def test_anat_reg_report(self, execdir):
subject_id = "subj01"
data_dir = execdir.mkdir("data")
mri_dir = data_dir.mkdir(subject_id).mkdir("mri")
shape = (12, 8, 4)
affine = np.eye(4)
cost_file = "cost.txt"
cost_array = np.random.uniform(0, 1, 5)
np.savetxt(cost_file, cost_array)
in_data = np.random.normal(100, 5, shape)
in_file = "func.nii.gz"
nib.save(nib.Nifti1Image(in_data, affine), in_file)
wm_data = np.random.randint(0, 2, shape).astype("uint8")
wm_file = mri_dir.join("wm.mgz")
nib.save(nib.MGHImage(wm_data, affine), str(wm_file))
aseg_data = np.random.randint(0, 5, shape).astype("uint8")
aseg_file = mri_dir.join("aseg.mgz")
nib.save(nib.MGHImage(aseg_data, affine), str(aseg_file))
out = preproc.AnatRegReport(
subject_id=subject_id,
data_dir=data_dir,
in_file=in_file,
cost_file=cost_file,
).run().outputs
assert out.out_file == execdir.join("reg.png")
assert op.exists(out.out_file)
def save_weights_as_datasurface(self, weights, output_dir):
import os
import nibabel as nib
import numpy as np
if self._images is None:
self.get_images()
sample = nib.load(self._images[0][0])
infinite_norm = np.max(np.abs(weights))
left_hemi_data = np.atleast_3d(
np.divide(weights[:np.int(weights.size / 2)], infinite_norm))
left_hemi_mgh = nib.MGHImage(left_hemi_data,
affine=sample.affine,
header=sample.header)
nib.save(left_hemi_mgh, os.path.join(output_dir, "weights_lh.mgh"))
right_hemi_data = np.atleast_3d(
np.divide(weights[np.int(weights.size / 2):], infinite_norm))
right_hemi_mgh = nib.MGHImage(right_hemi_data,
affine=sample.affine,
header=sample.header)
nib.save(right_hemi_mgh, os.path.join(output_dir, "weights_rh.mgh"))
def freesurfer(lyman_info):
subject = "subj01"
mri_dir = lyman_info["data_dir"].join(subject).join("mri")
seed = sum(map(ord, "freesurfer"))
rs = np.random.RandomState(seed)
affine = np.eye(4)
vol_shape = lyman_info["vol_shape"]
mask = rs.choice([0, 1], vol_shape, p=[.2, .8])
norm_data = rs.randint(0, 110, vol_shape) * mask
norm_file = str(mri_dir.join("norm.mgz"))
nib.save(nib.MGHImage(norm_data.astype("uint8"), affine), norm_file)
wmparc_vals = [1000, 10, 11, 16, 8, 3000, 5001, 7, 46, 4]
wmparc_data = rs.choice(wmparc_vals, vol_shape) * mask
wmparc_file = str(mri_dir.join("wmparc.mgz"))
nib.save(nib.MGHImage(wmparc_data.astype("int16"), affine), wmparc_file)
lyman_info.update(
subject=subject,
norm_file=norm_file,
wmparc_file=wmparc_file,
)
return lyman_info
def mric_solve(segmented, target, TR,TE, alpha, save , *args):
import nibabel as nb
import numpy as np
#Flatten array
fseg= nb.load(segmented).get_data().reshape(1,-1)[0]
rI = np.zeros(len(fseg))
vox2ras = nb.load(target).get_header().get_vox2ras()
init = nb.load(target).get_data().reshape(1,-1)[0].astype("float32")
#init[init==0]=0.1 # To avoid warnings
solver = np.vectorize(mric_brentq)
G = np.zeros(len(fseg))
k1 =TR*3.2
k2 =TE*3.9
G[fseg>0] = np.exp(-TR/1.084) #white assume all white
G[fseg>999] = np.exp(-TR/1.820) #grey
G[fseg==4] = 0 # np.exp(-TR/20.000)
G[fseg==43] = 0 # np.exp(-TR/20.000) #ve
for j in range(len(args)):
i = args[j]
