmask = pjoin(dir_src, 'nodif_brain_mask_' + par_dim_tag + '.nii.gz')
fmask = pjoin(dir_src, 'wm_mask_' + par_b_tag + '_' + par_dim_tag + '.nii.gz')
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=par_b0_threshold)
data, affine = load_nifti(fdwi, verbose)
mask, _ = load_nifti(fmask, verbose)
sphere = get_sphere('symmetric724')
response, ratio = auto_response(gtab, data, roi_radius=par_ar_radius,
fa_thr=par_ar_fa_th)
# print('Response function', response)
# Model fitting
csd_model = ConstrainedSphericalDeconvModel(gtab, response)
csd_peaks = peaks_from_model(csd_model,
data,
sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
parallel=False)
# Computation of streamlines
streamlines = EuDX(csd_peaks.peak_values,
csd_peaks.peak_indices,
seeds=par_eudx_seeds,
odf_vertices= sphere.vertices,
a_low=par_eudx_threshold)
# Saving tractography
voxel_size = (par_dim_vox,) * 3
dims = mask.shape[:3]
hdr = nib.trackvis.empty_header()
hdr['voxel_size'] = voxel_size
hdr['voxel_order'] = 'LAS'
hdr['dim'] = dims
hdr['vox_to_ras'] = affine
strm = ((sl, None, None) for sl in streamlines)
trk_name = 'tractogram_' + par_b_tag + '_' + par_dim_tag + '_' + par_csd_tag + '_' + par_eudx_tag + '.trk'
trk_out = os.path.join(dir_out, trk_name)
nib.trackvis.write(trk_out, strm, hdr, points_space='voxel')
def peaks_from_nifti(fdwi, fbvec=None, fbval=None, mask=None):
if '.' not in fdwi:
fbase = fdwi
fdwi = fdwi+".nii.gz"
if not fbval:
fbval = fbase+".bval"
if not fbvec:
fbvec = fbase+".bvec"
print fdwi
img = nib.load(fdwi)
data = img.get_data()
zooms = img.get_header().get_zooms()[:3]
affine = img.get_affine()
bval, bvec = dio.read_bvals_bvecs(fbval, fbvec)
gtab = dgrad.gradient_table(bval, bvec)
if not mask:
print 'generate mask'
maskdata, mask = median_otsu(data, 3, 1, False, vol_idx=range(10, 50), dilate=2)
else:
mask_img = nib.load(mask)
mask = mask_img.get_data()
from dipy.segment.mask import applymask
maskdata = applymask(data, mask)
print maskdata.shape, mask.shape
from dipy.reconst.shm import QballModel, CsaOdfModel
model = QballModel(gtab, 6)
sphere = get_sphere('symmetric724')
print "fit Qball peaks"
proc_num = multiprocessing.cpu_count()-1
print "peaks_from_model using core# =" + str(proc_num)
peaks = peaks_from_model(model=model, data=maskdata, relative_peak_threshold=.5,
min_separation_angle=25,
sphere=sphere, mask=mask, parallel=True, nbr_processes=proc_num)
return peaks
def load_bval_bvec(self, fbval, fbvec):
"""
Takes bval and bvec files and produces a structure in dipy format
**Positional Arguments:**
streamlines:
- Fiber streamlines either file or array in a dipy EuDX
or compatible format.
"""
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, atol=0.01)
print gtab.info
return gtab
def reconstruction(dwi,bval_file,bvec_file,mask=None,type='dti',b0=0.,order=4):
""" Uses Dipy to reconstruct an fODF for each voxel.
Parameters
----------
dwi: numpy array (mandatory)
Holds the diffusion weighted image in a 4D-array (see nibabel).
bval_file: string (mandatory)
Path to the b-value file (FSL format).
bvec_file: string (mandatory)
Path to the b-vectors file (FSL format).
mask: numpy array
Holds the mask in a 3D array (see nibabel).
type: string \in {'dti','csd','csa'} (default = 'dti')
The type of the ODF reconstruction.
b0: float (default = 0)
Threshold to use for defining b0 images.
order: int (default = 4)
Order to use for constrained spherical deconvolution (csd) or constant solid angle (csa).
Returns
-----------
model_fit: Dipy Object (depends on the type)
Represents the fitted model for each voxel.
