def remove_vols(dwifile, bvalfile, bvecfile, remove_Is, output_prefix):
import numpy as np
import nibabel as nib
# load data
dwidata = nib.load(dwifile)
data = dwidata.get_data()
bvals = np.genfromtxt(bvalfile)
bvecs = np.genfromtxt(bvecfile)
# bvecs = bvecs.T
# create output data
shape = (dwidata.shape[0], dwidata.shape[1], dwidata.shape[2], data.shape[3]-len(remove_Is))
print shape
writedata = np.empty(shape)
write_bvals = []
write_bvecs = []
g_all_i = 0
for g_i in range(data.shape[3]):
if not (g_i in remove_Is):
writedata[:,:,:,g_all_i] = data[:,:,:,g_i]
g_all_i = g_all_i + 1
write_bvals.append(bvals[g_i])
write_bvecs.append(bvecs[g_i])
# write output data
outfile = experiment_dir + '/' + output_prefix + '/' + output_prefix + 'subvolumes.nii.gz'
nib.save(nib.nifti1.Nifti1Image(writedata, dwidata.get_affine()), outfile)
bvecs = np.array(bvecs).T
bvalfile = experiment_dir + '/' + output_prefix + '/' + output_prefix + 'subvolumes.bval'
np.savetxt(bvalfile, bvals, fmt='%1.10f')
bvecfile = experiment_dir + '/' + output_prefix + '/' + output_prefix + 'subvolumes.bvec'
np.savetxt(bvecfile, bvecs, fmt='%1.10f')
return outfile, bvalfile, bvecfile
def _run_interface(self, runtime):
from dipy.reconst import dti
from dipy.io.utils import nifti1_symmat
gtab = self._get_gradient_table()
img = nb.load(self.inputs.in_file)
data = img.get_data()
affine = img.affine
mask = None
if isdefined(self.inputs.mask_file):
mask = nb.load(self.inputs.mask_file).get_data()
# Fit it
tenmodel = dti.TensorModel(gtab)
ten_fit = tenmodel.fit(data, mask)
lower_triangular = ten_fit.lower_triangular()
img = nifti1_symmat(lower_triangular, affine)
out_file = self._gen_filename('dti')
nb.save(img, out_file)
IFLOGGER.info('DTI parameters image saved as {i}'.format(i=out_file))
#FA MD RD and AD
for metric in ["fa", "md", "rd", "ad"]:
data = getattr(ten_fit,metric).astype("float32")
out_name = self._gen_filename(metric)
nb.Nifti1Image(data, affine).to_filename(out_name)
IFLOGGER.info('DTI {metric} image saved as {i}'.format(i=out_name, metric=metric))
return runtime
def export_lol_mask_file(rada_lol_file,Pajek_net_file,coords_file,mask_file):
import numpy as np
import nibabel as nib
import os
from dmgraphanalysis.utils_cor import return_mod_mask_corres,read_lol_file,read_Pajek_corres_nodes
print 'Loading Pajek_net_file for reading node_corres'
node_corres = read_Pajek_corres_nodes(Pajek_net_file)
print node_corres.shape
print 'Loading coords'
coords = np.array(np.loadtxt(coords_file),dtype = int)
print coords.shape
print 'Loading mask parameters'
mask = nib.load(mask_file)
data_mask_shape = mask.get_data().shape
mask_header = mask.get_header().copy()
mask_affine = np.copy(mask.get_affine())
print "Loading community belonging file" + rada_lol_file
community_vect = read_lol_file(rada_lol_file)
print community_vect
print "transforming to nii file"
lol_mask_data = return_mod_mask_corres(community_vect,node_corres,coords,data_mask_shape)
#print lol_mask_data
print lol_mask_data.shape
#print "saving npy file"
#mod_mask_file = os.path.abspath("mod_mask_data.npy")
#np.save(mod_mask_file ,np.array(mod_mask_data,dtype = int))
print "saving nii file"
lol_mask_file = os.path.abspath("lol_mask_data.nii")
nib.save(nib.Nifti1Image(np.array(lol_mask_data,dtype = int),mask_affine,mask_header),lol_mask_file)
#print "returning"
#lol_mask_file = ""
return lol_mask_file
def mask_brain(FeatDir, fMask=""):
'''
This function creates a brain mask based on the subject's normalized
T1_brain image. It can also incorporate an external mask.
Input parameters:
FeatDir: The .feat directory where segmentation results reside.
fMask: The file name for the binary mask image. If not provided,
then it will be omitted.
Returns:
NONE:
Output:
It produces a mask image callsed mask_brain.nii.gz under the
reg directory of the FeatDir.
'''
# directory and file names
RegDir = os.path.join(FeatDir, 'reg')
sBase = image_base(FeatDir)
fT1 = sBase + '.nii.gz'
fT1_bin = sBase + '_bin.nii.gz'
ffmri = os.path.join(RegDir, 'func2standard_r.nii.gz')
fIntersect = os.path.join(RegDir, 'mask_brain.nii.gz')
# threshold the T1 image
com_fslmaths = 'fslmaths ' + fT1
com_fslmaths += ' -bin ' + fT1_bin
res = os.system(com_fslmaths)
# reslicing the binarized T1 image to the fMRI space
fT1_bin_r = reslice_to_fMRI(fT1_bin, ffmri)
# if an external mask is provided
if fMask!="":
# first, copy the mask to the reg directory
MaskDir, fMaskImg = os.path.split(os.path.abspath(fMask))
fMaskCopy = os.path.join(RegDir, fMaskImg)
com_cp = 'cp ' + os.path.join(MaskDir, fMaskImg) + ' ' + RegDir
res = os.system(com_cp)
# then reslice the mask copy to the voxel size of fMRI data
fMaskCopy_r = reslice_to_fMRI(fMaskCopy, ffmri)
# multiplying the resliced external mask and the brain mask
# first, load mask images
img_mask = nib.load(fMaskCopy_r)
X_mask = img_mask.get_data()
img_brain = nib.load(fT1_bin_r)
X_brain = img_brain.get_data()
# then multiply masks
X_prod = X_mask * X_brain
# then saving the new mask image
maskimg = nib.Nifti1Image(X_prod, img_mask.get_affine())
nib.save(maskimg, fIntersect)
# if an external mask is not provided
else:
com_cp = 'cp ' + fT1_bin_r + ' ' + fIntersect
res = os.system(com_cp)
def _run_interface(self, runtime):
from dipy.reconst import dti
# Load the 4D image files
img = nb.load(self.inputs.in_file)
data = img.get_data()
affine = img.get_affine()
# Load the gradient strengths and directions
gtab = self._get_gradient_table()
# Mask the data so that tensors are not fit for
# unnecessary voxels
mask = data[..., 0] > 50
# Fit the tensors to the data
tenmodel = dti.TensorModel(gtab)
tenfit = tenmodel.fit(data, mask)
# Calculate the mode of each voxel's tensor
mode_data = tenfit.mode
# Write as a 3D Nifti image with the original affine
img = nb.Nifti1Image(mode_data, affine)
out_file = self._gen_filename('mode')
nb.save(img, out_file)
IFLOGGER.info('Tensor mode image saved as {i}'.format(i=out_file))
return runtime
def _run_interface(self, runtime):
from dipy.reconst import dki
from dipy.io.utils import nifti1_symmat
gtab = self._get_gradient_table()
img = nb.load(self.inputs.in_file)
data = img.get_data()
affine = img.affine
mask = None
if isdefined(self.inputs.mask_file):
mask = nb.load(self.inputs.mask_file).get_data()
# Fit the DKI model
kurtosis_model = dki.DiffusionKurtosisModel(gtab)
kurtosis_fit = kurtosis_model.fit(data, mask)
lower_triangular = kurtosis_fit.lower_triangular()
img = nifti1_symmat(lower_triangular, affine)
out_file = self._gen_filename('dki')
nb.save(img, out_file)
IFLOGGER.info('DKI parameters image saved as {i}.format(i=out_file)')
# FA, MD, RD, and AD
for metric in ['fa', 'md', 'rd', 'ad', 'mk', 'ak', 'rk']:
data = getattr(kurtosis_fit.metric).astype('float32')
out_name = self._gen_filename(metric)
nb.Nifti1Image(data, affine).to_filename(out_name)
IFLOGGER.info('DKI {metric} image saved as {i}'.format(i=out_name,
metric=metric))
return runtime
def intersect_masks(input_masks, output_filename=None, threshold=0.5, cc=True):
"""
Given a list of input mask images, generate the output image which
is the the threshold-level intersection of the inputs
Parameters
----------
input_masks: list of strings or ndarrays
paths of the input images nsubj set as len(input_mask_files), or
individual masks.
output_filename, string:
Path of the output image, if None no file is saved.
threshold: float within [0, 1[, optional
gives the level of the intersection.
threshold=1 corresponds to keeping the intersection of all
masks, whereas threshold=0 is the union of all masks.
cc: bool, optional
If true, extract the main connected component
Returns
-------
grp_mask, boolean array of shape the image shape
"""
grp_mask = None
if threshold > 1:
raise ValueError('The threshold should be < 1')
if threshold <0:
raise ValueError('The threshold should be > 0')
threshold = min(threshold, 1 - 1.e-7)
for this_mask in input_masks:
if isinstance(this_mask, basestring):
# We have a filename
this_mask = load(this_mask).get_data()
if grp_mask is None:
grp_mask = this_mask.copy().astype(np.int)
else:
grp_mask += this_mask
grp_mask = grp_mask > (threshold * len(list(input_masks)))
if np.any(grp_mask > 0) and cc:
grp_mask = largest_cc(grp_mask)
if output_filename is not None:
if isinstance(input_masks[0], basestring):
nim = load(input_masks[0])
header = nim.get_header()
affine = nim.get_affine()
else:
header = dict()
affine = np.eye(4)
header['descrip'] = 'mask image'
output_image = nifti1.Nifti1Image(grp_mask.astype(np.uint8),
affine=affine,
header=header,
)
save(output_image, output_filename)
return grp_mask > 0
def coefs_to_niftii(self, coefs, nii_name='coefs.nii.gz'):
"""
"""
print(coefs)
if self.n_features != len(coefs):
print("Num features {} does not match coef size {}. Did you downsize?".format(
self.n_features, len(coefs)))
raise(ValueError)
restored_coefs = self.restore_coefs(coefs)
print("restoring... num non-zero",np.count_nonzero(restored_coefs) )
try:
restored_coefs = restored_coefs.reshape(np.array(self.nii_shape))
print("Restored shape:", restored_coefs.shape)
except IndexError:
raise(IndexError, "Coefs don't match niftii shape")
sample_img = nib.load('tt29.nii')
affine = sample_img.affine.copy()
header = sample_img.header.copy()
header.set_data_dtype(np.float64)
assert(header.get_data_dtype()==np.float64)
print("Saving coefs as datatype", header.get_data_dtype())
i = nib.Nifti1Image(restored_coefs.astype(np.float64), affine, header)
nib.save(i, nii_name)
return restored_coefs
def to_image(self, path=None, data=None):
"""Write itself as a binary image, and returns it
Parameters
==========
path: string, path of the output image, if any
data: array of shape self.size,
data to put in the nonzer-region of the image
"""
if data is None:
wdata = np.zeros(self.shape, np.int8)
else:
wdata = np.zeros(self.shape, data.dtype)
wdata[self.ijk[:, 0], self.ijk[:, 1], self.ijk[:, 2]] = 1
if data is not None:
if data.size != self.size:
raise ValueError('incorrect data size')
wdata[wdata > 0] = data
nim = Nifti1Image(wdata, self.affine)
nim.get_header()['descrip'] = 'mask image representing domain %s' \
% self.id
if path is not None:
save(nim, path)
return nim
def _run_interface(self, runtime):
tracks, header = trk.read(self.inputs.in_file)
if not isdefined(self.inputs.data_dims):
data_dims = header['dim']
else:
data_dims = self.inputs.data_dims
if not isdefined(self.inputs.voxel_dims):
voxel_size = header['voxel_size']
else:
voxel_size = self.inputs.voxel_dims
affine = header['vox_to_ras']
streams = ((ii[0]) for ii in tracks)
data = density_map(streams, data_dims, voxel_size)
if data.max() < 2**15:
data = data.astype('int16')
img = nb.Nifti1Image(data,affine)
out_file = op.abspath(self.inputs.out_filename)
nb.save(img, out_file)
iflogger.info('Track density map saved as {i}'.format(i=out_file))
iflogger.info('Data Dimensions {d}'.format(d=data_dims))
iflogger.info('Voxel Dimensions {v}'.format(v=voxel_size))
return runtime
def generate_warping_field(fname_dest, warp_x, warp_y, fname_warp='warping_field.nii.gz', verbose=1):
"""
Generate an ITK warping field
:param fname_dest:
:param warp_x:
:param warp_y:
:param fname_warp:
:param verbose:
:return:
"""
sct.printv('\nGenerate warping field...', verbose)
# Get image dimensions
# sct.printv('Get destination dimension', verbose)
nx, ny, nz, nt, px, py, pz, pt = Image(fname_dest).dim
# sct.printv(' matrix size: '+str(nx)+' x '+str(ny)+' x '+str(nz), verbose)
# sct.printv(' voxel size: '+str(px)+'mm x '+str(py)+'mm x '+str(pz)+'mm', verbose)
# initialize
data_warp = np.zeros((nx, ny, nz, 1, 3))
# fill matrix
data_warp[:, :, :, 0, 0] = -warp_x # need to invert due to ITK conventions
data_warp[:, :, :, 0, 1] = -warp_y # need to invert due to ITK conventions
# save warping field
im_dest = load(fname_dest)
hdr_dest = im_dest.get_header()
hdr_warp = hdr_dest.copy()
hdr_warp.set_intent('vector', (), '')
hdr_warp.set_data_dtype('float32')
img = Nifti1Image(data_warp, None, hdr_warp)
save(img, fname_warp)
sct.printv(' --> '+fname_warp, verbose)
def export(self, nidm_version, export_dir):
"""
Create prov graph.