temp=nb.load(i).get_data().reshape(1,-1)[0].astype("float32")
rI[fseg>0] = temp[fseg>0]/init[fseg>0]
rI[np.isnan(rI)] = 1 # can be included
temp2 = np.array(solver(k1,k2,G,alpha,rI)).reshape(256,256,256)
img = nb.MGHImage(temp2.astype("float32"),vox2ras)
nb.save(img,save+str(j)+".mgz")
rI2 = temp/init
rI2[np.isnan(rI2)] = 1 #
temp3 = rI2.reshape(256,256,256)
img2 = nb.MGHImage(temp3.astype("float32"),vox2ras)
nb.save(img2,"testIR"+str(j)+".mgz")
def main(subject, bids_folder):
fn = op.join(bids_folder, 'derivatives', 'freesurfer', '{fs_subject}',
'surf', '{hemi}.{label}.mgz')
if subject == 'fsaverage':
for hemi in ['lh', 'rh']:
fs_subject = subject
im = nb.load(
fn.format(hemi=hemi,
label='wang2015_atlas',
fs_subject=fs_subject))
prob_mask = surface.load_surf_data(
fn.format(hemi=hemi,
label='wang2015_atlas',
fs_subject=fs_subject))
# print(prob_mask, op.exists(prob_mask))
label_mask = np.in1d(prob_mask, range(18, 24)).astype(np.int16)
new_im = nb.MGHImage(label_mask, im.affine, im.header)
new_im.to_filename(
fn.format(hemi=hemi, label='wang15_ips',
fs_subject=fs_subject))
else:
fs_subject = f'sub-{subject}'
for hemi in ['lh', 'rh']:
pts, poly = cortex.db.get_surf(f'sub-{subject}',
'pia',
hemisphere=hemi)
surf = cortex.polyutils.Surface(pts, poly)
im = nb.load(
fn.format(hemi=hemi,
label='wang15_fplbl',
fs_subject=fs_subject))
prob_mask = surface.load_surf_data(
fn.format(hemi=hemi,
label='wang15_fplbl',
fs_subject=fs_subject))
# print(prob_mask, op.exists(prob_mask))
label_mask = (prob_mask[18:24] > 0.05).any(0).astype(np.int16)
ix_mask = np.where(label_mask)[0]
ss = surf.create_subsurface(label_mask.astype(np.bool))
label_mask = ss.subsurface_vertex_mask
print(len(pts), len(label_mask))
new_im = nb.MGHImage(label_mask, im.affine, im.header)
new_im.to_filename(
fn.format(hemi=hemi, label='wang15_ips',
fs_subject=fs_subject))
def _reorient_image(img, axcodes='RAS'):
"""Reorient an image to a given orientation.
Parameters
----------
img : instance of SpatialImage
The MRI image.
axcodes : tuple | str
The axis codes specifying the orientation, e.g. "RAS".
See :func:`nibabel.orientations.aff2axcodes`.
Returns
-------
img_data : ndarray
The reoriented image data.
vox_ras_t : ndarray
The new transform from the new voxels to surface RAS.
Notes
-----
.. versionadded:: 0.24
"""
import nibabel as nib
orig_data = np.array(img.dataobj).astype(np.float32)
# reorient data to RAS
ornt = nib.orientations.axcodes2ornt(
nib.orientations.aff2axcodes(img.affine)).astype(int)
ras_ornt = nib.orientations.axcodes2ornt(axcodes)
ornt_trans = nib.orientations.ornt_transform(ornt, ras_ornt)
img_data = nib.orientations.apply_orientation(orig_data, ornt_trans)
orig_mgh = nib.MGHImage(orig_data, img.affine)
aff_trans = nib.orientations.inv_ornt_aff(ornt_trans, img.shape)
vox_ras_t = np.dot(orig_mgh.header.get_vox2ras_tkr(), aff_trans)
return img_data, vox_ras_t
def save_image(img_array, affine_info, header_info, save_as):
"""
Save an image (nibabel MGHImage), according to the desired output file format.
Supported formats are defined in supported_output_file_formats.