"""
#b-values and b-vectors
bvals, bvecs = read_bvals_bvecs(bval_file,bvec_file)
gtab = gradient_table(bvals, bvecs, b0_threshold=b0)
#reconstruction
if type == 'dti':
model = TensorModel(gtab,fit_method='WLS')
elif type == 'csd':
response, ratio = auto_response(gtab, dwi, roi_radius=10, fa_thr=0.7)
model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=order)
elif type == 'csa':
model = CsaOdfModel(gtab, order)
if mask is not None:
model_fit = model.fit(dwi,mask=mask)
else:
model_fit = model.fit(dwi)
return model_fit
def prepare_q4half(fimg, fbval, fbvec):
img = nib.load(fimg)
data = img.get_data()
affine = img.get_affine()
zooms = img.get_header().get_zooms()[:3]
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
bvecs[257: 257 + 256] = -bvecs[1:257]
bvals[257: 257 + 256] = bvals[1:257]
data[..., 257: 257 + 256] = data[..., 1:257]
bvals = np.delete(bvals, [513, 514], 0)
bvecs = np.delete(bvecs, [513, 514], 0)
data = np.delete(data, [513, 514], -1)
return data, affine, zooms, bvals, bvecs
def prepare_q5half(fimg, fbtext, fbval, fbvec, fmask, flipy):
img = nib.load(fimg)
data = img.get_data()
affine = img.get_affine()
zooms = img.get_header().get_zooms()[:3]
bvals, temp = read_bvals_bvecs(fbval, fbvec)
bmat = np.loadtxt(fbtext)
bvecs = bmat[:, 1:]
# Normalize bvec to unit norm
bvecs = bvecs / np.sqrt(np.sum(bvecs ** 2, axis=1))[:, None]
bvecs[np.isnan(bvecs)] = 0
if flipy:
bvecs[:,1] = -bvecs[:,1]
img_mask = nib.load(fmask)
mask = img_mask.get_data()
return data, affine, zooms, bvals, bvecs, mask
def make_dti_data(out_fbval, out_fbvec, out_fdata, out_shape=(5, 6, 7)):
"""
Create a synthetic data-set with a single shell acquisition
out_fbval, out_fbvec, out_fdata : str
Full paths to generated data and bval/bvec files
out_shape : tuple
The 3D shape of the output volum
"""
fimg, fbvals, fbvecs = dpd.get_data('small_64D')
img = nib.load(fimg)
bvals, bvecs = dio.read_bvals_bvecs(fbvals, fbvecs)
gtab = dpg.gradient_table(bvals, bvecs)
# Simulate a signal based on the DTI model:
signal = single_tensor(gtab, S0=100)
DWI = np.zeros(out_shape + (len(gtab.bvals), ))
DWI[:] = signal
nib.save(nib.Nifti1Image(DWI, img.affine), out_fdata)
np.savetxt(out_fbval, bvals)
np.savetxt(out_fbvec, bvecs)
def make_dki_data(out_fbval, out_fbvec, out_fdata, out_shape=(5, 6, 7)):
"""
Create a synthetic data-set with a 2-shell acquisition
out_fbval, out_fbvec, out_fdata : str
Full paths to generated data and bval/bvec files
out_shape : tuple
The 3D shape of the output volum
"""
# This is one-shell (b=1000) data:
fimg, fbvals, fbvecs = dpd.get_data('small_64D')
img = nib.load(fimg)
bvals, bvecs = dio.read_bvals_bvecs(fbvals, fbvecs)
# So we create two shells out of it
bvals_2s = np.concatenate((bvals, bvals * 2), axis=0)
bvecs_2s = np.concatenate((bvecs, bvecs), axis=0)
gtab_2s = dpg.gradient_table(bvals_2s, bvecs_2s)
# Simulate a signal based on the DKI model:
mevals_cross = np.array([[0.00099, 0, 0], [0.00226, 0.00087, 0.00087],
[0.00099, 0, 0], [0.00226, 0.00087, 0.00087]])
angles_cross = [(80, 10), (80, 10), (20, 30), (20, 30)]
fie = 0.49
frac_cross = [fie * 50, (1 - fie) * 50, fie * 50, (1 - fie) * 50]
# Noise free simulates
signal_cross, dt_cross, kt_cross = multi_tensor_dki(gtab_2s, mevals_cross,
S0=100,
angles=angles_cross,
fractions=frac_cross,
snr=None)
DWI = np.zeros(out_shape + (len(gtab_2s.bvals), ))
DWI[:] = signal_cross
nib.save(nib.Nifti1Image(DWI, img.affine), out_fdata)
np.savetxt(out_fbval, bvals_2s)
np.savetxt(out_fbvec, bvecs_2s)
def load_bval_bvec_dti(self, fbval, fbvec, dti_file, dti_file_out):
"""
Takes bval and bvec files and produces a structure in dipy format
**Positional Arguments:**
streamlines:
- Fiber streamlines either file or array in a dipy EuDX
or compatible format.