"""
if self.expl_mean_sq_file is None:
# Create Contrast Explained Mean Square Map as fstat<num>.nii.gz
# multiplied by sigmasquareds.nii.gz and save it in export_dir
fstat_img = nib.load(self.stat_file)
fstat = fstat_img.get_data()
sigma_sq_img = nib.load(self.sigma_sq_file)
sigma_sq = sigma_sq_img.get_data()
expl_mean_sq = nib.Nifti1Image(
fstat*sigma_sq, fstat_img.get_qform())
self.filename = ("ContrastExplainedMeanSquareMap" +
self.num + ".nii.gz")
self.expl_mean_sq_file = os.path.join(
export_dir, self.filename)
nib.save(expl_mean_sq, self.expl_mean_sq_file)
self.file = NIDMFile(self.id, self.expl_mean_sq_file,
filename=self.filename,
sha=self.sha, fmt=self.fmt)
# Contrast Explained Mean Square Map entity
path, filename = os.path.split(self.expl_mean_sq_file)
self.add_attributes((
(PROV['type'], self.type),
(NIDM_IN_COORDINATE_SPACE, self.coord_space.id),
(PROV['label'], self.label)))
def save_vol(vol, output_filename=None, output_dir=None, basename=None,
concat=False, **kwargs):
"""
Saves a single volume to disk.
"""
if not output_filename is None:
nibabel.save(vol, output_filename)
return output_filename
else:
if output_dir is None:
raise ValueError(
'One of output_filename and ouput_dir must be provided')
if not basename is None:
if isinstance(basename, list):
basename = basename[:1]
else:
basename = [basename]
# delegate to legacy save_vols
return save_vols([vol], output_dir, basenames=basename,
concat=False, **kwargs)[0]
def fill_nan(in_file, fill_value=0.):
"""Replace nan values with a given value
Parameters
----------
in_file : str
Path to image file
fill_value : float, optional
Value replacing nan
Returns
-------
out_file : str
Path to the filled file
"""
img = nibabel.load(in_file)
data = img.get_data()
if np.any(np.isnan(data)):
data[np.isnan(data)] = fill_value
img = nibabel.Nifti1Image(data, img.get_affine(), img.get_header())
out_file, _ = os.path.splitext(in_file)
out_file += '_no_nan.nii'
nibabel.save(img, out_file)
return out_file
def test_get_vox_dims():
# setup
affine = np.eye(4)
np.fill_diagonal(affine, [-3, 3, 3])
output_dir = os.path.join(OUTPUT_DIR, inspect.stack()[0][3])
if not os.path.exists(output_dir):
os.makedirs(output_dir)
# 3D vol
vol = create_random_image(affine=affine)
np.testing.assert_array_equal(get_vox_dims(vol), [3, 3, 3])
# 3D image file
saved_img_filename = os.path.join(output_dir, "vol.nii.gz")
nibabel.save(vol, saved_img_filename)
np.testing.assert_array_equal(get_vox_dims(vol), [3, 3, 3])
# 4D niimg
film = create_random_image(n_scans=10, affine=affine)
np.testing.assert_array_equal(get_vox_dims(film), [3, 3, 3])
# 4D image file
film = create_random_image(n_scans=10, affine=affine)
saved_img_filename = os.path.join(output_dir, "4D.nii.gz")
nibabel.save(film, saved_img_filename)
np.testing.assert_array_equal(get_vox_dims(film), [3, 3, 3])
def testset_predict(sess,clf,mean,std,masks,fold,img):
print "Predicting subject :",sess
flag = 0
metric_all = np.array([])
for sub in sess:
metric = np.ones(20)
test_set = read_test_sample(sub)
TE = test_set
#2. split x and y
X_cv = TE[:,masks]
y_cv = TE[:,-4]
coor = TE[:,-3:]
#3. Standardize
X_true = (X_cv - mean)/std
y_true = y_cv
y_pred = clf.predict(X_true)
list = [0,1,2,3,4]
for i,l in enumerate(list):
P = y_pred== l
T = y_true== l
di = dice(P,T)
if np.isnan(di):
metric[i] = 1
else:
metric[i] = di
#4. Compute metrics
precision = precision_score(y_true, y_pred,average=None)
recall = recall_score(y_true, y_pred,average=None)
f1 = f1_score(y_true,y_pred,average=None)
if len(precision)==len(list):
metric[5:10] = precision
if len(recall)==len(list):
metric[10:15] = recall
if len(f1)==len(list):
metric[15:20] = f1
#print metric
if flag==0:
metric_all = metric
flag = 1
else:
metric_all = np.vstack((metric_all,metric))
#construct the predicted image.
tmp = np.zeros_like(img.get_data())
for j,c in enumerate(coor):
tmp[tuple(c)] = y_pred[j]
img._data = tmp
nib.save(img,"pred_img_flod_%d/pred_img_%s.nii.gz"%(fold,sub))
print 'Saving pred_img_%s done!'%sub
print metric_all
filename = "test_metrics_sub_level_fold_%d.txt"%fold
np.savetxt(filename,metric_all,fmt='%1.8e',delimiter=',',newline='\n')
print "metric score for test set sub level have been saved in the %s"%filename
def saveImageToANewNiiWithHeaderFromOtherGivenExactFilePaths(labelImageCreatedByPredictions,
fullFilenameToSaveWith,
fullFilenameOfOriginalImageToCopyHeader,
npDtype = np.dtype(np.float32),
myLogger=None) :
fullFilenameToSaveWith = os.path.abspath(fullFilenameToSaveWith) # Cleans the .././/...
img_proxy_for_orig_image = nib.load(fullFilenameOfOriginalImageToCopyHeader)
hdr_for_orig_image = img_proxy_for_orig_image.header
affine_trans_to_ras = img_proxy_for_orig_image.affine
newLabelImg = nib.Nifti1Image(labelImageCreatedByPredictions, affine_trans_to_ras) #Nifti Constructor. data is the image itself, dimensions x,y,z,time. The second argument is the affine RAS transf.
newLabelImg.set_data_dtype(npDtype)
dimensionsOfTheGivenArrayImageToSave = len(labelImageCreatedByPredictions.shape)
newZooms = list(hdr_for_orig_image.get_zooms()[:dimensionsOfTheGivenArrayImageToSave])
if len(newZooms) < dimensionsOfTheGivenArrayImageToSave : #Eg if original image was 3D, but I need to save a multichannel image.
newZooms = newZooms + [1.0]*(dimensionsOfTheGivenArrayImageToSave - len(newZooms))
newLabelImg.header.set_zooms(newZooms)
if not fullFilenameToSaveWith.endswith(".nii.gz") :
fullFilenameToSaveWith = fullFilenameToSaveWith + ".nii.gz"
nib.save(newLabelImg, fullFilenameToSaveWith)
if myLogger<>None :
myLogger.print3("Image saved at: " + str(fullFilenameToSaveWith))
else :
print("Image saved at: " + str(fullFilenameToSaveWith))
def _run_interface(self, runtime): import nibabel as nib import numpy as np from dipy.denoise.nlmeans import nlmeans from nipype.utils.filemanip import split_filename fname = self.inputs.in_file img = nib.load(fname) data = img.get_data() affine = img.get_affine() mask = data[..., 0] > 80 a = data.shape denoised_data = np.ndarray(shape=data.shape) for image in range(0,a[3]): print(str(image + 1) + '/' + str(a[3] + 1)) dat = data[...,image] sigma = np.std(dat[~mask]) # Calculating the standard deviation of the noise den = nlmeans(dat, sigma=sigma, mask=mask) denoised_data[:,:,:,image] = den _, base, _ = split_filename(fname) nib.save(nib.Nifti1Image(denoised_data, affine), base + '_denoised.nii') return runtime
def _run_interface(self, runtime):
from nilearn.input_data import NiftiMasker, NiftiLabelsMasker
from nipype.utils.filemanip import split_filename
import nibabel as nib
import os
functional_filename = self.inputs.in_file
atlas_filename = self.inputs.atlas_filename
mask_filename = self.inputs.mask_filename
# Extracting the ROI signals
masker = NiftiLabelsMasker(labels_img=atlas_filename,
background_label = 0,
standardize=True,
detrend = True,
verbose = 1
)
time_series = masker.fit_transform(functional_filename)
# Removing the ROI signal from the time series
nifti_masker = NiftiMasker(mask_img=mask_filename)
masked_data = nifti_masker.fit_transform(functional_filename, confounds=time_series[...,0])
masked_img = nifti_masker.inverse_transform(masked_data)
# Saving the result to disk
outputs = self._outputs().get()
fname = self.inputs.in_file
_, base, _ = split_filename(fname)
nib.save(masked_img, os.path.abspath(base + '_regressed.nii.gz'))
return runtime
def sphere(file_roi, vol, mm_x=0, mm_y=0, mm_z=0, radius=4, dtype=np.uint8):
img = nibabel.load(vol)
header = img.get_header()
voxels_size= header.get_zooms()
coord_center_voxel = mm_to_voxel(vol, [[mm_x, mm_y, mm_z]])
shape_x, shape_y, shape_z = img.shape[0], img.shape[1], img.shape[2]
roi = np.zeros((shape_x, shape_y, shape_z))
radius = radius / voxels_size[0]
if radius > 1 :
radius -= 1
first_x = coord_center_voxel[0][0] - radius
first_y = coord_center_voxel[0][1] - radius
first_z = coord_center_voxel[0][2] - radius
elem = morphology.ball(radius)
#check voxel size is isotropic
#check radius is at least one voxel
for x in range(0,elem.shape[0]):
for y in range(0, elem.shape[1]):
for z in range(0, elem.shape[2]):
x_ = int(first_x) + x
y_ = int(first_y) + y
z_ = int(first_z) + z
roi[x_, y_, z_] = elem[x,y,z]
roi_img = nibabel.Nifti1Image(roi, img.get_affine(),img.get_header() )
nibabel.save(roi_img, file_roi)
def _run_interface(self, runtime): import dipy.reconst.dti as dti import dipy.denoise.noise_estimate as ne from dipy.core.gradients import gradient_table from nipype.utils.filemanip import split_filename import nibabel as nib fname = self.inputs.in_file img = nib.load(fname) data = img.get_data() affine = img.get_affine() bvals = self.inputs.bval bvecs = self.inputs.bvec gtab = gradient_table(bvals, bvecs) sigma = ne.estimate_sigma(data) dti = dti.TensorModel(gtab,fit_method='RESTORE', sigma=sigma) dtifit = dti.fit(data) fa = dtifit.fa _, base, _ = split_filename(fname) nib.save(nib.Nifti1Image(fa, affine), base + '_FA.nii') return runtime
def siemens_ph_wrap(in_file, out_file=None, irange=8192, orange=4096.00):
import nibabel as nb
import os.path as op
import numpy as np
import math
if out_file is None:
fname, fext = op.splitext(op.basename(in_file))
if fext == '.gz':
fname, _ = op.splitext(fname)
out_file = op.abspath('./%s_wrapped.nii.gz' % fname)
im = nb.load(in_file)
imdata = im.get_data().astype(np.float32)
imdata = (imdata - np.median(imdata)).astype(np.int16)
imax = int(irange * 0.5)
imin = int(irange * -0.5) + 1
imdata[imdata > imax] = imdata[imdata > imax] - irange
imdata[imdata < imin] = imdata[imdata < imin] + irange
imdata = imdata.astype(np.float32) / (1.0 * irange)
imdata = imdata * orange
hdr = im.get_header().copy()
hdr.set_data_dtype(np.int16)
hdr['datatype'] = 4
nii = nb.Nifti1Image(imdata.astype(np.int16), im.get_affine(), hdr)
nb.save(nii, out_file)
return out_file
def reconst_flow_core(flow, extra_args=[]):
with TemporaryDirectory() as out_dir:
data_path, bval_path, bvec_path = get_data('small_25')
vol_img = nib.load(data_path)
volume = vol_img.get_data()
mask = np.ones_like(volume[:, :, :, 0])
mask_img = nib.Nifti1Image(mask.astype(np.uint8), vol_img.affine)
mask_path = join(out_dir, 'tmp_mask.nii.gz')
nib.save(mask_img, mask_path)
dti_flow = flow()
args = [data_path, bval_path, bvec_path, mask_path]
args.extend(extra_args)
dti_flow.run(*args, out_dir=out_dir)
fa_path = dti_flow.last_generated_outputs['out_fa']
fa_data = nib.load(fa_path).get_data()
assert_equal(fa_data.shape, volume.shape[:-1])
tensor_path = dti_flow.last_generated_outputs['out_tensor']
tensor_data = nib.load(tensor_path)
assert_equal(tensor_data.shape[-1], 6)
assert_equal(tensor_data.shape[:-1], volume.shape[:-1])
ga_path = dti_flow.last_generated_outputs['out_ga']
ga_data = nib.load(ga_path).get_data()
assert_equal(ga_data.shape, volume.shape[:-1])
rgb_path = dti_flow.last_generated_outputs['out_rgb']
rgb_data = nib.load(rgb_path)
assert_equal(rgb_data.shape[-1], 3)
assert_equal(rgb_data.shape[:-1], volume.shape[:-1])
md_path = dti_flow.last_generated_outputs['out_md']
md_data = nib.load(md_path).get_data()
assert_equal(md_data.shape, volume.shape[:-1])
ad_path = dti_flow.last_generated_outputs['out_ad']
ad_data = nib.load(ad_path).get_data()
assert_equal(ad_data.shape, volume.shape[:-1])
rd_path = dti_flow.last_generated_outputs['out_rd']
rd_data = nib.load(rd_path).get_data()
assert_equal(rd_data.shape, volume.shape[:-1])
mode_path = dti_flow.last_generated_outputs['out_mode']
mode_data = nib.load(mode_path).get_data()
assert_equal(mode_data.shape, volume.shape[:-1])
evecs_path = dti_flow.last_generated_outputs['out_evec']
evecs_data = nib.load(evecs_path).get_data()
assert_equal(evecs_data.shape[-2:], tuple((3, 3)))
assert_equal(evecs_data.shape[:-2], volume.shape[:-1])
evals_path = dti_flow.last_generated_outputs['out_eval']
evals_data = nib.load(evals_path).get_data()
assert_equal(evals_data.shape[-1], 3)
assert_equal(evals_data.shape[:-1], volume.shape[:-1])
def labels_to_rd(labels_ct_native_nii, rd_nii, correct_cta, output_dir):
""" Register the rd to the ct space.