:param numpy.ndarray img_array: an array containing image data
:param numpy.ndarray affine_info: image affine information
:param nibabel.freesurfer.mghformat.MGHHeader header_info: image header information
:param str save_as: name under which to save prediction; this determines output file format
:return None: saves predictions to save_as
"""
assert any(save_as.endswith(file_ext) for file_ext in supported_output_file_formats), \
'Output filename does not contain a supported file format (' + ', '.join(file_ext for file_ext in supported_output_file_formats) + ')!'
mgh_img = None
if save_as.endswith('mgz'):
mgh_img = nib.MGHImage(img_array, affine_info, header_info)
elif any(save_as.endswith(file_ext) for file_ext in ['nii', 'nii.gz']):
mgh_img = nib.nifti1.Nifti1Pair(img_array, affine_info, header_info)
if any(save_as.endswith(file_ext) for file_ext in ['mgz', 'nii']):
nib.save(mgh_img, save_as)
elif save_as.endswith('nii.gz'):
## For correct outputs, nii.gz files should be saved using the nifti1 sub-module's save():
nib.nifti1.save(mgh_img, save_as)
def _fake_CT_coords(skull_size=5, contact_size=2):
"""Make somewhat realistic CT data with contacts."""
import nibabel as nib
brain = nib.load(op.join(subjects_dir, subject, 'mri', 'brain.mgz'))
verts = mne.read_surface(
op.join(subjects_dir, subject, 'bem', 'outer_skull.surf'))[0]
verts = apply_trans(np.linalg.inv(brain.header.get_vox2ras_tkr()), verts)
x, y, z = np.array(brain.shape).astype(int) // 2
coords = [(x, y - 14, z), (x - 10, y - 15, z), (x - 20, y - 16, z + 1),
(x - 30, y - 16, z + 1)]
center = np.array(brain.shape) / 2
# make image
np.random.seed(99)
ct_data = np.random.random(brain.shape).astype(np.float32) * 100
# make skull
for vert in verts:
x, y, z = np.round(vert).astype(int)
ct_data[slice(x - skull_size, x + skull_size + 1),
slice(y - skull_size, y + skull_size + 1),
slice(z - skull_size, z + skull_size + 1)] = 1000
# add electrode with contacts
for (x, y, z) in coords:
# make sure not in skull
assert np.linalg.norm(center - np.array((x, y, z))) < 50
ct_data[slice(x - contact_size, x + contact_size + 1),
slice(y - contact_size, y + contact_size + 1),
slice(z - contact_size, z + contact_size + 1)] = \
1000 - np.linalg.norm(np.array(np.meshgrid(
*[range(-contact_size, contact_size + 1)] * 3)), axis=0)
ct = nib.MGHImage(ct_data, brain.affine)
coords = apply_trans(ct.header.get_vox2ras_tkr(), np.array(coords))
return ct, coords
def epi_to_surf_xfm(epi_fname, reg_fname):
"""Obtain a transformation from epi voxels -> Freesurfer surf coords.
Parameters
----------
epi_fname : string
Filename pointing at image defining the epi space.
reg_fname : string
Filename pointing at registration file (from bbregister) that maps
``epi_img_fname`` to the Freesurfer anatomy.
Returns
-------
xfm : 4 x 4 numpy array
Transformation matrix that can be applied to surf coords.
"""
# Load the Freesurfer "tkreg" style transform file
# Confusingly, this file actually encodes the anat-to-func transform
anat2func_xfm = np.genfromtxt(reg_fname, skip_header=4, skip_footer=1)
func2anat_xfm = np.linalg.inv(anat2func_xfm)
# Get a tkreg-compatibile mapping from IJK to RAS
epi_img = nib.load(epi_fname)
mgh_img = nib.MGHImage(np.zeros(epi_img.shape[:3]), epi_img.get_affine(),
epi_img.get_header())
vox2ras_tkr = mgh_img.get_header().get_vox2ras_tkr()
# Combine the two transformations
xfm = np.dot(func2anat_xfm, vox2ras_tkr)
return xfm
def asmgh(infile):
outfile = op.basename(fslimage.removeExt(infile))
outfile = outfile + '.mgh'
inimg = fslimage.Image(infile)
outimg = nib.MGHImage(inimg.data, inimg.voxToWorldMat)
outimg.to_filename(outfile)
return outfile
def test_slice_browser_io(_slice_browser):
"""Test the input/output of the slice browser GUI."""