"""
# Load Data
startTime = datetime.now()
img = nb.load(dti_file)
data = img.get_data()
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
# Get rid of spurrious scans
idx = np.where((bvecs[:, 0] == 100) & (bvecs[:, 1] == 100) &
(bvecs[:, 2] == 100))
bvecs = np.delete(bvecs, idx, axis=0)
bvals = np.delete(bvals, idx, axis=0)
data = np.delete(data, idx, axis=3)
# Save corrected DTI volume
dti_new = nb.Nifti1Image(data, affine=img.get_affine(),
header=img.get_header())
dti_new.update_header()
nb.save(dti_new, dti_file_out)
gtab = gradient_table(bvals, bvecs, atol=0.01)
print gtab.info
return gtab
def shell_extraction(src_dwi, src_bvec, src_bval, out_b0,
delta=100, verbose=False):
shell = [0]
bvals, bvecs = read_bvals_bvecs(src_bval, src_bvec)
img = nib.load(src_dwi)
data = img.get_data()
affine = img.get_affine()
header = img.header
sind = np.zeros((bvals.size), dtype=bool)
for b in shell:
tind = (bvals < b+delta) & (bvals > b-delta)
sind = sind | tind
shell_data = data[..., sind].mean(axis=3)
shell_img = nib.Nifti1Image(shell_data, affine, header)
shell_img.update_header()
nib.save(shell_img, out_b0)
return sind.sum()
def compute_dti(fname_in, fname_bvals, fname_bvecs, prefix, method, evecs, file_mask):
"""
Compute DTI.
:param fname_in: input 4d file.
:param bvals: bvals txt file
:param bvecs: bvecs txt file
:param prefix: output prefix. Example: "dti_"
:param method: algo for computing dti
:param evecs: bool: output diffusion tensor eigenvectors and eigenvalues
:return: True/False
"""
# Open file.
from spinalcordtoolbox.image import Image
nii = Image(fname_in)
data = nii.data
sct.printv('data.shape (%d, %d, %d, %d)' % data.shape)
# open bvecs/bvals
bvals, bvecs = read_bvals_bvecs(fname_bvals, fname_bvecs)
gtab = gradient_table(bvals, bvecs)
# mask and crop the data. This is a quick way to avoid calculating Tensors on the background of the image.
if not file_mask == '':
sct.printv('Open mask file...', param.verbose)
# open mask file
nii_mask = Image(file_mask)
mask = nii_mask.data
# fit tensor model
sct.printv('Computing tensor using "' + method + '" method...', param.verbose)
import dipy.reconst.dti as dti
if method == 'standard':
tenmodel = dti.TensorModel(gtab)
if file_mask == '':
tenfit = tenmodel.fit(data)
else:
tenfit = tenmodel.fit(data, mask)
elif method == 'restore':
import dipy.denoise.noise_estimate as ne
sigma = ne.estimate_sigma(data)
dti_restore = dti.TensorModel(gtab, fit_method='RESTORE', sigma=sigma)
if file_mask == '':
tenfit = dti_restore.fit(data)
else:
tenfit = dti_restore.fit(data, mask)
# Compute metrics
sct.printv('Computing metrics...', param.verbose)
# FA
nii.data = tenfit.fa
nii.save(prefix + 'FA.nii.gz', dtype='float32')
# MD
nii.data = tenfit.md
nii.save(prefix + 'MD.nii.gz', dtype='float32')
# RD
nii.data = tenfit.rd
nii.save(prefix + 'RD.nii.gz', dtype='float32')
# AD
nii.data = tenfit.ad
nii.save(prefix + 'AD.nii.gz', dtype='float32')
if evecs:
data_evecs = tenfit.evecs
data_evals = tenfit.evals
# output 1st (V1), 2nd (V2) and 3rd (V3) eigenvectors as 4d data
for idim in range(3):
nii.data = data_evecs[:, :, :, :, idim]
nii.save(prefix + 'V' + str(idim+1) + '.nii.gz', dtype="float32")
nii.data = data_evals[:, :, :, idim]
nii.save(prefix + 'E' + str(idim+1) + '.nii.gz', dtype="float32")
return True
def compute_dti(fname_in, fname_bvals, fname_bvecs, prefix, method, file_mask):
"""
Compute DTI.