"""
# Output autocompletion
labels_rescale_file = os.path.join(output_dir, "BrainMask_to_rd.nii.gz")
# Load images
labels_ct_native_im = nibabel.load(labels_ct_native_nii)
labels_data = labels_ct_native_im.get_data()
rd_im = nibabel.load(rd_nii)
rd_data = rd_im.get_data()
cta = labels_ct_native_im.get_affine()
rda = rd_im.get_affine()
# Correct the rda affine matrix
print cta
#cta[1, 3] += 21
cta[2, 2] = correct_cta
print cta
# Inverse affine transformation
icta = inverse_affine(cta)
t = numpy.dot(icta, rda)
numpy.savetxt(os.path.join(output_dir,"t_icta_rda.txt"), t)
# Matricial dot product
labels_rescale = numpy.zeros(rd_data.shape)
dot_image = numpy.zeros(rd_data.shape + (3, ))
x = numpy.linspace(0, rd_data.shape[0] - 1, rd_data.shape[0])
y = numpy.linspace(0, rd_data.shape[1] - 1, rd_data.shape[1])
z = numpy.linspace(0, rd_data.shape[2] - 1, rd_data.shape[2])
xg, yg, zg = numpy.meshgrid(y, x, z)
print 'dot image shape: ', dot_image.shape
print 'yg shape: ', yg.shape
print 'xg shape: ', xg.shape
print 'zg shape: ', zg.shape
dot_image[..., 0] = yg
dot_image[..., 1] = xg
dot_image[..., 2] = zg
dot_image = threed_dot(t, dot_image)
cnt = 0
print rd_data.size
for x in range(rd_data.shape[0]):
for y in range(rd_data.shape[1]):
for z in range(rd_data.shape[2]):
#for z in range(cut_brain_index, rd_data.shape[2]):
if cnt % 100000 == 0:
print cnt
cnt += 1
voxel_labels = dot_image[x, y, z]
if (voxel_labels > 0).all() and (voxel_labels < (numpy.asarray(labels_data.shape) - 1)).all():
voxel_labels = numpy.round(voxel_labels)
labels_rescale[x, y, z] = labels_data[voxel_labels[0], voxel_labels[1], voxel_labels[2]]
labels_rescale_im = nibabel.Nifti1Image(labels_rescale, rda)
nibabel.save(labels_rescale_im, labels_rescale_file)
return labels_rescale_file
def _run_interface(self, runtime):
nii1 = nb.load(self.inputs.volume1)
nii2 = nb.load(self.inputs.volume2)
origdata1 = np.logical_not(np.logical_or(nii1.get_data() == 0, np.isnan(nii1.get_data())))
origdata2 = np.logical_not(np.logical_or(nii2.get_data() == 0, np.isnan(nii2.get_data())))
if isdefined(self.inputs.mask_volume):
maskdata = nb.load(self.inputs.mask_volume).get_data()
maskdata = np.logical_not(np.logical_or(maskdata == 0, np.isnan(maskdata)))
origdata1 = np.logical_and(maskdata, origdata1)
origdata2 = np.logical_and(maskdata, origdata2)
for method in ("dice", "jaccard"):
setattr(self, "_" + method, self._bool_vec_dissimilarity(origdata1, origdata2, method=method))
self._volume = int(origdata1.sum() - origdata2.sum())
both_data = np.zeros(origdata1.shape)
both_data[origdata1] = 1
both_data[origdata2] += 2
nb.save(nb.Nifti1Image(both_data, nii1.get_affine(), nii1.get_header()), self.inputs.out_file)
return runtime
def data_for_neuronal_network(seg_src_path, seg_dest_path):
ih.createPathIfNotExists(seg_dest_path)
seg_list = os.listdir(seg_src_path) # seg_list: list of all files in segmentation directory
print ("List of input files:")
print (seg_list)
file_num = 0
for f in seg_list:
print("file number: " + str(file_num))
print("read file...", f)
path = seg_src_path + "/" + f
print(path)
image = nib.load(path)
headers = image.header
# print(headers)
matrix = image.affine
# matrix[np.where(matrix > 1)] = 1
# matrix[np.where(matrix < 1)] = 0
print(matrix)
# manipulations.....
#numbers
dest_file = seg_dest_path + "/" + f
nib.save(image, dest_file)
def reorient_image(input_axes, in_file, output_dir):
""" Rectify the orientation of an image.
"""
# get the transformation to the RAS space
rotation = swap_affine(input_axes)
det = numpy.linalg.det(rotation)
if det != 1:
raise Exception("Determinant must be equal to "
"one got: {0}.".format(det))
# load image
image = nibabel.load(in_file)
# get affine transform (qform or sform)
affine = image.get_affine()
# apply transformation
transformation = numpy.dot(rotation, affine)
image.set_qform(transformation)
image.set_sform(transformation)
# save result
reoriented_file = os.path.join(output_dir, "im_reorient.nii.gz")
nibabel.save(image, reoriented_file)
return reoriented_file
def nifti_image_files(outdir, filelist, shape):
for f in filelist:
hdr = nb.Nifti1Header()
hdr.set_data_shape(shape)
img = np.random.random(shape)
nb.save(nb.Nifti1Image(img, np.eye(4), hdr),
os.path.join(outdir, f))
def save2nifti(data, affine, file_name):
"""
Save data to a nifti file.
"""
img = nib.Nifti1Image(data, affine)
nib.save(img, file_name)
def save(self, path, result):
"""
When we aggregate a result we store new single subject results
"""
name_ = result.name
radius_ = np.int(result._radius)
map_ = result._map
print map_.get_affine()
# If map is obtained via folding we average across maps
if len(map_.get_data().shape) > 3:
mean_map = map_.get_data().mean(axis=3)
mean_img = ni.Nifti1Image(mean_map, affine=map_.get_affine())
fname = "%s_radius_%s_searchlight_mean_map.nii.gz" % (name_, str(radius_))
ni.save(mean_img, os.path.join(path,fname))
return_map = mean_map
else:
return_map = map_.get_data()
fname = "%s_radius_%s_searchlight_total_map.nii.gz" % (name_, str(radius_))
ni.save(map_, os.path.join(path,fname))
result._mean_map = return_map
def tissue2dwi_align(self):
"""alignment of ventricle and CC ROI's from MNI space --> dwi and CC and CSF from T1w space --> dwi
A function to generate and perform dwi space alignment of avoidance/waypoint masks for tractography.
First creates ventricle and CC ROI. Then creates transforms from stock MNI template to dwi space.
NOTE: for this to work, must first have called both t1w2dwi_align and atlas2t1w2dwi_align.
Raises
------
ValueError
Raised if FSL atlas for ventricle reference not found
"""
# Create MNI-space ventricle mask
print("Creating MNI-space ventricle ROI...")
if not os.path.isfile(self.mni_atlas):
raise ValueError("FSL atlas for ventricle reference not found!")
cmd = f"fslmaths {self.mni_vent_loc} -thr 0.1 -bin {self.mni_vent_loc}"
gen_utils.run(cmd)
cmd = f"fslmaths {self.corpuscallosum} -bin {self.corpuscallosum}"
gen_utils.run(cmd)
cmd = f"fslmaths {self.corpuscallosum} -sub {self.mni_vent_loc} -bin {self.corpuscallosum}"
gen_utils.run(cmd)
# Create a transform from the atlas onto T1w. This will be used to transform the ventricles to dwi space.
reg_utils.align(
self.mni_atlas,
self.input_mni,
xfm=self.xfm_roi2mni_init,
init=None,
bins=None,
dof=6,
cost="mutualinfo",
searchrad=True,
interp="spline",
out=None,
)
# Create transform to align roi to mni and T1w using flirt
reg_utils.applyxfm(self.input_mni, self.mni_vent_loc,
self.xfm_roi2mni_init, self.vent_mask_mni)
if self.simple is False:
# Apply warp resulting from the inverse MNI->T1w created earlier
reg_utils.apply_warp(
self.t1w_brain,
self.vent_mask_mni,
self.vent_mask_t1w,
warp=self.mni2t1w_warp,
interp="nn",
sup=True,
)
# Apply warp resulting from the inverse MNI->T1w created earlier
reg_utils.apply_warp(
self.t1w_brain,
self.corpuscallosum,
self.corpuscallosum_mask_t1w,
warp=self.mni2t1w_warp,
interp="nn",
sup=True,
)
# Applyxfm tissue maps to dwi space
reg_utils.applyxfm(
self.nodif_B0,
self.vent_mask_t1w,
self.t1wtissue2dwi_xfm,
self.vent_mask_dwi,
)
reg_mri_pngs(self.vent_mask_dwi, self.nodif_B0, self.qa_reg)
reg_utils.applyxfm(
self.nodif_B0,
self.corpuscallosum_mask_t1w,
self.t1wtissue2dwi_xfm,
self.corpuscallosum_dwi,
)
reg_mri_pngs(self.corpuscallosum_dwi, self.nodif_B0, self.qa_reg)
reg_utils.applyxfm(self.nodif_B0, self.csf_mask,
self.t1wtissue2dwi_xfm, self.csf_mask_dwi)
reg_mri_pngs(self.csf_mask_dwi, self.nodif_B0, self.qa_reg)
reg_utils.applyxfm(self.nodif_B0, self.gm_mask, self.t1wtissue2dwi_xfm,
self.gm_in_dwi)
reg_mri_pngs(self.gm_in_dwi, self.nodif_B0, self.qa_reg)
reg_utils.applyxfm(self.nodif_B0, self.wm_mask, self.t1wtissue2dwi_xfm,
self.wm_in_dwi)
reg_mri_pngs(self.wm_in_dwi, self.nodif_B0, self.qa_reg)
# Threshold WM to binary in dwi space
thr_img = nib.load(self.wm_in_dwi)
thr_img.get_data()[thr_img.get_data() < 0.15] = 0
nib.save(thr_img, self.wm_in_dwi_bin)
# Threshold GM to binary in dwi space
thr_img = nib.load(self.gm_in_dwi)
thr_img.get_data()[thr_img.get_data() < 0.15] = 0
nib.save(thr_img, self.gm_in_dwi_bin)
# Threshold CSF to binary in dwi space
thr_img = nib.load(self.csf_mask_dwi)
thr_img.get_data()[thr_img.get_data() < 0.99] = 0
nib.save(thr_img, self.csf_mask_dwi)
# Threshold WM to binary in dwi space
self.t_img = load_img(self.wm_in_dwi_bin)
self.mask = math_img("img > 0", img=self.t_img)
self.mask.to_filename(self.wm_in_dwi_bin)
# Threshold GM to binary in dwi space
self.t_img = load_img(self.gm_in_dwi_bin)
self.mask = math_img("img > 0", img=self.t_img)
self.mask.to_filename(self.gm_in_dwi_bin)
# Threshold CSF to binary in dwi space
self.t_img = load_img(self.csf_mask_dwi)
self.mask = math_img("img > 0", img=self.t_img)
self.mask.to_filename(self.csf_mask_dwi_bin)
# Create ventricular CSF mask
print("Creating ventricular CSF mask...")
cmd = f"fslmaths {self.vent_mask_dwi} -kernel sphere 10 -ero -bin {self.vent_mask_dwi}"
gen_utils.run(cmd)
print("Creating Corpus Callosum mask...")
cmd = f"fslmaths {self.corpuscallosum_dwi} -mas {self.wm_in_dwi_bin} -bin {self.corpuscallosum_dwi}"
gen_utils.run(cmd)
cmd = f"fslmaths {self.csf_mask_dwi} -add {self.vent_mask_dwi} -bin {self.vent_csf_in_dwi}"
gen_utils.run(cmd)
# Create gm-wm interface image
cmd = (
f"fslmaths {self.gm_in_dwi_bin} -mul {self.wm_in_dwi_bin} -add {self.corpuscallosum_dwi} "
f"-sub {self.vent_csf_in_dwi} -mas {self.nodif_B0_mask} -bin {self.wm_gm_int_in_dwi}"
)
gen_utils.run(cmd)
import numpy as np
import nibabel as nib
import os
import glob
np_dir = '/data/hejy/MedicalZooPytorch_2cls/datasets/MICCAI_2020_ribfrac/generated/train_vol_512x512x96_0.6'
nii_out_dir = '/data/hejy/MedicalZooPytorch_2cls/datasets/MICCAI_2020_ribfrac/generated/train_vol_512x512x96_0.6_nii'
if not os.path.exists(nii_out_dir):
os.makedirs(nii_out_dir)
for i, np_path in enumerate(glob.glob(np_dir+'/*seg.npy')):
if i % 100 == 0:
print(i)
nii_save_name = os.path.join(nii_out_dir, os.path.basename(np_path).split('.')[0] + '.nii.gz')
np_file = np.load(np_path)
if len(np_file.shape) ==3:
np_file = np_file.squeeze(0)
else:
_, h, w, d = np_file.shape
np_file_new = np.zeros((h,w,d))
index_ = np.where(np_file!=0)
np_file_new[(index_[1], index_[2], index_[3])] = index_[0]
np_file = np_file_new
new_image = nib.Nifti1Image(np_file, np.eye(4))
nib.save(new_image, nii_save_name)
k_data = np.zeros((91, 109, 91, 7))
z_data = np.zeros((91, 109, 91, 7))
thresh = np.zeros((91, 109, 91))
maxval_per_maxK = np.zeros((91, 109, 91, 7))
lengths = [10, 15, 20, 25, 30, 35, 40]
for i in range(len(lengths)):
data = nib.load(datadir + str(lengths[i]) +
'_sec_events.nii.gz').get_data()
z = nib.load(datadir + str(lengths[i]) + '_sec_events_Z.nii.gz').get_data()
k_data[:, :, :, i] = data
z_data[:, :, :, i] = z
max_K = np.argmax(k_data, axis=3)
max_K[np.sum(k_data, axis=3) == 0] = 0
for i in range(91):
for j in range(109):
for k in range(91):
thresh[i, j, k] = z_data[i, j, k, max_K[i, j, k]]
max_K[thresh < 0] = 0
# save final map as nifti
maxval = np.max(max_K)
minval = np.min(max_K)
img = nib.Nifti1Image(max_K, affine=nii_template.affine)
img.header['cal_min'] = minval
img.header['cal_max'] = maxval
nib.save(img, datadir + 'best_event_length_map.nii.gz')
def mask(in_path, out_path, mask_path):
in_volume = np.flipud(nib.load(in_path).get_data())
mask_volume = binary_fill_holes(np.flipud(nib.load(mask_path).get_data()))
out_volume = np.multiply(in_volume, mask_volume).astype(in_volume.dtype)
nib.save(nib.Nifti1Image(out_volume, np.eye(4)), out_path)
return
for qq in range(0, imgsize[3]):
myvoxel_zeroed[idx_sort[qq]] = myvoxel[qq]
# Pass voxel through SARDU-net
myvoxel_up = net(Tensor(myvoxel_zeroed))
myvoxel_up = myvoxel_up.detach().numpy()
# Bring voxel back to original signal space
myvoxel_up = myvoxel_up * (smax - smin) + smin
# Store voxel
sout_data[xx, yy, zz, :] = myvoxel_up
# Save the predicted NIFTI file as output
print('')
print(' ... saving output file as 4D NIFTI ...')