import nibabel as nib
with pytest.raises(ValueError, match='Base image is not aligned to MRI'):
_slice_browser(nib.MGHImage(
np.ones((96, 96, 96), dtype=np.float32), np.eye(4)),
subject=subject, subjects_dir=subjects_dir)
def mgh_from_sitk(sitk_img, orig_mgh_header=None):
if orig_mgh_header:
h1 = MGHHeader.from_header(orig_mgh_header)
else:
h1 = MGHHeader()
# get voxels sizes and set zooms (=delta in h1 header)
spacing = sitk_img.GetSpacing()
h1.set_zooms(np.asarray(spacing))
# Get direction cosines from sitk image, reshape to 3x3 Matrix
direction = np.asarray(sitk_img.GetDirection()).reshape(
3, 3, order="F") * [-1, -1, 1]
h1["Mdc"] = direction
# compute affine
origin = np.asarray(sitk_img.GetOrigin()).reshape(3, 1) * [[-1], [-1], [1]]
affine = np.vstack(
[np.hstack([h1['Mdc'].T * h1["delta"], origin]), [0, 0, 0, 1]])
# get dims and calculate and set new image center in world coords
dims = np.array(sitk_img.GetSize())
if dims.size == 3:
dims = np.hstack((dims, [1]))
h1['dims'] = dims
h1['Pxyz_c'] = affine.dot(np.hstack((dims[:3] / 2.0, [1])))[:3]
# swap axes as data is stored differently between sITK and Nibabel
data = np.swapaxes(sitk.GetArrayFromImage(sitk_img), 0, 2)
# assemble MGHImage from header, image data and affine
mgh_img = nib.MGHImage(data, affine, h1)
return mgh_img
def mric_RI(save, *args):
import numpy as np
import nibabel as nb
target = args[0][0]
vox2ras = nb.load(target).get_header().get_vox2ras()
idata = nb.load(target).get_data()
init = idata.reshape(1, -1)[0].astype("float32")
for j in range(1, len(args[0])):
i = args[0][j]
temp = nb.load(i).get_data().reshape(1, -1)[0].astype("float32")
rI2 = temp / init
rI2[np.isnan(rI2)] = 1 #
temp3 = rI2.reshape(idata.shape)
img2 = nb.MGHImage(temp3.astype("float32"), vox2ras)
print save + "/" + str(i).split("/")[-1]
nb.save(img2, save + "/" + str(i).split("/")[-1])
def write(self, outfile):
log.info('Writing output to ' + outfile)
if outfile.endswith('.nii') or outfile.endswith('.nii.gz'):
img = nib.Nifti1Image(self.out, self.m_rcs2ras)
if outfile.endswith('.mgh') or outfile.endswith('.mgz'):
self.out = self.out.astype(np.float32)
img = nib.MGHImage(self.out, self.m_rcs2ras)
nib.save(img, outfile)
def save_mgh(filename, array, demo):
""" save mgh file using nibabel and imported demo mgh file"""
mmap = np.memmap('/tmp/tmp',
dtype='float32',
mode='w+',
shape=demo.get_data().shape)
mmap[:, 0, 0] = array[:]
output = nb.MGHImage(mmap, demo.affine, demo.header)
nb.save(output, filename)
def test_ieeg_elec_locate_gui_io(_locate_ieeg):
"""Test the input/output of the intracranial location GUI."""