:param fname_in: input 4d file.
:param bvals: bvals txt file
:param bvecs: bvecs txt file
:param prefix: output prefix. Example: "dti_"
:param method: algo for computing dti
:return: True/False
"""
# Open file.
from msct_image import Image
nii = Image(fname_in)
data = nii.data
print('data.shape (%d, %d, %d, %d)' % data.shape)
# open bvecs/bvals
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fname_bvals, fname_bvecs)
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs)
# mask and crop the data. This is a quick way to avoid calculating Tensors on the background of the image.
if not file_mask == '':
printv('Open mask file...', param.verbose)
# open mask file
nii_mask = Image(file_mask)
mask = nii_mask.data
# fit tensor model
printv('Computing tensor using "'+method+'" method...', param.verbose)
import dipy.reconst.dti as dti
if method == 'standard':
tenmodel = dti.TensorModel(gtab)
if file_mask == '':
tenfit = tenmodel.fit(data)
else:
tenfit = tenmodel.fit(data, mask)
elif method == 'restore':
import dipy.denoise.noise_estimate as ne
sigma = ne.estimate_sigma(data)
dti_restore = dti.TensorModel(gtab, fit_method='RESTORE', sigma=sigma)
if file_mask == '':
tenfit = dti_restore.fit(data)
else:
tenfit = dti_restore.fit(data, mask)
# Compute metrics
printv('Computing metrics...', param.verbose)
# FA
from dipy.reconst.dti import fractional_anisotropy
nii.data = fractional_anisotropy(tenfit.evals)
nii.setFileName(prefix+'FA.nii.gz')
nii.save('float32')
# MD
from dipy.reconst.dti import mean_diffusivity
nii.data = mean_diffusivity(tenfit.evals)
nii.setFileName(prefix+'MD.nii.gz')
nii.save('float32')
# RD
from dipy.reconst.dti import radial_diffusivity
nii.data = radial_diffusivity(tenfit.evals)
nii.setFileName(prefix+'RD.nii.gz')
nii.save('float32')
# AD
from dipy.reconst.dti import axial_diffusivity
nii.data = axial_diffusivity(tenfit.evals)
nii.setFileName(prefix+'AD.nii.gz')
nii.save('float32')
return True
plt.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
plt.show()
plt.savefig('data.png', bbox_inches='tight')
"""
.. figure:: data.png
:align: center
**Showing the middle axial slice without (left) and with (right) diffusion weighting**.
The next step is to load the b-values and b-vectors from the disk using
the function ``read_bvals_bvecs``.
"""
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
"""
In Dipy, we use an object called ``GradientTable`` which holds all the acquision
specific parameters, e.g. b-values, b-vectors, timings and others. To create this
object you can use the function ``gradient_table``.