buffer_header = sin_obj.header
if (nbit == 64):
buffer_header.set_data_dtype(
'float64'
) # Make sure we save output files float64, even if input is not
elif (nbit == 32):
buffer_header.set_data_dtype(
'float32'
) # Make sure we save output files float64, even if input is not
sout_obj = nib.Nifti1Image(sout_data, sin_obj.affine, buffer_header)
nib.save(sout_obj, args.nifti_out)
print('')
print(' Done!')
print('')
sys.exit(0)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
assert_inputs_exist(parser,
[args.input, args.bvals, args.bvecs, args.frf_file])
assert_outputs_exist(parser, args, args.out_fODF)
# Loading data
full_frf = np.loadtxt(args.frf_file)
vol = nib.load(args.input)
data = vol.get_fdata(dtype=np.float32)
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
# Checking mask
if args.mask is None:
mask = None
else:
mask = get_data_as_mask(nib.load(args.mask), dtype=bool)
if mask.shape != data.shape[:-1]:
raise ValueError("Mask is not the same shape as data.")
sh_order = args.sh_order
# Checking data and sh_order
check_b0_threshold(args.force_b0_threshold, bvals.min())
if data.shape[-1] < (sh_order + 1) * (sh_order + 2) / 2:
logging.warning(
'We recommend having at least {} unique DWI volumes, but you '
'currently have {} volumes. Try lowering the parameter sh_order '
'in case of non convergence.'.format(
(sh_order + 1) * (sh_order + 2) / 2, data.shape[-1]))
# Checking bvals, bvecs values and loading gtab
if not is_normalized_bvecs(bvecs):
logging.warning('Your b-vectors do not seem normalized...')
bvecs = normalize_bvecs(bvecs)
gtab = gradient_table(bvals, bvecs, b0_threshold=bvals.min())
# Checking full_frf and separating it
if not full_frf.shape[0] == 4:
raise ValueError('FRF file did not contain 4 elements. '
'Invalid or deprecated FRF format')
frf = full_frf[0:3]
mean_b0_val = full_frf[3]
# Loading the sphere
reg_sphere = get_sphere('symmetric362')
# Computing CSD
csd_model = ConstrainedSphericalDeconvModel(gtab, (frf, mean_b0_val),
reg_sphere=reg_sphere,
sh_order=sh_order)
# Computing CSD fit
csd_fit = fit_from_model(csd_model,
data,
mask=mask,
nbr_processes=args.nbr_processes)
# Saving results
shm_coeff = csd_fit.shm_coeff
if args.sh_basis == 'tournier07':
shm_coeff = convert_sh_basis(shm_coeff,
reg_sphere,
mask=mask,
nbr_processes=args.nbr_processes)
nib.save(nib.Nifti1Image(shm_coeff.astype(np.float32), vol.affine),
args.out_fODF)
end = time.time()
time_elapsed = end - start
print("\nDone (in %2.2f seconds)!" % (time_elapsed))
# save the normalised voxel-wise mean
if apply_norm:
# save the volume containing the normalised voxel-wise mean
print('Saving the normalised voxel-wise mean volume at %s...' %
(out_path)),
sys.stdout.flush()
nifti_to_save = nib.Nifti1Image(norm_voxelwise_mean,
affine=data_header.get_sform(),
header=data_header)
nib.save(nifti_to_save, os.path.join(out_path,
'norm_voxelwise_mean.nii.gz'))
print("Done.")
# save the volume containing the voxel-wise mean
print('Saving the voxel-wise mean volume at %s...' % (out_path)),
sys.stdout.flush()
nifti_to_save = nib.Nifti1Image(voxelwise_mean,
affine=data_header.get_sform(),
header=data_header)
nib.save(nifti_to_save, os.path.join(out_path, 'voxelwise_mean.nii.gz'))
print("Done.")
# at this point, the variable average_subject subject contains the actual saved volume
# for this reason, don't load it from the .nii.gz but use the variable instead
# compute the voxelwise mean
print("Computing the voxel-wise standard deviation...")
from monai.data.synthetic import create_test_image_3d
from monai.handlers.utils import stopping_fn_from_metric
from monai.networks.utils import predict_segmentation
monai.config.print_config()
logging.basicConfig(stream=sys.stdout, level=logging.INFO)
# Create a temporary directory and 40 random image, mask paris
tempdir = tempfile.mkdtemp()
print(
'generating synthetic data to {} (this may take a while)'.format(tempdir))
for i in range(40):
im, seg = create_test_image_3d(128, 128, 128, num_seg_classes=1)
n = nib.Nifti1Image(im, np.eye(4))
nib.save(n, os.path.join(tempdir, 'im%i.nii.gz' % i))
n = nib.Nifti1Image(seg, np.eye(4))
nib.save(n, os.path.join(tempdir, 'seg%i.nii.gz' % i))
images = sorted(glob(os.path.join(tempdir, 'im*.nii.gz')))
segs = sorted(glob(os.path.join(tempdir, 'seg*.nii.gz')))
# Define transforms for image and segmentation
train_imtrans = transforms.Compose(
[Rescale(), AddChannel(),
UniformRandomPatch((96, 96, 96))])
train_segtrans = transforms.Compose(
[AddChannel(), UniformRandomPatch((96, 96, 96))])
val_imtrans = transforms.Compose(
[Rescale(), AddChannel(), Resize((96, 96, 96))])
def save_nii(path_to_file, img):
"""Saves ``img`` of type `numpy.ndarray` in nifty format."""
nb.save(nb.Nifti1Image(img, np.eye(4)), path_to_file)
def atlas2t1w2dwi_align(self, atlas, dsn=True):
"""alignment from atlas to t1w to dwi. A function to perform atlas alignmet. Tries nonlinear registration first, and if that fails, does a liner
registration instead.
Note: for this to work, must first have called t1w2dwi_align.
Parameters
----------
atlas : str
path to atlas file you want to use
dsn : bool, optional
is your space for tractography native-dsn, by default True
Returns
-------
str
path to aligned atlas file
"""
self.atlas = atlas
self.atlas_name = gen_utils.get_filename(self.atlas)
self.aligned_atlas_t1mni = (
f"{self.reg_a}/{self.atlas_name}_aligned_atlas_t1w_mni.nii.gz")
self.aligned_atlas_skull = (
f"{self.reg_a}/{self.atlas_name}_aligned_atlas_skull.nii.gz")
self.dwi_aligned_atlas = (
f"{self.reg_anat}/{self.atlas_name}_aligned_atlas.nii.gz")
reg_utils.align(
self.atlas,
self.t1_aligned_mni,
init=None,
xfm=None,
out=self.aligned_atlas_t1mni,
dof=12,
searchrad=True,
interp="nearestneighbour",
cost="mutualinfo",
)
if (self.simple is False) and (dsn is False):
try:
# Apply warp resulting from the inverse of T1w-->MNI created earlier
reg_utils.apply_warp(
self.t1w_brain,
self.aligned_atlas_t1mni,
self.aligned_atlas_skull,
warp=self.mni2t1w_warp,
interp="nn",
sup=True,
)
# Apply transform to dwi space
reg_utils.align(
self.aligned_atlas_skull,
self.nodif_B0,
init=self.t1wtissue2dwi_xfm,
xfm=None,
out=self.dwi_aligned_atlas,
dof=6,
searchrad=True,
interp="nearestneighbour",
cost="mutualinfo",
)
except:
print(
"Warning: Atlas is not in correct dimensions, or input is low quality,\nusing linear template registration."
)
# Create transform to align atlas to T1w using flirt
reg_utils.align(
self.atlas,
self.t1w_brain,
xfm=self.xfm_atlas2t1w_init,
init=None,
bins=None,
dof=6,
cost="mutualinfo",
searchrad=True,
interp="spline",
out=None,
sch=None,
)
reg_utils.align(
self.atlas,
self.t1_aligned_mni,
xfm=self.xfm_atlas2t1w,
out=None,
dof=6,
searchrad=True,
bins=None,
interp="spline",
cost="mutualinfo",
init=self.xfm_atlas2t1w_init,
)
# Combine our linear transform from t1w to template with our transform from dwi to t1w space to get a transform from atlas ->(-> t1w ->)-> dwi
reg_utils.combine_xfms(self.xfm_atlas2t1w,
self.t1wtissue2dwi_xfm,
self.temp2dwi_xfm)
# Apply linear transformation from template to dwi space
reg_utils.applyxfm(self.nodif_B0, self.atlas,
self.temp2dwi_xfm, self.dwi_aligned_atlas)
elif dsn is False:
# Create transform to align atlas to T1w using flirt
reg_utils.align(
self.atlas,
self.t1w_brain,
xfm=self.xfm_atlas2t1w_init,
init=None,
bins=None,
dof=6,
cost="mutualinfo",
searchrad=None,
interp="spline",
out=None,
sch=None,
)
reg_utils.align(
self.atlas,
self.t1w_brain,
xfm=self.xfm_atlas2t1w,
out=None,
dof=6,
searchrad=True,
bins=None,
interp="spline",
cost="mutualinfo",
init=self.xfm_atlas2t1w_init,
)
# Combine our linear transform from t1w to template with our transform from dwi to t1w space to get a transform from atlas ->(-> t1w ->)-> dwi
reg_utils.combine_xfms(self.xfm_atlas2t1w, self.t1wtissue2dwi_xfm,
self.temp2dwi_xfm)
# Apply linear transformation from template to dwi space
reg_utils.applyxfm(self.nodif_B0, self.atlas, self.temp2dwi_xfm,
self.dwi_aligned_atlas)
else:
pass
# Set intensities to int
if dsn is False:
self.atlas_img = nib.load(self.dwi_aligned_atlas)
else:
self.atlas_img = nib.load(self.aligned_atlas_t1mni)
self.atlas_data = np.around(self.atlas_img.get_data()).astype("int16")
node_num = len(np.unique(self.atlas_data))
self.atlas_data[self.atlas_data > node_num] = 0
t_img = load_img(self.wm_gm_int_in_dwi)
mask = math_img("img > 0", img=t_img)
mask.to_filename(self.wm_gm_int_in_dwi_bin)
if dsn is False:
nib.save(
nib.Nifti1Image(
self.atlas_data.astype(np.int32),
affine=self.atlas_img.affine,
header=self.atlas_img.header,
),
self.dwi_aligned_atlas,
)
reg_mri_pngs(self.dwi_aligned_atlas, self.nodif_B0, self.qa_reg)
return self.dwi_aligned_atlas
else:
nib.save(
nib.Nifti1Image(
self.atlas_data.astype(np.int32),
affine=self.atlas_img.affine,
header=self.atlas_img.header,
),
self.aligned_atlas_t1mni,
)
reg_mri_pngs(self.aligned_atlas_t1mni, self.t1_aligned_mni,
self.qa_reg)
return self.aligned_atlas_t1mni
def group_std_masks():
from nilearn.image import get_data, new_img_like, resample_img
import nibabel as nib
saa = {}
thr = {'mOFC': [1014,2014],
'dACC': [1002,2002],
'lh_amyg': [18],
'rh_amyg': [54],
'lh_hpc': [17],
'rh_hpc': [53]}
masks = {}
for roi in thr: masks[roi] = {}
for sub in all_sub_args:
subj = bids_meta(sub)
print(sub)
# os.system('flirt -in %s -out %s -ref %s -applyxfm -init %s -interp nearestneighbour'%(subj.faa,subj.saa,std_2009_brain,subj.ref2std))
saa[sub] = get_data(subj.faa)
for roi in thr:
if len(thr[roi]) == 2:
l = np.zeros(saa[sub].shape)
l[np.where(saa[sub] == thr[roi][0])] = 1
r = np.zeros(saa[sub].shape)
r[np.where(saa[sub] == thr[roi][1])] = 1
m = l+r
else:
m = np.zeros(saa[sub].shape)
m[np.where(saa[sub] == thr[roi][0])] = 1
masks[roi][sub] = m
for roi in masks:
masks[roi] = np.array([masks[roi][i] for i in masks[roi]])
masks[roi] = np.sum(masks[roi],axis=0) / 48
masks[roi] = new_img_like(subj.faa,masks[roi],copy_header=False)
# masks[roi].header['pixdim'] = [1.,3., 3., 3., 0., 0., 0., 0.,]
# masks[roi] = new_img_like(std_2009_brain,masks[roi],copy_header=False)
std = nib.load(std_2009_brain)
masks[roi] = resample_img(masks[roi],target_affine=std.affine,target_shape=std.shape,interpolation='nearest')
# nib.save(masks[roi],os.path.join(group_masks,'%s_3mm_raw.nii.gz'%(roi)))
# nib.save(masks[roi],os.path.join(group_masks,'%s_1mm_raw.nii.gz'%(roi)))
nib.save(masks[roi],os.path.join(group_masks,'%s_1mm.nii.gz'%(roi)))
os.system('fslmaths %s -bin %s'%(os.path.join(group_masks,'%s_1mm.nii.gz'%(roi)), os.path.join(group_masks,'%s_group_mask.nii.gz'%(roi))))
for hemi in ['l','r']:
amyg = get_data(os.path.join(group_masks,'%sh_amyg_1mm.nii.gz'%(hemi)))
hpc = get_data(os.path.join(group_masks,'%sh_hpc_1mm.nii.gz'%(hemi)))
a_bin = np.where(amyg > hpc, 1, 0)
h_bin = np.where(hpc > amyg, 1, 0)
a_out = new_img_like(std_2009_brain,a_bin,copy_header=False)
h_out = new_img_like(std_2009_brain,h_bin,copy_header=False)
nib.save(a_out,os.path.join(group_masks,'%sh_amyg_group_mask.nii.gz'%(hemi)))
nib.save(h_out,os.path.join(group_masks,'%sh_hpc_group_mask.nii.gz'%(hemi)))
def btnConvert_click(self):
msgBox = QMessageBox()
# OutFile
OutFile = ui.txtOutFile.text()
if not len(OutFile):
msgBox.setText("Please enter out file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
ThresholdType = ui.cbThType.currentData()
MinTh = None
MaxTh = None
if (ThresholdType == "min") or (ThresholdType == "ext"):
try:
MinTh = np.double(ui.txtThMin.text())
except:
msgBox.setText("Min Threshold must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Min Threshold is valid")
if (ThresholdType == "max") or (ThresholdType == "ext"):
try:
MaxTh = np.double(ui.txtThMax.text())
except:
msgBox.setText("Max Threshold must be a number")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return False
print("Max Threshold is valid")
# OutFile
AFNI = ui.txtAFNI.text()
if not len(AFNI):
AFNI = None
else:
CopyFile = ui.txtFAFNI.text()
if not len(CopyFile):
msgBox.setText("Please select 3dcopy command!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isfile(CopyFile):
msgBox.setText("Please select 3dcopy command!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
RefitFile = ui.txtFSUMA.text()
if not len(RefitFile):
msgBox.setText("Please select 3drefit command!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isfile(RefitFile):
msgBox.setText("Please select 3drefit command!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
# InFile
InFile = ui.txtInFile.text()
if not len(InFile):
msgBox.setText("Please enter input file!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isfile(InFile):
msgBox.setText("Input file not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not len(ui.txtMatrix.currentText()):
msgBox.setText("Matrix name not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not len(ui.txtCoord.currentText()):
msgBox.setText("Coordinate name not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not len(ui.txtTime.text()):
msgBox.setText("Time points not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
AffineFile = ui.txtSSSpace.currentText()
if not len(AffineFile):
msgBox.setText("Please enter affine reference!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
if not os.path.isfile(AffineFile):
msgBox.setText("Affine reference not found!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
AffineHDR = nb.load(AffineFile)
Affine = AffineHDR.affine
Time = strRange(ui.txtTime.text())
if Time is None:
msgBox.setText("Time points is wrong!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
try:
InData = io.loadmat(InFile)
Mat = InData[ui.txtMatrix.currentText()]
Coord = InData[ui.txtCoord.currentText()]
imgShape = InData["imgShape"][0]
except:
print("Cannot load data!")