import nibabel as nib
info = mne.create_info([], 1000)
aligned_ct = nib.MGHImage(np.zeros((256, 256, 256), dtype=np.float32),
np.eye(4))
trans = mne.transforms.Transform('head', 'mri')
with pytest.raises(ValueError,
match='No channels found in `info` to locate'):
_locate_ieeg(info, trans, aligned_ct, subject, subjects_dir)
def freesurfer(lyman_info):
subject = "subj01"
mri_dir = lyman_info["data_dir"].join(subject).join("mri")
label_dir = lyman_info["data_dir"].join(subject).join("label")
seed = sum(map(ord, "freesurfer"))
rs = np.random.RandomState(seed)
affine = np.eye(4)
vol_shape = lyman_info["vol_shape"]
mask = rs.choice([0, 1], vol_shape, p=[.2, .8])
norm_data = rs.randint(0, 110, vol_shape) * mask
norm_file = str(mri_dir.join("norm.mgz"))
nib.save(nib.MGHImage(norm_data.astype("uint8"), affine), norm_file)
orig_file = str(mri_dir.join("orig.mgz"))
nib.save(nib.MGHImage(norm_data.astype("uint8"), affine), orig_file)
wmparc_vals = [1000, 10, 11, 16, 8, 3000, 5001, 7, 46, 4]
wmparc_data = rs.choice(wmparc_vals, vol_shape) * mask
wmparc_file = str(mri_dir.join("wmparc.mgz"))
nib.save(nib.MGHImage(wmparc_data.astype("int16"), affine), wmparc_file)
n = 10
fmt = ["%d", "%.3f", "%.3f", "%.3f", "%.9f"]
label_data = np.c_[np.arange(n), np.zeros((n, 4))]
label_files = {}
for hemi in ["lh", "rh"]:
fname = str(label_dir.join("{}.cortex.label".format(hemi)))
label_files[hemi] = fname
np.savetxt(fname, label_data, fmt=fmt, header=str(n))
lyman_info.update(
subject=subject,
norm_file=norm_file,
orig_file=orig_file,
wmparc_file=wmparc_file,
label_files=label_files,
)
return lyman_info
def write(self, outfile):
log.info('Writing output to ' + outfile)
# if out datatype is float64 make it float32
if self.out.dtype == np.float64:
self.out = self.out.astype(np.float32)
if outfile.endswith('.nii') or outfile.endswith('.nii.gz'):
img = nib.Nifti1Image(self.out, self.m_rcs2ras)
if outfile.endswith('.mgh') or outfile.endswith('.mgz'):
#self.out = self.out.astype(self.vol.dtype)
img = nib.MGHImage(self.out, self.m_rcs2ras)
nib.save(img, outfile)
def _ensure_image_in_surface_RAS(image, subject, subjects_dir):
"""Check if the image is in Freesurfer surface RAS space."""
import nibabel as nib
if not isinstance(image, nib.spatialimages.SpatialImage):
image = nib.load(image)
image = nib.MGHImage(image.dataobj.astype(np.float32), image.affine)
fs_img = nib.load(op.join(subjects_dir, subject, 'mri', 'brain.mgz'))
if not np.allclose(image.affine, fs_img.affine, atol=1e-6):
raise RuntimeError('The `image` is not aligned to Freesurfer '
'surface RAS space. This space is required as '
'it is the space where the anatomical '
'segmentation and reconstructed surfaces are')
return image # returns MGH image for header
def save_weights_as_datasurface(self, weights, output_dir):
import numpy as np
import nibabel as nib
import os
if self._images is None:
self.get_images()
sample = nib.load(self._images[0][0])
left_hemi_data = np.atleast_3d(weights[:weights.size / 2])
left_hemi_mgh = nib.MGHImage(left_hemi_data,
affine=sample.affine,
header=sample.header)
nib.save(left_hemi_mgh, os.path.join(output_dir, 'weights_lh.mgh'))
right_hemi_data = np.atleast_3d(weights[weights.size / 2:])
right_hemi_mgh = nib.MGHImage(right_hemi_data,
affine=sample.affine,
header=sample.header)
nib.save(right_hemi_mgh, os.path.join(output_dir, 'weights_rh.mgh'))
pass
def predict_segmentation(input_arr, model_name, header):
batch_size = 10
count = 0
result = []
model = torch.load('api/pytorch_models/' + model_name + '.model')
input_arr = input_arr.reshape(
(-1, 1, input_arr.shape[-2], input_arr.shape[-1]))
if model_name == "quicknat":
input_arr = np.transpose(input_arr, [0, 1, 3, 2])
while count <= input_arr.shape[0]:
last_index = count + batch_size - 1
if last_index > input_arr.shape[0]:
last_index = input_arr.shape[0]
out = model(
Variable(torch.Tensor(input_arr[count:last_index]).cuda(),
volatile=True))
result.append(out)
count += batch_size - 1
result = torch.cat(result)
result = F.softmax(result, dim=1)
max_val, idx = torch.max(result, 1)
idx = idx.data.cpu().numpy()
color_map = [
label for label in SEG_LABELS_LIST[model_name] if label["id"] != 0
]
stats = {'color_map': color_map}
if model_name == "quicknat":
idx = np.transpose(idx, [0, 2, 1])
indexes, counts = np.unique(np.ravel(idx), return_counts=True)
indexes = indexes[1:]
counts = counts[1:]
indexes = [str(i) for i in indexes]
counts = [str(c) for c in counts]
stats['volume_estimates'] = dict(zip(indexes, counts))
feature_matrix = np.loadtxt('api/age_estimation/feature_matrix.csv')
predicted_age, uncertainty = estimate_age(
np.expand_dims(feature_matrix[1],
axis=0), 'api/age_estimation/gpr_model.sav',
'api/age_estimation/gpr_scaler.sav')
stats['predicted_age'] = np.round(predicted_age[0], 2)
stats['predicted_age_uncertainty'] = np.round(uncertainty[0], 2)
# Create a new file
nifti_img = nib.MGHImage(idx, np.eye(4), header=header)
result = np.array([label_img_to_rgb(frame, model_name) for frame in idx])
return {'result': result, 'stats': stats, 'nifti_img': nifti_img}
def conform(img, order=1):
"""
Python version of mri_convert -c, which turns image intensity values into UCHAR, reslices images to standard position, fills up
slices to standard 256x256x256 format and enforces 1 mm isotropic voxel sizes.