"""
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs)
"""
Finally, you can use ``gtab`` (the GradientTable object) to show some information about the
acquisition parameters
"""
def identify_b0(fname_bvecs, fname_bvals, bval_min, verbose):
# Identify b=0 and DWI images
sct.printv('\nIdentify b=0 and DWI images...', verbose)
index_b0 = []
index_dwi = []
# if bval is not provided
if not fname_bvals:
# Open bvecs file
bvecs = []
with open(fname_bvecs) as f:
for line in f:
bvecs_new = [x for x in map(float, line.split())]
bvecs.append(bvecs_new)
# Check if bvecs file is nx3
if not len(bvecs[0][:]) == 3:
sct.printv(' WARNING: bvecs file is 3xn instead of nx3. Consider using sct_dmri_transpose_bvecs.', verbose, 'warning')
sct.printv(' Transpose bvecs...', verbose)
# transpose bvecs
bvecs = list(zip(*bvecs))
# get number of lines
nt = len(bvecs)
# identify b=0 and dwi
for it in range(0, nt):
if math.sqrt(math.fsum([i**2 for i in bvecs[it]])) < 0.01:
index_b0.append(it)
else:
index_dwi.append(it)
# if bval is provided
else:
# Open bvals file
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(fname_bvals, fname_bvecs)
# get number of lines
nt = len(bvals)
# Identify b=0 and DWI images
sct.printv('\nIdentify b=0 and DWI images...', verbose)
for it in range(0, nt):
if bvals[it] < bval_min:
index_b0.append(it)
else:
index_dwi.append(it)
# check if no b=0 images were detected
if index_b0 == []:
sct.printv('ERROR: no b=0 images detected. Maybe you are using non-null low bvals? in that case use flag -bvalmin. Exit program.', 1, 'error')
sys.exit(2)
# display stuff
nb_b0 = len(index_b0)
nb_dwi = len(index_dwi)
sct.printv(' Number of b=0: ' + str(nb_b0) + ' ' + str(index_b0), verbose)
sct.printv(' Number of DWI: ' + str(nb_dwi) + ' ' + str(index_dwi), verbose)
# return
return index_b0, index_dwi, nb_b0, nb_dwi
import sys
import numpy as np
import nibabel as nib
import dipy.reconst.dti as dti
from dipy.core.gradients import gradient_table
from dipy.io import read_bvals_bvecs
fval = sys.argv[7]+'.bval'
fvec = sys.argv[7]+'.bvec'
bvals,bvecs = read_bvals_bvecs(fval,fvec)
fname = sys.argv[7]+'.nii.gz'
gtab=gradient_table(bvals,bvecs)
img=nib.load(fname)
data = img.get_data()
print('data.shape (%d, %d, %d, %d)' % data.shape)
x_f=int(sys.argv[1])
y_f=int(sys.argv[2])
z_f=int(sys.argv[3])
x_t=int(sys.argv[4])
y_t=int(sys.argv[5])
z_t=int(sys.argv[6])
mask = data[..., 0] > 50
tenmodel = dti.TensorModel(gtab)
print('Tensor fitting computation')
tenfit = tenmodel.fit(data, mask)
print('Computing anisotropy measures (FA, MD, RGB)')
from dipy.reconst.dti import fractional_anisotropy, color_fa, lower_triangular
FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
fa_img = nib.Nifti1Image(FA.astype(np.float32), img.get_affine())
nib.save(fa_img, sys.argv[7]+'_fa.nii.gz')
evecs_img = nib.Nifti1Image(tenfit.evecs.astype(np.float32), img.get_affine())
def run(rawargs):
arguments = docopt(doc, argv=rawargs, version='Fit v{0}'.format(Version))
configuration = {}
#Try to load the image data. If successful, save it to configuration as "data"
try:
configuration["data"] = nib.load(arguments["--image"])
except:
print("The image you specified does not exist, or cannot be read.")
sys.exit(1)
#Try to load the mask data. If successful, save it to configuration as "mask"
if arguments["--mask"] != None and arguments["--mask"] != "None":
try:
configuration["mask"] = nib.load(arguments["--mask"])
except:
print("The mask image you specified does not exist, or cannot be read.")