msgBox.setText("Cannot load data!")
msgBox.setIcon(QMessageBox.Critical)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
return
ImgData = None
# Filter Mat
for t in Time:
vox = Mat[t, :]
if ui.cbScale.isChecked():
vox = preprocessing.scale(vox)
print("Time Point: " + str(t) + " is normalized.")
if MinTh is not None:
vox[np.where(vox < MinTh)] = 0
print("Time Point: " + str(t) +
", Lower band thresholding is done!")
if MaxTh is not None:
vox[np.where(vox > MaxTh)] = 0
print("Time Point: " + str(t) +
", Upper band thresholding is done!")
img = np.zeros([imgShape[0], imgShape[1], imgShape[2], 1])
for coIndx, _ in enumerate(Coord[0]):
img[Coord[0][coIndx], Coord[1][coIndx], Coord[2][coIndx],
0] = vox[coIndx]
ImgData = img if ImgData is None else np.concatenate(
(ImgData, img), axis=3)
print("Time point: " + str(t) + " is done.")
print("Saving image ...")
NIF = nb.Nifti1Image(ImgData, Affine)
nb.save(NIF, OutFile)
if AFNI is not None:
cmd = CopyFile + " " + OutFile + " " + AFNI
print("Running: " + cmd)
os.system(cmd)
cmd = RefitFile + " -view tlrc -space MNI " + AFNI + " " + AFNI + "+tlrc."
print("Running: " + cmd)
os.system(cmd)
print("DONE!")
msgBox.setText("Image file is generated.")
msgBox.setIcon(QMessageBox.Information)
msgBox.setStandardButtons(QMessageBox.Ok)
msgBox.exec_()
subj_dst_dir = os.path.join(DST_DIR, subj)
if not os.path.exists(subj_dst_dir):
os.makedirs(subj_dst_dir)
# crop the new CT
# WIP code:
#x_pad[np.ix_((x_pad > thresh).any(1),
#(x_pad > thresh).any(0))]
# Save CT
x = np.array(new_img)
x = np.rollaxis(x, 0, 3)
# ensure air is constant
x[np.where(x < -1024)] = -1024
new_nii_obj = nib.Nifti1Image(x, affine=orig.affine, header=orig.header)
new_filename = os.path.join(subj_dst_dir, subj + "_CT.nii.gz")
nib.save(new_nii_obj, new_filename)
# Save mask
x = np.array(new_mask)
x = np.rollaxis(x, 0, 3)
# ensure binary mask
# This shouldn't be a problem, but just in case
x[np.where(x < 0.5)] = 0
x[np.where(x >= 0.5)] = 1
new_nii_obj = nib.Nifti1Image(x, affine=orig.affine, header=orig.header)
new_filename = os.path.join(subj_dst_dir, subj + "_mask.nii.gz")
nib.save(new_nii_obj, new_filename)
def main(*args):
t1_overall = time.time()
# Change to blm directory
os.chdir(os.path.dirname(os.path.realpath(__file__)))
batchNo = args[0]
if len(args) == 1 or (not args[1]):
# Load in inputs
with open(os.path.join(os.getcwd(), '..', 'blmm_config.yml'),
'r') as stream:
inputs = yaml.load(stream, Loader=yaml.FullLoader)
else:
if type(args[1]) is str:
# In this case inputs file is first argument
with open(os.path.join(args[1]), 'r') as stream:
inputs = yaml.load(stream, Loader=yaml.FullLoader)
else:
# In this case inputs structure is first argument.
inputs = args[1]
if 'MAXMEM' in inputs:
MAXMEM = eval(inputs['MAXMEM'])
else:
MAXMEM = 2**32
OutDir = inputs['outdir']
# Get number of ffx parameters
c1 = blmm_eval(inputs['contrasts'][0]['c' + str(1)]['vector'])
c1 = np.array(c1)
n_p = c1.shape[0]
del c1
# Y volumes
with open(inputs['Y_files']) as a:
Y_files = []
i = 0
for line in a.readlines():
Y_files.append(line.replace('\n', ''))
# Load in one nifti to check NIFTI size
try:
Y0 = blmm_load(Y_files[0])
except Exception as error:
raise ValueError('The NIFTI "' + Y_files[0] + '"does not exist')
d0 = Y0.get_data()
# Get the maximum memory a NIFTI could take in storage.
NIFTIsize = sys.getsizeof(np.zeros(d0.shape, dtype='uint64'))
# Similar to blksize in SwE, we divide by 8 times the size of a nifti
# to work out how many blocks we use.
blksize = int(np.floor(MAXMEM / 8 / NIFTIsize / n_p))
# Reduce X to X for this block.
X = blmm_load(inputs['X'])
X = X[(blksize * (batchNo - 1)):min((blksize * batchNo), len(Y_files))]
# Number of random effects factors.
n_f = len(inputs['Z'])
# Read in each factor
for i in range(0, n_f):
Zi_factor = blmm_load(inputs['Z'][i]['f' + str(i + 1)]['factor'])
Zi_design = blmm_load(inputs['Z'][i]['f' + str(i + 1)]['design'])
# Number of levels for factor i
l_i = np.amax(Zi_factor)
# Number of parameters for factor i
q_i = Zi_design.shape[1]
# One hot encode the factor vector
Zi_factor = pd.get_dummies(pd.DataFrame(Zi_factor)[0]).values
# Reduce to block.
Zi_design = Zi_design[(blksize *
(batchNo - 1)):min((blksize *
batchNo), len(Y_files))]
Zi_factor = Zi_factor[(blksize *
(batchNo - 1)):min((blksize *
batchNo), len(Y_files))]
# Repeat Zi_factor for each parameter
Zi = np.repeat(Zi_factor, q_i, axis=1).astype(np.float64)
# Fill the one values with the design
Zi[Zi == 1] = Zi_design.reshape(Zi[Zi == 1].shape)
# Concatenate Z's Horizontally
if i == 0:
Z = Zi
else:
Z = np.hstack((Z, Zi))
# Mask volumes (if they are given)
if 'data_mask_files' in inputs:
with open(inputs['data_mask_files']) as a:
M_files = []
i = 0
for line in a.readlines():
M_files.append(line.replace('\n', ''))
# If we have a mask for each Y, reduce the list to just for this block
if len(M_files) == len(Y_files):
# In this case we have a mask per Y volume
M_files = M_files[(blksize *
(batchNo - 1)):min((blksize *
batchNo), len(M_files))]
else:
if len(M_files) > len(Y_files):
raise ValueError('Too many data_masks specified!')
else:
raise ValueError('Too few data_masks specified!')
# Otherwise we have no masks
else:
# There is not a mask for each Y as there are no masks at all!
M_files = []
# Mask threshold for Y (if given)
if 'data_mask_thresh' in inputs:
M_t = float(inputs['data_mask_thresh'])
else:
M_t = None
# Mask volumes (if they are given)
if 'analysis_mask' in inputs:
M_a = blmm_load(inputs['analysis_mask']).get_data()
else:
M_a = None
# Reduce Y_files to only Y files for this block
Y_files = Y_files[(blksize *
(batchNo - 1)):min((blksize * batchNo), len(Y_files))]
# Verify input
verifyInput(Y_files, M_files, Y0)
# Obtain Y, mask for Y and nmap. This mask is just for voxels
# with no studies present.
Y, Mask, nmap, M, Mmap = obtainY(Y_files, M_files, M_t, M_a)
# Work out voxel specific designs
MX = blkMX(X, Y, M)
MZ = blkMX(Z, Y, M) # MIGHT NEED TO THINK ABOUT SPARSITY HERE LATER
# Get X transpose Y, Z transpose Y and Y transpose Y.
XtY = blkXtY(X, Y, Mask)
YtY = blkYtY(Y, Mask)
ZtY = blkXtY(Z, Y, Mask) # REVISIT ONCE SPARSED
# In a spatially varying design XtX has dimensions n_voxels
# by n_parameters by n_parameters. We reshape to n_voxels by
# n_parameters^2 so that we can save as a csv.
XtX = blkXtX(MX)
XtX = XtX.reshape([XtX.shape[0], XtX.shape[1] * XtX.shape[2]])
# In a spatially varying design ZtX has dimensions n_voxels
# by n_q by n_parameters. We reshape to n_voxels by
# n_parameters^2 so that we can save as a csv.
ZtX = blkZtX(MZ, MX)
ZtX = ZtX.reshape([ZtX.shape[0], ZtX.shape[1] * ZtX.shape[2]])
# ======================================================================
# NEED TO THINK ABOUT SPARSE HERE
# ======================================================================
#
# In a spatially varying design ZtZ has dimensions n_voxels
# by n_q by n_q. We reshape to n_voxels by n_q^2 so that we
# can save as a csv.
ZtZ = blkXtX(MZ)
ZtZ = ZtZ.reshape([ZtZ.shape[0], ZtZ.shape[1] * ZtZ.shape[2]])
# ======================================================================
# Pandas reads and writes files much more quickly with nrows <<
# number of columns
XtY = XtY.transpose()
ZtY = ZtY.transpose()
if (len(args) == 1) or (type(args[1]) is str):
# Record product matrices
np.save(os.path.join(OutDir, "tmp", "XtX" + str(batchNo)), XtX)
np.save(os.path.join(OutDir, "tmp", "XtY" + str(batchNo)), XtY)
np.save(os.path.join(OutDir, "tmp", "YtY" + str(batchNo)), YtY)
np.save(os.path.join(OutDir, "tmp", "ZtY" + str(batchNo)), ZtY)
np.save(os.path.join(OutDir, "tmp", "ZtX" + str(batchNo)), ZtX)
np.save(os.path.join(OutDir, "tmp", "ZtZ" + str(batchNo)), ZtZ)
# Get map of number of scans at voxel.
nmap = nib.Nifti1Image(nmap, Y0.affine, header=Y0.header)
nib.save(
nmap,
os.path.join(OutDir, 'tmp',
'blmm_vox_n_batch' + str(batchNo) + '.nii'))
# Get map of number of scans at voxel.
Mmap = nib.Nifti1Image(Mmap, Y0.affine, header=Y0.header)
nib.save(
Mmap,
os.path.join(OutDir, 'tmp',
'blmm_vox_uniqueM_batch' + str(batchNo) + '.nii'))
else:
# Return XtX, XtY, YtY, nB
return (XtX, XtY, YtY, nmap)
w.resetwarnings()
t2_overall = time.time()
print('TIME: ', t2_overall - t1_overall)
#!/usr/bin/python
import nibabel as nib
import scipy.signal
import os
path_main = '/home/andreabertana/Projects/HCP/results/MNI/mc/'
subj = os.listdir('./Projects/HCP/MNI/')
for s in subj:
path = path_main + s + '_mc.nii.gz'
print path
print "Loading data"
fmri = nib.load(path)
data = fmri #.data.astype('float32')
#fmri= unload()
#detrend. Axis 0 should be time.bp should run detrend taking 12 different parts,each with 121vol (12 steps: 1452/121 = 12) that respect one block in Haxby design.