Difference to mri_convert -c is that we first interpolate (float image), and then rescale to uchar. mri_convert is
doing it the other way. However, we compute the scale factor from the input to be more similar again
:param nibabel.MGHImage img: loaded source image
:param int order: interpolation order (0=nearest,1=linear(default),2=quadratic,3=cubic)
:return:nibabel.MGHImage new_img: conformed image
"""
from nibabel.freesurfer.mghformat import MGHHeader
cwidth = 256
csize = 1
h1 = MGHHeader.from_header(
img.header) # may copy some parameters if input was MGH format
h1.set_data_shape([cwidth, cwidth, cwidth, 1])
h1.set_zooms([csize, csize, csize])
h1['Mdc'] = [[-1, 0, 0], [0, 0, -1], [0, 1, 0]]
h1['fov'] = cwidth
h1['Pxyz_c'] = img.affine.dot(
np.hstack((np.array(img.shape[:3]) / 2.0, [1])))[:3]
# from_header does not compute Pxyz_c (and probably others) when importing from nii
# Pxyz is the center of the image in world coords
# get scale for conversion on original input before mapping to be more similar to mri_convert
src_min, scale = getscale(img.get_data(), 0, 255)
mapped_data = map_image(img,
h1.get_affine(),
h1.get_data_shape(),
order=order)
# print("max: "+format(np.max(mapped_data)))
if not img.get_data_dtype() == np.dtype(np.uint8):
if np.max(mapped_data) > 255:
mapped_data = scalecrop(mapped_data, 0, 255, src_min, scale)
new_data = np.uint8(np.rint(mapped_data))
new_img = nib.MGHImage(new_data, h1.get_affine(), h1)
# make sure we store uchar
new_img.set_data_dtype(np.uint8)
return new_img
def synthesize_image(self, in_img_file, out_img_filename, step_size):
in_img = nib.load(in_img_file)
(in_patches, in_indices, padded_img_size) = self.feature_generator.extract_patches(in_img_file, intensity_threshold=0,
step_size=step_size, is_label_img=False,
indices=None)
out_patches = self.model.predict(in_patches)
patch_crop_size = [1, 1, 1] # should be filter_size/2
out_img_data, count_img_data = self.feature_generator.build_image_from_patches(out_patches, in_indices,
padded_img_size, patch_crop_size)
out_img_data = intensity_standardize_utils.wm_peak_normalize(out_img_data)
out_img_data[out_img_data > 255] = 255
out_img = nib.MGHImage(out_img_data, in_img.affine, in_img.header)
nib.save(out_img, out_img_filename)
def avgerage_brainimg_pr(projectdir,
sessidlist,
funcname,
analysis_name,
runlist,
savepath,
outfmt="mgz"):
"""Average result per run after doing zscore, doing to all sessions.
Parameters
----------
projectdir: name of where your session data placed, type: str.
sessidlist: list of sessid, type: list[str].
funcname: name of your func, under sessid dir.
analysis_name: analysis dir name in mkanalysis-sess.
runlist: list of runid.
savepath: dir of where to put average result file.
outfmt: suffix of out file.