sys.exit(1)
else:
configuration["mask"] = None
#Try to load the bvec, bvals files. If successful, save it to configuration as "gradient_table"
try:
bvals, bvecs = read_bvals_bvecs(arguments["--bvals"], arguments["--bvecs"])
configuration["gradient_table"] = gradient_table(bvals, bvecs)
except:
print("Could not read bvec and/or bval file")
sys.exit(1)
#Update configuration with more basic settings
lookup = {"--out_dti": "out_dti",
"--out_dki": "out_dki",
"--out_residual": "out_residual",
"--out_noise": "out_noise",
"--out_snr": "out_snr",
"--out_fa": "out_fa",
"--out_md": "out_md",
"--out_rd": "out_rd",
"--out_ad": "out_ad",
"--out_mk": "out_mk",
"--out_rk": "out_rk",
"--out_ak": "out_ak",
"--mask_median_radius": "median_radius",
"--mask_numpass": "******"}
for key, value in lookup.iteritems():
if arguments[key] == "None" or arguments[key] == None:
configuration[value] = None
else:
configuration[value] = arguments[key]
if arguments["--fit_method"].upper() in ["WLS", "OLS"]:
configuration["fit_method"] = arguments["--fit_method"].upper()
else:
print("'{0}' is not a valid fit method. Choose either 'WLS', 'OLS'".format(arguments["--fit_method"].upper()))
sys.exit(1)
fitter = Fitter(**configuration)
fitter.apply_mask()
fitter.fit()
fitter.extract_scalars()
fitter.save()
sys.exit(0)
wm_data_bin = np.copy(wm_data)
wm_data_bin[wm_data_bin > 0] = 1
# Mask the dwi_data so that you're only investigating voxels inside the brain!
dwi_data = dwi_data * wm_data_bin.reshape([wm_data_bin.shape[0],
wm_data_bin.shape[1],
wm_data_bin.shape[2],
1])
parcellation_img = nib.load(parcellation_file)
parcellation_data = parcellation_img.get_data().astype(np.int)
wm_img = nib.load(wm_file)
wm_data = wm_img.get_data()
bvals, bvecs = read_bvals_bvecs(bvals_file, bvecs_file)
gtab = gradient_table(bvals, bvecs)
mask_data_bin[mask_data_bin > 0] = 1
wm_data_bin = np.copy(wm_data)
wm_data_bin[wm_data_bin > 0] = 1
parcellation_data = parcellation_data * mask_data_bin
parcellation_wm_data = parcellation_data * wm_data_bin
parcellation_wm_data = parcellation_wm_data.astype(np.int)
#=============================================================================
# Track all of white matter using EuDX
#=============================================================================
if not os.path.exists(Msym_file) and not os.path.exists(Mdir_file):
def run(self, data_files, bvals_files, bvecs_files, mask_files,
bbox_threshold=[0.6, 1, 0, 0.1, 0, 0.1], out_dir='',
out_file='product.json', out_mask_cc='cc.nii.gz',
out_mask_noise='mask_noise.nii.gz'):
"""Compute the signal-to-noise ratio in the corpus callosum.
Parameters
----------
data_files : string
Path to the dwi.nii.gz file. This path may contain wildcards to
process multiple inputs at once.
bvals_files : string
Path of bvals.
bvecs_files : string
Path of bvecs.
mask_files : string
Path of brain mask
bbox_threshold : variable float, optional
Threshold for bounding box, values separated with commas for ex.
[0.6,1,0,0.1,0,0.1]. (default (0.6, 1, 0, 0.1, 0, 0.1))
out_dir : string, optional
Where the resulting file will be saved. (default '')
out_file : string, optional
Name of the result file to be saved. (default 'product.json')
out_mask_cc : string, optional
Name of the CC mask volume to be saved (default 'cc.nii.gz')
out_mask_noise : string, optional
Name of the mask noise volume to be saved
(default 'mask_noise.nii.gz')
"""
io_it = self.get_io_iterator()
for dwi_path, bvals_path, bvecs_path, mask_path, out_path, \
cc_mask_path, mask_noise_path in io_it:
data, affine = load_nifti(dwi_path)
bvals, bvecs = read_bvals_bvecs(bvals_path, bvecs_path)
gtab = gradient_table(bvals=bvals, bvecs=bvecs)
logging.info('Computing brain mask...')
_, calc_mask = median_otsu(data)
mask, affine = load_nifti(mask_path)
mask = np.array(calc_mask == mask.astype(bool)).astype(int)
logging.info('Computing tensors...')
tenmodel = TensorModel(gtab)
tensorfit = tenmodel.fit(data, mask=mask)
logging.info(
'Computing worst-case/best-case SNR using the CC...')