print "Detrending"
detrended = scipy.signal.detrend(data.get_data(),
axis=3,
type='linear',
bp=[405])
filename = ('/home/andreabertana/Projects/HCP/results/MNI/detrend/' + s +
'_detrend.nii.gz')
print 'Store detrended data for later re-use'
affine = data.get_affine()
img = nib.AnalyzeImage(detrended, affine=affine)
nib.save(img, filename)
print "Done."
print "All Done"
def save_array_as_nifty_volume(data, filename):
# numpy data shape [D, H, W]
# nifty image shape [W, H, W]
data = np.transpose(data, [2, 1, 0])
seg = nibabel.Nifti1Image(data, np.eye(4))
nibabel.save(seg, filename)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.INFO)
required_args = [args.input_dwi, args.bvals, args.bvecs, args.reverse_b0]
optional_args = [args.output_b0s]
assert_inputs_exist(parser, required_args)
assert_outputs_exist(parser, args, [], optional_args)
if os.path.splitext(args.output_prefix)[1] != '':
parser.error('The prefix must not contain any extension.')
bvals, bvecs = read_bvals_bvecs(args.bvals, args.bvecs)
bvals_min = bvals.min()
# TODO refactor this
b0_threshold = args.b0_thr
if bvals_min < 0 or bvals_min > b0_threshold:
raise ValueError('The minimal b-value is lesser than 0 or greater '
'than {0}. This is highly suspicious. Please check '
'your data to ensure everything is correct. '
'Value found: {1}'.format(b0_threshold, bvals_min))
gtab = gradient_table(bvals, bvecs, b0_threshold=b0_threshold)
acqparams = create_acqparams(gtab, args.readout, args.encoding_direction)
if not os.path.exists(args.output_directory):
os.makedirs(args.output_directory)
acqparams_path = os.path.join(args.output_directory, 'acqparams.txt')
np.savetxt(acqparams_path, acqparams, fmt='%1.4f', delimiter=' ')
rev_b0_img = nib.load(args.reverse_b0)
rev_b0 = rev_b0_img.get_data()
dwi_image = nib.load(args.input_dwi)
dwi = dwi_image.get_data()
b0s = dwi[..., gtab.b0s_mask]
b0_idx = np.where(gtab.b0s_mask)[0]
fused_b0s = np.zeros(b0s.shape[:-1] + (len(b0_idx) + 1, ))
fused_b0s[..., 0:-1] = b0s
fused_b0s[..., -1] = rev_b0
fused_b0s_path = os.path.join(args.output_directory, args.output_b0s)
nib.save(nib.Nifti1Image(fused_b0s, rev_b0_img.affine), fused_b0s_path)
output_path = os.path.join(args.output_directory, args.output_prefix)
fout_path = os.path.join(args.output_directory, "correction_field")
iout_path = os.path.join(args.output_directory, "corrected_b0s")
topup = 'topup --imain={0} --datain={1}'\
' --config={2} --verbose --out={3}'\
' --fout={4} --iout={5} --subsamp=1 \n'\
.format(fused_b0s_path, acqparams_path, args.config, output_path,
fout_path, iout_path)
if args.output_script:
with open("topup.sh", 'w') as f:
f.write(topup)
else:
print(topup)
# Plot outlier regions to a brain map in the patient's anatomical space
print "Plotting accuracy outlier ROIs to a brain map..."
ROI_atlas = nibabel.load(
'/usr/share/fsl/5.0/data/atlases/HarvardOxford/HarvardOxford-cortl-maxprob-thr25-2mm.nii.gz'
)
orig_ROI_data = ROI_atlas.get_data()
affine = ROI_atlas.get_affine()
acc_roi_data = np.zeros(np.shape(orig_ROI_data))
for i in range(1, roin):
ids = np.where(orig_ROI_data == i)
acc_roi_data[ids[0], ids[1], ids[2]] = diff_acc[i]
acc_roi_data[np.where(acc_roi_data > 0)] = 1 #remove positive values
acc_img = nibabel.Nifti1Image(-acc_roi_data,
affine) #change sign to positive
nibabel.save(
acc_img,
patient_results + 'subj' + test_subj + '_diff_accuracy.nii.gz')
# Transform to native anatomical space
print "Transforming to native space..."
flirt = fsl.FLIRT(bins=800, cost='mutualinfo', reference=anat)
flirt.inputs.in_file = patient_results + 'subj' + test_subj + '_diff_accuracy.nii.gz'
flirt.inputs.out_file = patient_results + 'subj' + test_subj + '_diff_accuracy_transformed.nii.gz'
flirt.run()
# Make box & whiskers plots for each Harvard-Oxford region
plt.figure(figsize=(10, 20))
plt.boxplot(reproducibility.T, vert=0, showmeans=True)
ticks, labels = plt.yticks(np.arange(1,
np.shape(cort_labels)[0] + 1),
cort_labels,
plt.savefig('denoised_ascm.png', bbox_inches='tight')
print("The ascm result saved in denoised_ascm.png")
"""
.. figure:: denoised_ascm.png
:align: center
**Showing the axial slice without (left) and with (middle) ASCM denoising**.
"""
"""
From the above figure we can see that the residual is really uniform in nature
which dictates that ASCM denoises the data while preserving the sharpness of
the features.
"""
nib.save(nib.Nifti1Image(den_final, affine), 'denoised_ascm.nii.gz')
print("Saving the entire denoised output in denoised_ascm.nii.gz")
"""
For comparison propose we also plot the outputs of the ``non_local_means``
(both with the larger as well as with the smaller patch radius) with the ASCM
output.
"""
fig, ax = plt.subplots(1, 4)
ax[0].imshow(original, cmap='gray', origin='lower')
ax[0].set_title('Original')
ax[1].imshow(den_small[..., axial_middle].T,
cmap='gray',
origin='lower',
interpolation='none')
# Create random dictionary
np.random.seed(12345)
input_image = nibabel.load(args.input)
data = input_image.get_data().astype(float)
maxval = 0
if args.normalize == True:
maxval = np.max(data)
data /= maxval
if args.rician == False:
data += np.random.normal(args.mean, args.std, data.shape)
else:
data += rice.rvs(args.b,
loc=args.mean,
scale=args.std,
size=data.shape)
if args.normalize == True:
data *= maxval
nibabel.save(nibabel.Nifti1Image(data, input_image.affine), args.output)
"""A Rice continuous random variable. (from scipy code)
Notes
-----
The probability density function for `rice` is::
rice.pdf(x, b) = x * exp(-(x**2+b**2)/2) * I[0](x*b)
for ``x > 0``, ``b > 0``.
"""
def execute_spm_auditory_glm(data, reg_motion=False):
reg_motion = reg_motion and 'realignment_parameters' in data
tr = 7.
n_scans = 96
_duration = 6
epoch_duration = _duration * tr
conditions = ['rest', 'active'] * 8
duration = epoch_duration * np.ones(len(conditions))
onset = np.linspace(0, (len(conditions) - 1) * epoch_duration,
len(conditions))
paradigm = BlockParadigm(con_id=conditions, onset=onset, duration=duration)
hfcut = 2 * 2 * epoch_duration
# construct design matrix
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
add_reg_names = None
add_regs = None
if reg_motion:
add_reg_names = ['tx', 'ty', 'tz', 'rx', 'ry', 'rz']
add_regs = data['realignment_parameters'][0]
if isinstance(add_regs, basestring):
add_regs = np.loadtxt(add_regs)
design_matrix = make_dmtx(frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
add_reg_names=add_reg_names,
add_regs=add_regs)
# plot and save design matrix
ax = design_matrix.show()
ax.set_position([.05, .25, .9, .65])
ax.set_title('Design matrix')
dmat_outfile = os.path.join(data['output_dir'],
'design_matrix.png')
pl.savefig(dmat_outfile, bbox_inches="tight", dpi=200)
pl.close()
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# more interesting contrasts"""
contrasts['active-rest'] = contrasts['active'] - contrasts['rest']
# fit GLM
print('\r\nFitting a GLM (this takes time)...')
fmri_glm = FMRILinearModel(load_4D_img(data['func'][0]),
design_matrix.matrix,
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(data['output_dir'], "mask.nii.gz")
print "Saving mask image %s..." % mask_path
nibabel.save(fmri_glm.mask, mask_path)
# compute bg unto which activation will be projected
anat_img = load_vol(data['anat'])
anat = anat_img.get_data()
if anat.ndim == 4:
anat = anat[..., 0]
anat_affine = anat_img.get_affine()
print "Computing contrasts..."
z_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, t_map, eff_map, var_map = fmri_glm.contrast(
contrasts[contrast_id],
con_id=contrast_id,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True,
)
# store stat maps to disk
for dtype, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, eff_map, var_map]):
map_dir = os.path.join(
data['output_dir'], '%s_maps' % dtype)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if contrast_id == 'active-rest' and dtype == "z":
z_maps[contrast_id] = map_path
print "\t\t%s map: %s" % (dtype, map_path)
print
# do stats report
stats_report_filename = os.path.join(data['reports_output_dir'],
"report_stats.html")
contrasts = dict((contrast_id, contrasts[contrast_id])
for contrast_id in z_maps.keys())
generate_subject_stats_report(
stats_report_filename,
contrasts,
z_maps,
fmri_glm.mask,
design_matrices=[design_matrix],
subject_id=data['subject_id'],
anat=anat,
anat_affine=anat_affine,
cluster_th=50, # we're only interested in this 'large' clusters
# additional ``kwargs`` for more informative report
paradigm=paradigm.__dict__,
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
frametimes=frametimes,
drift_model=drift_model,
hrf_model=hrf_model,
)
ProgressReport().finish_dir(data['output_dir'])
print "\r\nStatistic report written to %s\r\n" % stats_report_filename
def test_AFQ_data_waypoint():
"""
Test with some actual data again, this time for track segmentation
"""
tmpdir = nbtmp.InTemporaryDirectory()
afd.organize_stanford_data(path=tmpdir.name)
dmriprep_path = op.join(tmpdir.name, 'stanford_hardi',
'derivatives', 'dmriprep')
bundle_names = ["SLF", "ARC", "CST", "FP"]
tracking_params = dict(odf_model="DTI")
segmentation_params = dict(filter_by_endpoints=False,
seg_algo="AFQ",
return_idx=True)
clean_params = dict(return_idx=True)
myafq = api.AFQ(dmriprep_path=dmriprep_path,
sub_prefix='sub',
bundle_names=bundle_names,
scalars=["dti_fa", "dti_md"],
tracking_params=tracking_params,
segmentation_params=segmentation_params,
clean_params=clean_params)
# Replace the mapping and streamlines with precomputed:
file_dict = afd.read_stanford_hardi_tractography()
mapping = file_dict['mapping.nii.gz']
streamlines = file_dict['tractography_subsampled.trk']
streamlines = dts.Streamlines(
dtu.transform_tracking_output(
[s for s in streamlines if s.shape[0] > 100],
np.linalg.inv(myafq.dwi_affine[0])))
sl_file = op.join(
myafq.data_frame.results_dir[0],
'sub-01_sess-01_dwi_space-RASMM_model-DTI_desc-det_tractography.trk')
sft = StatefulTractogram(streamlines, myafq.data_frame.dwi_file[0],
Space.VOX)
save_tractogram(sft, sl_file, bbox_valid_check=False)
mapping_file = op.join(
myafq.data_frame.results_dir[0],
'sub-01_sess-01_dwi_mapping_from-DWI_to_MNI_xfm.nii.gz')
nib.save(mapping, mapping_file)
reg_prealign_file = op.join(
myafq.data_frame.results_dir[0],
'sub-01_sess-01_dwi_prealign_from-DWI_to-MNI_xfm.npy')
np.save(reg_prealign_file, np.eye(4))
tgram = load_tractogram(myafq.bundles[0], myafq.dwi_img[0])
bundles = aus.tgram_to_bundles(tgram, myafq.bundle_dict, myafq.dwi_img[0])
npt.assert_(len(bundles['CST_R']) > 0)
# Test ROI exporting:
myafq.export_rois()
assert op.exists(op.join(
myafq.data_frame['results_dir'][0],
'ROIs',
'sub-01_sess-01_dwi_desc-ROI-CST_R-1-include.json'))
# Test bundles exporting:
myafq.export_bundles()
assert op.exists(op.join(
myafq.data_frame['results_dir'][0],
'bundles',
'sub-01_sess-01_dwi_space-RASMM_model-DTI_desc-det-AFQ-CST_L_tractography.trk')) # noqa
# Test creation of file with bundle indices:
assert op.exists(op.join(
myafq.data_frame['results_dir'][0],
'sub-01_sess-01_dwi_space-RASMM_model-DTI_desc-det-AFQ-clean_tractography_idx.json')) # noqa
tract_profiles = pd.read_csv(myafq.tract_profiles[0])
assert tract_profiles.shape == (800, 5)
# Before we run the CLI, we'll remove the bundles and ROI folders, to see
# that the CLI generates them
shutil.rmtree(op.join(myafq.data_frame['results_dir'][0],
'bundles'))
shutil.rmtree(op.join(myafq.data_frame['results_dir'][0],
'ROIs'))
# Test the CLI:
print("Running the CLI:")
# Bare bones config only points to the files
config = dict(files=dict(dmriprep_path=dmriprep_path))
config_file = op.join(tmpdir.name, "afq_config.toml")
with open(config_file, 'w') as ff:
toml.dump(config, ff)
cmd = "pyAFQ " + config_file
out = os.system(cmd)
assert out == 0
# The combined tract profiles should already exist from the CLI Run:
from_file = pd.read_csv(op.join(myafq.afq_dir, 'tract_profiles.csv'))
# And should be identical to what we would get by rerunning this:
combined_profiles = myafq.combine_profiles()
assert combined_profiles.shape == (800, 7)
assert_frame_equal(combined_profiles, from_file)
# Make sure the CLI did indeed generate these:
myafq.export_rois()
assert op.exists(op.join(
myafq.data_frame['results_dir'][0],
'ROIs',
'sub-01_sess-01_dwi_desc-ROI-CST_R-1-include.json'))
myafq.export_bundles()
assert op.exists(op.join(
myafq.data_frame['results_dir'][0],
'bundles',
'sub-01_sess-01_dwi_space-RASMM_model-DTI_desc-det-AFQ-CST_L_tractography.trk')) # noqa
def main(tempdir):
monai.config.print_config()
logging.basicConfig(stream=sys.stdout, level=logging.INFO)
# create a temporary directory and 40 random image, mask pairs
print(f"generating synthetic data to {tempdir} (this may take a while)")
for i in range(40):
im, seg = create_test_image_3d(128,
128,
128,
num_seg_classes=1,
channel_dim=-1)
n = nib.Nifti1Image(im, np.eye(4))
nib.save(n, os.path.join(tempdir, f"img{i:d}.nii.gz"))
n = nib.Nifti1Image(seg, np.eye(4))