"""
for runid in runlist:
prid = "pr%s" % runid
check_dir(savepath)
result_name = "mean_res_%s.%s" % (runid, outfmt)
result_path = os.path.join(savepath, result_name)
data = []
for sessid in sessidlist:
fileroot = os.path.join(projectdir, sessid, funcname,
analysis_name, prid, "res")
filename = "res-%s.nii.gz" % runid
filepath = os.path.join(fileroot, filename)
print("loading %s" % filepath)
result_run = nib.load(filepath)
result_data = stats.zscore(result_run.get_data()[:, 0, 0, :],
axis=1) # doing zscore before average.
data.append(result_data)
print("Shape of img: {}: ".format(np.shape(data)))
avg_data = np.mean(data, axis=0)
print("Shape of avg_data: {}: ".format(np.shape(avg_data)))
avg_data = np.reshape(avg_data, result_run.shape)
data_file = nib.MGHImage(avg_data, None, result_run.get_header())
nib.save(data_file, result_path)
print("Saving %s" % result_path)
print("===" * 10)
def test_lossless_slice_noscaling(tmp_path):
fname = tmp_path / 'image.mgh'
img = nb.MGHImage(np.random.uniform(-20000, 20000,
(5, 5, 5, 5)).astype("float32"),
affine=np.eye(4))
img.to_filename(fname)
img1 = nb.load(fname)
sliced_fname = tmp_path / 'sliced.mgh'
lossless_slice(
img1,
(slice(None), slice(None), slice(2, 4))).to_filename(sliced_fname)
img2 = nb.load(sliced_fname)
assert np.array_equal(img1.get_fdata()[:, :, 2:4], img2.get_fdata())
assert np.array_equal(img1.dataobj.get_unscaled()[:, :, 2:4],
img2.dataobj.get_unscaled())
assert img1.dataobj.slope == img2.dataobj.slope
assert img1.dataobj.inter == img2.dataobj.inter
def save2mgh(fpath, data, affine=None, header=None):
"""
Save to a MGH/MGZ file
The .mgh file format is used to store high-resolution structural data and
other data which are to be overlaid on the high-resolution structural volume.
A .mgz (or .mgh.gz) file is a .mgh file that has been compressed with ZLib.
NOTE!!! MGH file format seemingly has 3D dimensions at least. As a result, it essentially
regards the first dimensions as a volume and the forth dimension as the number of volumes.
References:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
http://nipy.org/nibabel/reference/nibabel.freesurfer.html#nibabel.freesurfer.mghformat.MGHImage
:param fpath: str
The file path to output. valid_exts = ('.mgh', '.mgz')
:param data: numpy array
:param affine: numpy array
:param header: MGHHeader
"""
img = nib.MGHImage(data, affine, header=header)
nib.save(img, fpath)
def save_brainimg(imgpath, data, header):
"""
Save brain image identified by its suffix
suffix now support
Nifti: .nii.gz
freesurfer: .mgz, .mgh
cifti: .dscalar.nii, .dlabel.nii, .dtseries.nii
Parameters:
------------
imgpath: brain image path to be saved
data: brain image data matrix
header: brain image header
Returns:
--------
"""
imgname = os.path.basename(imgpath)
imgsuffix = imgname.split('.')[1:]
imgsuffix = '.'.join(imgsuffix)
if imgsuffix == 'nii.gz':
data = np.transpose(data, (1, 2, 3, 0))
outimg = nib.Nifti1Image(data, None, header)
nib.save(outimg, imgpath)
elif imgsuffix == 'mgz' or imgsuffix == 'mgh':
data = np.transpose(data, (1, 2, 3, 0))
outimg = nib.MGHImage(data, None, header)
nib.save(outimg, imgpath)
elif imgsuffix == 'dscalar.nii' or imgsuffix == 'dlabel.nii' or imgsuffix == 'dtseries.nii':
data = data[..., 0, 0]
map_name = [''] * data.shape[0]
bm_full = header[1]
cifti.write(imgpath, data,
(cifti.Scalar.from_names(map_names), bm_full))
else:
raise Exception(
'Not support this format of brain image data, please contact with author to update this function.'