if np.ndim(data) == 4:
CC_box = np.zeros_like(data[..., 0])
elif np.ndim(data) == 3:
CC_box = np.zeros_like(data)
else:
raise IOError('DWI data has invalid dimensions')
mins, maxs = bounding_box(mask)
mins = np.array(mins)
maxs = np.array(maxs)
diff = (maxs - mins) // 4
bounds_min = mins + diff
bounds_max = maxs - diff
CC_box[bounds_min[0]:bounds_max[0],
bounds_min[1]:bounds_max[1],
bounds_min[2]:bounds_max[2]] = 1
if len(bbox_threshold) != 6:
raise IOError('bbox_threshold should have 6 float values')
mask_cc_part, cfa = segment_from_cfa(tensorfit, CC_box,
bbox_threshold,
return_cfa=True)
save_nifti(cc_mask_path, mask_cc_part.astype(np.uint8), affine)
logging.info('CC mask saved as {0}'.format(cc_mask_path))
mean_signal = np.mean(data[mask_cc_part], axis=0)
mask_noise = binary_dilation(mask, iterations=10)
mask_noise[..., :mask_noise.shape[-1]//2] = 1
mask_noise = ~mask_noise
save_nifti(mask_noise_path, mask_noise.astype(np.uint8), affine)
logging.info('Mask noise saved as {0}'.format(mask_noise_path))
noise_std = np.std(data[mask_noise, :])
logging.info('Noise standard deviation sigma= ' + str(noise_std))
idx = np.sum(gtab.bvecs, axis=-1) == 0
gtab.bvecs[idx] = np.inf
axis_X = np.argmin(
np.sum((gtab.bvecs-np.array([1, 0, 0])) ** 2, axis=-1))
axis_Y = np.argmin(
np.sum((gtab.bvecs-np.array([0, 1, 0])) ** 2, axis=-1))
axis_Z = np.argmin(
np.sum((gtab.bvecs-np.array([0, 0, 1])) ** 2, axis=-1))
SNR_output = []
SNR_directions = []
for direction in ['b0', axis_X, axis_Y, axis_Z]:
if direction == 'b0':
SNR = mean_signal[0]/noise_std
logging.info("SNR for the b=0 image is :" + str(SNR))
else:
logging.info("SNR for direction " + str(direction) +
" " + str(gtab.bvecs[direction]) + "is :" +
str(SNR))
SNR_directions.append(direction)
SNR = mean_signal[direction]/noise_std
SNR_output.append(SNR)
data = []
data.append({
'data': str(SNR_output[0]) + ' ' + str(SNR_output[1]) +
' ' + str(SNR_output[2]) + ' ' + str(SNR_output[3]),
'directions': 'b0' + ' ' + str(SNR_directions[0]) +
' ' + str(SNR_directions[1]) + ' ' +
str(SNR_directions[2])
})
with open(os.path.join(out_dir, out_path), 'w') as myfile:
json.dump(data, myfile)
def load_data(fraw, fmask, fbval, fbvec):
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs, b0_threshold=10)
data, affine = load_nifti(fraw)
mask, _ = load_nifti(fmask)
return gtab, data, affine, mask
print(image.get_header().get_zooms()[:3])
import matplotlib.pyplot as plt
axial_middle = data.shape[2] / 2
plt.figure('Showing the datasets')
plt.subplot(1,2,1).set_axis_off()
plt.imshow(data[:,:, axial_middle, 0].T, cmap='gray', origin='lower')
plt.subplot(1,2,2).set_axis_off()
plt.imshow(data[:,:, axial_middle, 10].T, cmap='gray', origin='lower')
plt.show()
from dipy.io import read_bvals_bvecs
bvals, bvecs = read_bvals_bvecs(file_bval, file_bvec)
from dipy.core.gradients import gradient_table
gtab = gradient_table(bvals, bvecs)
print(gtab.info)
print(gtab.bvals)
print(gtab.bvecs[:10,:])
S0s = data[:,:,:, gtab.b0s_mask]
print(S0s.shape)
nib.save(nib.Nifti1Image(S0s, image.get_affine()), 'teste_S0s.nii.gz')
import numpy as np
def run(rawargs):
arguments = docopt(doc, argv=rawargs, version='Orientation Check v{0}'.format(Version))
inputs = [{"Value":"image file", "Flag": "--image"}, {"Value":"bvec file", "Flag": "--bvecs"}, {"Value":"bvec file", "Flag": "--bvecs"}]
for inputinfo in inputs:
if not exists(arguments[inputinfo["Flag"]]):
print("The {0} specified does not exist!".format(inputinfo["Value"]))
sys.exit(1)
rawimage = nib.load(arguments["--image"])
bvals, bvecs = read_bvals_bvecs(arguments['--bvals'], arguments['--bvecs'])
print("Generating gradient table.")