nib.save(n, os.path.join(tempdir, f"seg{i:d}.nii.gz"))
images = sorted(glob(os.path.join(tempdir, "img*.nii.gz")))
segs = sorted(glob(os.path.join(tempdir, "seg*.nii.gz")))
train_files = [{
"image": img,
"label": seg
} for img, seg in zip(images[:20], segs[:20])]
val_files = [{
"image": img,
"label": seg
} for img, seg in zip(images[-20:], segs[-20:])]
# define transforms for image and segmentation
train_transforms = Compose([
LoadNiftid(keys=["image", "label"]),
AsChannelFirstd(keys=["image", "label"], channel_dim=-1),
ScaleIntensityd(keys="image"),
RandCropByPosNegLabeld(keys=["image", "label"],
label_key="label",
spatial_size=[96, 96, 96],
pos=1,
neg=1,
num_samples=4),
RandRotate90d(keys=["image", "label"], prob=0.5, spatial_axes=[0, 2]),
ToTensord(keys=["image", "label"]),
])
val_transforms = Compose([
LoadNiftid(keys=["image", "label"]),
AsChannelFirstd(keys=["image", "label"], channel_dim=-1),
ScaleIntensityd(keys="image"),
ToTensord(keys=["image", "label"]),
])
# create a training data loader
train_ds = monai.data.CacheDataset(data=train_files,
transform=train_transforms,
cache_rate=0.5)
# use batch_size=2 to load images and use RandCropByPosNegLabeld to generate 2 x 4 images for network training
train_loader = monai.data.DataLoader(train_ds,
batch_size=2,
shuffle=True,
num_workers=4)
# create a validation data loader
val_ds = monai.data.CacheDataset(data=val_files,
transform=val_transforms,
cache_rate=1.0)
val_loader = monai.data.DataLoader(val_ds, batch_size=1, num_workers=4)
# create UNet, DiceLoss and Adam optimizer
device = torch.device("cuda:0")
net = monai.networks.nets.UNet(
dimensions=3,
in_channels=1,
out_channels=1,
channels=(16, 32, 64, 128, 256),
strides=(2, 2, 2, 2),
num_res_units=2,
).to(device)
loss = monai.losses.DiceLoss(sigmoid=True)
opt = torch.optim.Adam(net.parameters(), 1e-3)
lr_scheduler = torch.optim.lr_scheduler.StepLR(opt, step_size=2, gamma=0.1)
val_post_transforms = Compose([
Activationsd(keys="pred", sigmoid=True),
AsDiscreted(keys="pred", threshold_values=True),
KeepLargestConnectedComponentd(keys="pred", applied_labels=[1]),
])
val_handlers = [
StatsHandler(output_transform=lambda x: None),
TensorBoardStatsHandler(log_dir="./runs/",
output_transform=lambda x: None),
TensorBoardImageHandler(
log_dir="./runs/",
batch_transform=lambda x: (x["image"], x["label"]),
output_transform=lambda x: x["pred"],
),
CheckpointSaver(save_dir="./runs/",
save_dict={"net": net},
save_key_metric=True),
]
evaluator = SupervisedEvaluator(
device=device,
val_data_loader=val_loader,
network=net,
inferer=SlidingWindowInferer(roi_size=(96, 96, 96),
sw_batch_size=4,
overlap=0.5),
post_transform=val_post_transforms,
key_val_metric={
"val_mean_dice":
MeanDice(include_background=True,
output_transform=lambda x: (x["pred"], x["label"]))
},
additional_metrics={
"val_acc":
Accuracy(output_transform=lambda x: (x["pred"], x["label"]))
},
val_handlers=val_handlers,
# if no FP16 support in GPU or PyTorch version < 1.6, will not enable AMP evaluation
amp=True if monai.config.get_torch_version_tuple() >=
(1, 6) else False,
)
train_post_transforms = Compose([
Activationsd(keys="pred", sigmoid=True),
AsDiscreted(keys="pred", threshold_values=True),
KeepLargestConnectedComponentd(keys="pred", applied_labels=[1]),
])
train_handlers = [
LrScheduleHandler(lr_scheduler=lr_scheduler, print_lr=True),
ValidationHandler(validator=evaluator, interval=2, epoch_level=True),
StatsHandler(tag_name="train_loss",
output_transform=lambda x: x["loss"]),
TensorBoardStatsHandler(log_dir="./runs/",
tag_name="train_loss",
output_transform=lambda x: x["loss"]),
CheckpointSaver(save_dir="./runs/",
save_dict={
"net": net,
"opt": opt
},
save_interval=2,
epoch_level=True),
]
trainer = SupervisedTrainer(
device=device,
max_epochs=5,
train_data_loader=train_loader,
network=net,
optimizer=opt,
loss_function=loss,
inferer=SimpleInferer(),
post_transform=train_post_transforms,
key_train_metric={
"train_acc":
Accuracy(output_transform=lambda x: (x["pred"], x["label"]))
},
train_handlers=train_handlers,
# if no FP16 support in GPU or PyTorch version < 1.6, will not enable AMP training
amp=True if monai.config.get_torch_version_tuple() >=
(1, 6) else False,
)
trainer.run()
try:
from nilearn.decomposition.canica import CanICA
t0 = time.time()
canica = CanICA(n_components=n_components,
mask=mask_img,
smoothing_fwhm=6.,
memory="nilearn_cache",
memory_level=1,
threshold=None,
random_state=1,
n_jobs=-1)
canica.fit(dataset.func)
print('Canica: %f' % (time.time() - t0))
canica_components = masking.unmask(canica.components_, mask_img)
nibabel.save(
nibabel.Nifti1Image(canica_components, mask_img.get_affine()),
join(path, 'canica.nii.gz'))
except ImportError:
import warnings
warnings.warn('nilearn must be installed to run CanICA')
canica_dmn = nibabel.load(join(path, 'canica.nii.gz')).get_data()[..., 4]
### Melodic ICA ############################################################
# To have MELODIC results, please use my melodic branch of nilearn
melodic_dmn = nibabel.load(join(path, 'melodic.nii.gz')).get_data()[..., 3]
### FastICA ##################################################################
# Concatenate all the subjects
data_df = pd.DataFrame(data, columns=col_names, index=gf.index, dtype=float)
df = pd.concat([gf, data_df], axis=1)
# selecting just specific groups
groups = gf.group.tolist()
idx = [i for i, v in enumerate(groups) if v in test_groups]
res = np.zeros([gv.shape[0], 3]) # ttest and pval
res[:] = np.nan
gv_idx = np.nonzero(gv)[0]
for v in range(nvoxels):
good_subjs = np.nonzero(~np.isnan(df['v%d' % v]))[0]
keep = np.intersect1d(good_subjs, idx)
est = smf.ols(formula='v%d ~ group + age + gender' % v,
data=df.iloc[keep]).fit()
# find the coefficient with group term
sx = [x for x, i in enumerate(est.tvalues.keys()) if i.find('group') == 0]
if len(sx) > 0:
sx = sx[0]
# convert from coefficient to beta
beta = est.tvalues[sx]
res[gv_idx[v], 0] = beta
res[gv_idx[v], 1] = 1 - est.pvalues[sx]
else:
res[gv_idx[v], 0] = 0
res[gv_idx[v], 1] = 0
fname = '%s/%sAgeGender_IC%02d.nii' % (res_dir, test_fname, comp)
print 'Saving results to %s' % fname
res = res.reshape(mask.get_data().shape[:3] + tuple([-1]))
nb.save(nb.Nifti1Image(res, img.get_affine()), fname)
def execute_spm_multimodal_fmri_glm(data, reg_motion=False):
reg_motion = reg_motion and 'realignment_parameters' in data
# experimental paradigm meta-params
stats_start_time = time.ctime()
tr = 2.
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
hfcut = 128.
# make design matrices
design_matrices = []
for x in xrange(2):
n_scans = data['func'][x].shape[-1]
timing = scipy.io.loadmat(data['trials_ses%i' % (x + 1)],
squeeze_me=True, struct_as_record=False)
faces_onsets = timing['onsets'][0].ravel()
scrambled_onsets = timing['onsets'][1].ravel()
onsets = np.hstack((faces_onsets, scrambled_onsets))
onsets *= tr # because onsets were reporting in 'scans' units
conditions = ['faces'] * len(faces_onsets) + ['scrambled'] * len(
scrambled_onsets)
paradigm = EventRelatedParadigm(conditions, onsets)
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
add_reg_names = None
add_regs = None
if reg_motion:
add_reg_names = ['tx', 'ty', 'tz', 'rx', 'ry', 'rz']
add_regs = np.loadtxt(data['realignment_parameters'][x])
if isinstance(add_regs):
add_regs = np.loadtxt(add_regs)
design_matrix = make_dmtx(
frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
add_reg_names=add_reg_names,
add_regs=add_regs
)
design_matrices.append(design_matrix)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# more interesting contrasts
contrasts['faces-scrambled'] = contrasts['faces'] - contrasts['scrambled']
contrasts['scrambled-faces'] = contrasts['scrambled'] - contrasts['faces']
contrasts['effects_of_interest'] = contrasts[
'faces'] + contrasts['scrambled']
# we've thesame contrasts over sessions, so let's replicate
contrasts = dict((contrast_id, [contrast_val] * 2)
for contrast_id, contrast_val in contrasts.iteritems())
# fit GLM
print('\r\nFitting a GLM (this takes time)...')
fmri_glm = FMRILinearModel([load_4D_img(sess_func)
for sess_func in data['func']],
[dmat.matrix for dmat in design_matrices],
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(data['output_dir'], "mask.nii.gz")
print "Saving mask image %s" % mask_path
nibabel.save(fmri_glm.mask, mask_path)
# compute bg unto which activation will be projected
anat_img = load_vol(data['anat'])
anat = anat_img.get_data()
if anat.ndim == 4:
anat = anat[..., 0]
anat_affine = anat_img.get_affine()
print "Computing contrasts .."
z_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, t_map, eff_map, var_map = fmri_glm.contrast(
contrast_val,
con_id=contrast_id,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True,
)
# store stat maps to disk
for dtype, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, eff_map, var_map]):
map_dir = os.path.join(
data['output_dir'], '%s_maps' % dtype)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if dtype == 'z':
z_maps[contrast_id] = map_path
print "\t\t%s map: %s" % (dtype, map_path)
# do stats report
data['stats_report_filename'] = os.path.join(data['reports_output_dir'],
"report_stats.html")
contrasts = dict((contrast_id, contrasts[contrast_id])
for contrast_id in z_maps.keys())
generate_subject_stats_report(
data['stats_report_filename'],
contrasts,
z_maps,
fmri_glm.mask,
anat=anat,
anat_affine=anat_affine,
design_matrices=design_matrices,
subject_id=data['subject_id'],
cluster_th=15, # we're only interested in this 'large' clusters
start_time=stats_start_time,
# additional ``kwargs`` for more informative report
paradigm=paradigm.__dict__,
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
frametimes=frametimes,
drift_model=drift_model,
hrf_model=hrf_model,
)
ProgressReport().finish_dir(data['reports_output_dir'])
print "\r\nStatistic report written to %s\r\n" % data[
'stats_report_filename']
return data
def __getitem__(self, index):
data = self.testing[index]
modalities = ['T1c', 'T1w', 'FLR', 'ENT', 'T2w']
return_obj = []
bbox = None
missing_modalities = []
if not self.targets:
for modality in modalities:
if modality == 'ENT' and data[modality] is not None:
ent_map = nib.load(data[modality]).get_fdata()
try:
bbox = bbox_3d_new(ent_map, self.size)
except:
print(data['id'])
raise ValueError(
"Not able to generate bounding box, check mask dimensions"
)
for modality in modalities:
if modality != 'ENT':
path = data[modality]
if path is not None:
if self.normalize:
nifti_img = nib.load(data[modality])
min_ = nifti_img.get_fdata().min()
max_ = nifti_img.get_fdata().max()
if min_ == -0 and max_ == -0:
image = nib.load(data[modality])
else:
if self.normalize == 'fcm' and modality == 'T1c':
self.tissue_mask = norm_main(
nifti_img,
contrast=modality,
method=self.normalize)
image = norm_main(
nifti_img,
contrast=modality,
method='zscore').get_fdata()
elif self.normalize == 'fcm' and modality != 'T1c':
image = norm_main(
nifti_img,
contrast=modality,
method=self.normalize,
fcm=self.tissue_mask).get_fdata()
else:
image = norm_main(
nifti_img,
contrast=modality,
method=self.normalize).get_fdata()
elif not self.normalize:
image = nib.load(data[modality]).get_fdata()
min_ = image.min()
max_ = image.max()
if min_ == -0 and max_ == -0:
missing_modalities.append(modality)
zeros = (self.size, self.size, self.size)
image_numpy = np.zeros(zeros)
return_obj.append(
torch.as_tensor(
np.ascontiguousarray(image_numpy)))
else:
if bbox is not None:
image_numpy = np.array(image[bbox])
if image_numpy.shape != (64, 64, 64):
image_numpy = pad_image(
image_numpy, self.size)
else:
image_numpy = np.array(image)
return_obj.append(
torch.as_tensor(
np.ascontiguousarray(image_numpy)))
if self.montage:
returnMontage(image_numpy, modality)
if self.save:
ni_img = nib.Nifti1Image(image_numpy, np.eye(4))
nib.save(
ni_img, '{}_bounding_box_{}.nii.gz'.format(
data['id'], modality))
else:
missing_modalities.append(modality)
zeros = (self.size, self.size, self.size)
image_numpy = np.zeros(zeros)
return_obj.append(
torch.as_tensor(np.ascontiguousarray(image_numpy)))
if not self.montage:
if self.targets:
return np.array(([x['group'] for x in self.testing
], [x['event'] for x in self.testing],
[x['surv'] for x in self.testing]))
else:
time, event = tuple((torch.tensor(np.array(data['group'])),
torch.tensor(np.array(data['event']))))
id_ = data['id']
if self.only_modality:
torch_images = (return_obj[0][None])
if torch_images.size() != torch.Size(
[1, self.size, self.size, self.size]):
return id_
else:
torch_images = torch.cat(
tuple((return_obj[0][None], return_obj[1][None],
return_obj[2][None], return_obj[3][None])))
if torch_images.size() != torch.Size(
[4, self.size, self.size, self.size]):
print(torch_images.size())
return id_
return torch_images.float()
def segmentVoxel(imgLoc, model):
'''
Segment the image and store the results
:param imgLoc: location of the flair image. Other modalities locations can be computed using this one.