)
def get_diff_data(editp, uneditp, vol, subnum, savediff, diffp):
# Calculate difference image
if vol == "brain.finalsurfs":
edit_img = nib.load(path.join(editp, 'mri/%s.manedit.mgz') % (vol))
else:
edit_img = nib.load(path.join(editp, 'mri/%s.mgz') % (vol))
edit_data = edit_img.get_fdata()
unedit_img = nib.load(
path.join(uneditp, 'sub-%s/mri/%s.mgz') % (subnum, vol))
unedit_data = unedit_img.get_fdata()
diff_data = unedit_data - edit_data
if savediff:
diff_img = nib.MGHImage(diff_data.astype(np.int32), edit_img.affine)
nib.save(diff_img, os.path.join(diffp, 'diff_%s.mgz') % (vol))
# Extract non-zero values from difference data and arrange in df
out = pd.DataFrame(np.asarray(
np.asarray(diff_data != 0).nonzero()).T).rename(columns={
0: "Sag",
1: "Axe",
2: "Cor"
})
out['diff_val'] = diff_data[np.where(diff_data != 0)]
out['Action'] = np.where(out.diff_val > 0, "delete voxel", "add voxel")
# When WM edits are not perfect it can look like voxel additions
# For the clarity of the summary drop these
if vol == "wm" or vol == "brainmask":
out = out.query("diff_val != -1")
out = out.drop(columns="diff_val")
out['Vol'] = vol
out = out.sort_values(by=['Cor'])
out.reset_index(drop=True)
return (out)
def main(subject, bids_folder):
(pts_l, poly_l), (pts_r, poly_r) = cortex.db.get_surf(f'sub-{subject}', 'pia')
surf_l = cortex.polyutils.Surface(pts_l, poly_l)
surf_r = cortex.polyutils.Surface(pts_r, poly_r)
for hemi, surf in [('lh', surf_l), ('rh', surf_r)]:
im = nb.load(op.join(bids_folder, 'derivatives', 'freesurfer', f'sub-{subject}', 'surf', f'{hemi}.wang15_ips.mgz'))
mask = np.squeeze(im.get_data().astype(bool))
print(mask.sum())
ss = surf.create_subsurface(mask)
nlverts = len(ss.pts)
dist_matrix = np.zeros((nlverts, nlverts))
for i in tqdm(range(len(dist_matrix))):
dist_matrix[i] = ss.geodesic_distance(i)
v1 = dist_matrix[np.triu_indices(nlverts, k = 1)]
v2 = dist_matrix[np.tril_indices(nlverts, k = -1)]
v = (v1 + v2) / 2.
# see https://stackoverflow.com/questions/17527693/transform-the-upper-lower-triangular-part-of-a-symmetric-matrix-2d-array-into/58806626#58806626
dist_matrix_ = np.zeros((nlverts,nlverts))
dist_matrix_[np.triu_indices(nlverts, k = 1)] = v
dist_matrix_ = dist_matrix_ + dist_matrix_.T
print(dist_matrix - dist_matrix_)
print(np.array_equal(dist_matrix, dist_matrix_))
# im = gifti.GiftiImage(darrays=[gifti.GiftiDataArray(v)])
# im.to_filename(op.join(bids_folder, 'derivatives', 'freesurfer', f'sub-{subject}', 'surf', f'{hemi}.wang15_ips_distance.gii'))
new_im = nb.MGHImage(v, im.affine, im.header)
new_im.to_filename(op.join(bids_folder, 'derivatives', 'freesurfer', f'sub-{subject}', 'surf', f'{hemi}.wang15_ips_distance.mgz'))
def test_inject_skullstrip(tmp_path):
t1_mgz = tmp_path / "sub-01" / "mri" / "T1.mgz"
t1_mgz.parent.mkdir(parents=True)
# T1.mgz images are uint8
nb.MGHImage(np.ones((5, 5, 5), dtype=np.uint8), np.eye(4)).to_filename(str(t1_mgz))
mask_nii = tmp_path / "mask.nii.gz"
# Masks may be in a different space (and need resampling), but should be boolean,
# or uint8 in NIfTI
nb.Nifti1Image(np.ones((6, 6, 6), dtype=np.uint8), np.eye(4)).to_filename(
str(mask_nii)
)
FSInjectBrainExtracted(
subjects_dir=str(tmp_path), subject_id="sub-01", in_brain=str(mask_nii)
).run()
assert Path.exists(tmp_path / "sub-01" / "mri" / "brainmask.auto.mgz")
assert Path.exists(tmp_path / "sub-01" / "mri" / "brainmask.mgz")
# Run a second time to hit "already exists" condition
FSInjectBrainExtracted(
subjects_dir=str(tmp_path), subject_id="sub-01", in_brain=str(mask_nii)
).run()