gtab = gradient_table(bvals, bvecs)
#Define the tensor model
print("Generating the tensor model.")
dti_wls = dti.TensorModel(gtab, fit_method="NLLS")
image_data = rawimage.get_data()
print("Masking the brain.")
image_masked, mask = median_otsu(image_data, 3, 1, autocrop=True, dilate=2)
#print(image_masked)
#image_masked_data = nib.nifti1.Nifti1Image(image_masked.astype(np.float32), image_data.get_affine())
#print("Saving masked brain image")
#nib.nifti1.save(image_masked_data, "./imagemasked.nii.gz")
print("Resampling the brain to a standard resolution.")
image, affine1 = reslice(image_masked, rawimage.get_affine(), rawimage.get_header().get_zooms()[:3], (3.0,3.0,3.0))
mask, maskaffine1 = reslice(mask.astype(numpy.int), rawimage.get_affine(), rawimage.get_header().get_zooms()[:3], (3.0,3.0,3.0))
#print(len([type(mask) for i in range(0,image.shape[3])]))
#mask = numpy.expand_dims(mask,3)
#print(mask)
#print(mask.shape)
#image=image*mask
print(image[0][0][0])
print("Checking the image dimensions")
Xsize, Ysize, Zsize, directions = image.shape
print("X: {0}\nY: {1}\nZ: {2}".format(Xsize, Ysize, Zsize))
#Define Image Scopes
print("Defining the image scopes.")
imagedict = {"axial": {"dropdim": [0,1], "scope": (slice(0,Xsize), slice(0,Ysize), slice(math.floor(Zsize/2),math.floor(Zsize/2)+1))},
"coronal": {"dropdim": [0,2], "scope": (slice(0,Xsize), slice(math.floor(Ysize/2),math.floor(Ysize/2)+1), slice(0, Zsize))},
"sagittal": {"dropdim": [1,2], "scope": (slice(math.floor(Xsize/2),math.floor(Xsize/2)+1), slice(0,Ysize), slice(0, Zsize))}}
#roi_idx = (slice(0,image.shape[0]), slice(0,image.shape[1]), slice(middleslice,middleslice+1))#(slice(0,image.shape[0]), slice(0,image.shape[1]), slice(int(image.shape[2]/2),int(image.shape[2]/2)+1))
print("Defining sphere.")
sphere = get_sphere('symmetric724')
#sphere = dpd.get_sphere('symmetric362')
#Slice the whole dataset by the scope
print("Slicing the dataset with the scopes.")
for view in ["sagittal", "coronal", "axial"]:
imagedict[view]["image"] = image[imagedict[view]["scope"]]
imagedict[view]["mask"] = mask[imagedict[view]["scope"]]
print("Fitting {0} data.".format(view))
fit_wls = dti_wls.fit(imagedict[view]["image"])
print("Extracting {0} FA.".format(view))
fa1 = fit_wls.fa * imagedict[view]["mask"]
print("Extracting {0} EVALS.".format(view))
evals1 = fit_wls.evals
print("Extracting {0} EVECS.".format(view))
evecs1 = fit_wls.evecs
print("Extracting {0} Color FA.".format(view))
cfa1 = dti.color_fa(fa1, evecs1)
cfa1 = cfa1/cfa1.max()
print("Defining {0} renderer.".format(view))
render = fvtk.ren()
print("Generating {0} image.".format(view))
x =cfa1.shape[imagedict[view]["dropdim"][0]]
y =cfa1.shape[imagedict[view]["dropdim"][1]]
#print(x, y, 1, 3)
cfa2 = cfa1.reshape(x, y, 1, 3)
evals2 = evals1.reshape(x, y, 1, 3)*1.25
evecs2 = evecs1.reshape(x, y, 1, 3, 3)*1.25
print("Adding render.")
fvtk.add(render, fvtk.tensor(evals2, evecs2, cfa2, sphere))
print("Recording render.")
with Xvfb() as xvfb:
fvtk.record(render, out_path=arguments["--out"+view], size=(800,800), magnification=2)
print("Image Saved")
sys.exit(0)