:param model: Segmentation Network
:return: dice scores
'''
t1_loc = imgLoc.replace('flair', 't1')
t1ce_loc = imgLoc.replace('flair', 't1ce')
t2_loc = imgLoc.replace('flair', 't2')
label_loc = imgLoc.replace('flair', 'seg')
# get the 4 modalities
img_flair = nib.load(imgLoc).get_data()
gth_dummy = np.copy(img_flair)
img_t1 = nib.load(t1_loc).get_data()
img_t1ce = nib.load(t1ce_loc).get_data()
img_t2 = nib.load(t2_loc).get_data()
# Crop and min-max normalize them
wi_st, wi_en, hi_st, hi_en, ch_st, ch_en = cropVolumes(img_flair, img_t1, img_t1ce, img_t2)
img_flair = norm(img_flair[wi_st:wi_en, hi_st:hi_en, ch_st:ch_en])
img_t1 = norm(img_t1[wi_st:wi_en, hi_st:hi_en, ch_st:ch_en])
img_t1ce = norm(img_t1ce[wi_st:wi_en, hi_st:hi_en, ch_st:ch_en])
img_t2 = norm(img_t2[wi_st:wi_en, hi_st:hi_en, ch_st:ch_en])
# convert to Tensor
resize = (1, img_flair.shape[0], img_flair.shape[1], img_flair.shape[2])
img_flair = img_flair.reshape(resize)
img_t1 = img_t1.reshape(resize)
img_t1ce = img_t1ce.reshape(resize)
img_t2 = img_t2.reshape(resize)
tensor_flair = torch.from_numpy(img_flair)
tensor_t1 = torch.from_numpy(img_t1)
inputB = torch.from_numpy(img_t1ce)
tensor_t2 = torch.from_numpy(img_t2)
del img_flair, img_t1, img_t1ce, img_t2
# concat the tensors and then feed them to the model
tensor_concat = torch.cat([tensor_flair, tensor_t1, inputB, tensor_t2], 0) # inputB #
tensor_concat = torch.unsqueeze(tensor_concat, 0)
tensor_concat = tensor_concat.cuda()
#convert to variable.
# If you are using PyTorch version > 0.3, then you don't need this
tensor_concat_var = torch.autograd.Variable(tensor_concat, volatile=True)
# Average ensembling at multiple resolutions
# We found by experiments that ensembling at original and 144x144x144 gives best results.
test_resolutions = [None, (144, 144, 144)]
output = None
for res in test_resolutions:
if output is not None:
# test at the scaled resolution and combine them
output = output + model(tensor_concat_var, inp_res=res)
else:
# test at the original resolution
output = model(tensor_concat_var, inp_res=res)
output = output / len(test_resolutions)
del tensor_concat, tensor_concat_var
# convert the output to segmentation mask and move to CPU
output_ = output[0].max(0)[1].data.byte().cpu().numpy()
output_numpy = np.zeros_like(gth_dummy)
output_numpy[wi_st:wi_en, hi_st:hi_en, ch_st:ch_en] = output_
# rename the label 3 back to label 4
output_numpy[output_numpy == 3] = 4
# We need headers, so reload the flair image again
img1 = nib.load(imgLoc)
img1_new = nib.Nifti1Image(output_numpy, img1.affine, img1.header)
name = imgLoc.replace('_flair', '').split('/')[-1]
out_dir = './predictions'
if not os.path.isdir(out_dir):
os.mkdir(out_dir)
file_name = out_dir + os.sep + name
nib.save(img1_new, file_name)
def run_command(context, n_gif=0, thr_increment=None, resume_training=False):
"""Run main command.
This function is central in the ivadomed project as training / testing / evaluation commands are run via this
function. All the process parameters are defined in the config.
Args:
context (dict): Dictionary containing all parameters that are needed for a given process. See
:doc:`configuration_file` for more details.
n_gif (int): Generates a GIF during training if larger than zero, one frame per epoch for a given slice. The
parameter indicates the number of 2D slices used to generate GIFs, one GIF per slice. A GIF shows
predictions of a given slice from the validation sub-dataset. They are saved within the log directory.
thr_increment (float): A threshold analysis is performed at the end of the training using the trained model and
the training + validation sub-dataset to find the optimal binarization threshold. The specified value
indicates the increment between 0 and 1 used during the ROC analysis (e.g. 0.1).
resume_training (bool): Load a saved model ("checkpoint.pth.tar" in the log_directory) for resume training.
This training state is saved everytime a new best model is saved in the log
directory.
Returns:
Float or pandas Dataframe:
If "train" command: Returns floats: best loss score for both training and validation.
If "test" command: Returns a pandas Dataframe: of metrics computed for each subject of the testing
sub dataset and return the prediction metrics before evaluation.
If "segment" command: No return value.
"""
command = copy.deepcopy(context["command"])
log_directory = copy.deepcopy(context["log_directory"])
if not os.path.isdir(log_directory):
print('Creating log directory: {}'.format(log_directory))
os.makedirs(log_directory)
else:
print('Log directory already exists: {}'.format(log_directory))
# Define device
cuda_available, device = imed_utils.define_device(context['gpu'])
# Get subject lists. "segment" command uses all participants of BIDS path, hence no need to split
if command != "segment":
train_lst, valid_lst, test_lst = imed_loader_utils.get_subdatasets_subjects_list(
context["split_dataset"],
context['loader_parameters']['bids_path'], log_directory,
context["loader_parameters"]['subject_selection'])
# Loader params
loader_params = copy.deepcopy(context["loader_parameters"])
if command == "train":
loader_params["contrast_params"]["contrast_lst"] = loader_params[
"contrast_params"]["training_validation"]
else:
loader_params["contrast_params"]["contrast_lst"] = loader_params[
"contrast_params"]["testing"]
if "FiLMedUnet" in context and context["FiLMedUnet"]["applied"]:
loader_params.update(
{"metadata_type": context["FiLMedUnet"]["metadata"]})
# Load metadata necessary to balance the loader
if context['training_parameters']['balance_samples']['applied'] and \
context['training_parameters']['balance_samples']['type'] != 'gt':
loader_params.update({
"metadata_type":
context['training_parameters']['balance_samples']['type']
})
# Get transforms for each subdataset
transform_train_params, transform_valid_params, transform_test_params = \
imed_transforms.get_subdatasets_transforms(context["transformation"])
# MODEL PARAMETERS
model_params = copy.deepcopy(context["default_model"])
model_params["folder_name"] = copy.deepcopy(context["model_name"])
model_context_list = [
model_name for model_name in MODEL_LIST
if model_name in context and context[model_name]["applied"]
]
if len(model_context_list) == 1:
model_params["name"] = model_context_list[0]
model_params.update(context[model_context_list[0]])
elif 'Modified3DUNet' in model_context_list and 'FiLMedUnet' in model_context_list and len(
model_context_list) == 2:
model_params["name"] = 'Modified3DUNet'
for i in range(len(model_context_list)):
model_params.update(context[model_context_list[i]])
elif len(model_context_list) > 1:
print(
'ERROR: Several models are selected in the configuration file: {}.'
'Please select only one (i.e. only one where: "applied": true).'.
format(model_context_list))
exit()
model_params['is_2d'] = False if "Modified3DUNet" in model_params[
'name'] else model_params['is_2d']
# Get in_channel from contrast_lst
if loader_params["multichannel"]:
model_params["in_channel"] = len(
loader_params["contrast_params"]["contrast_lst"])
else:
model_params["in_channel"] = 1
# Get out_channel from target_suffix
model_params["out_channel"] = len(loader_params["target_suffix"])
# If multi-class output, then add background class
if model_params["out_channel"] > 1:
model_params.update({"out_channel": model_params["out_channel"] + 1})
# Display for spec' check
imed_utils.display_selected_model_spec(params=model_params)
# Update loader params
if 'object_detection_params' in context:
object_detection_params = context['object_detection_params']
object_detection_params.update({
"gpu":
context['gpu'],
"log_directory":
context['log_directory']
})
loader_params.update(
{"object_detection_params": object_detection_params})
loader_params.update({"model_params": model_params})
# TESTING PARAMS
# Aleatoric uncertainty
if context['uncertainty'][
'aleatoric'] and context['uncertainty']['n_it'] > 0:
transformation_dict = transform_train_params
else:
transformation_dict = transform_test_params
undo_transforms = imed_transforms.UndoCompose(
imed_transforms.Compose(transformation_dict, requires_undo=True))
testing_params = copy.deepcopy(context["training_parameters"])
testing_params.update({'uncertainty': context["uncertainty"]})
testing_params.update({
'target_suffix': loader_params["target_suffix"],
'undo_transforms': undo_transforms,
'slice_axis': loader_params['slice_axis']
})
if command == "train":
imed_utils.display_selected_transfoms(transform_train_params,
dataset_type=["training"])
imed_utils.display_selected_transfoms(transform_valid_params,
dataset_type=["validation"])
elif command == "test":
imed_utils.display_selected_transfoms(transformation_dict,
dataset_type=["testing"])
# Check if multiple raters
if any([
isinstance(class_suffix, list)
for class_suffix in loader_params["target_suffix"]
]):
print(
"\nAnnotations from multiple raters will be used during model training, one annotation from one rater "
"randomly selected at each iteration.\n")
if command != "train":
print(
"\nERROR: Please provide only one annotation per class in 'target_suffix' when not training a model.\n"
)
exit()
if command == 'train':
# LOAD DATASET
# Get Validation dataset
ds_valid = imed_loader.load_dataset(**{
**loader_params,
**{
'data_list': valid_lst,
'transforms_params': transform_valid_params,
'dataset_type': 'validation'
}
},
device=device,
cuda_available=cuda_available)
# Get Training dataset
ds_train = imed_loader.load_dataset(**{
**loader_params,
**{
'data_list': train_lst,
'transforms_params': transform_train_params,
'dataset_type': 'training'
}
},
device=device,
cuda_available=cuda_available)
metric_fns = imed_metrics.get_metric_fns(ds_train.task)
# If FiLM, normalize data
if 'film_layers' in model_params and any(model_params['film_layers']):
# Normalize metadata before sending to the FiLM network
results = imed_film.get_film_metadata_models(
ds_train=ds_train,
metadata_type=model_params['metadata'],
debugging=context["debugging"])
ds_train, train_onehotencoder, metadata_clustering_models = results
ds_valid = imed_film.normalize_metadata(
ds_valid, metadata_clustering_models, context["debugging"],
model_params['metadata'])
model_params.update({
"film_onehotencoder":
train_onehotencoder,
"n_metadata":
len([ll for l in train_onehotencoder.categories_ for ll in l])
})
joblib.dump(metadata_clustering_models,
"./" + log_directory + "/clustering_models.joblib")
joblib.dump(train_onehotencoder,
"./" + log_directory + "/one_hot_encoder.joblib")
# Model directory
path_model = os.path.join(log_directory, context["model_name"])
if not os.path.isdir(path_model):
print('Creating model directory: {}'.format(path_model))
os.makedirs(path_model)
if 'film_layers' in model_params and any(
model_params['film_layers']):
joblib.dump(train_onehotencoder,
os.path.join(path_model, "one_hot_encoder.joblib"))
if 'metadata_dict' in ds_train[0]['input_metadata'][0]:
metadata_dict = ds_train[0]['input_metadata'][0][
'metadata_dict']
joblib.dump(
metadata_dict,
os.path.join(path_model, "metadata_dict.joblib"))
else:
print('Model directory already exists: {}'.format(path_model))
save_config_file(context, log_directory)
# RUN TRAINING
best_training_dice, best_training_loss, best_validation_dice, best_validation_loss = imed_training.train(
model_params=model_params,
dataset_train=ds_train,
dataset_val=ds_valid,
training_params=context["training_parameters"],
log_directory=log_directory,
device=device,
cuda_available=cuda_available,
metric_fns=metric_fns,
n_gif=n_gif,
resume_training=resume_training,
debugging=context["debugging"])
if thr_increment:
# LOAD DATASET
if command != 'train': # If command == train, then ds_valid already load
# Get Validation dataset
ds_valid = imed_loader.load_dataset(**{
**loader_params,
**{
'data_list': valid_lst,
'transforms_params': transform_valid_params,
'dataset_type': 'validation'
}
},
device=device,
cuda_available=cuda_available)
# Get Training dataset with no Data Augmentation
ds_train = imed_loader.load_dataset(**{
**loader_params,
**{
'data_list': train_lst,
'transforms_params': transform_valid_params,
'dataset_type': 'training'
}
},
device=device,
cuda_available=cuda_available)
# Choice of optimisation metric
metric = "recall_specificity" if model_params[
"name"] in imed_utils.CLASSIFIER_LIST else "dice"
# Model path
model_path = os.path.join(log_directory, "best_model.pt")
# Run analysis
thr = imed_testing.threshold_analysis(model_path=model_path,
ds_lst=[ds_train, ds_valid],
model_params=model_params,
testing_params=testing_params,
metric=metric,
increment=thr_increment,
fname_out=os.path.join(
log_directory, "roc.png"),
cuda_available=cuda_available)
# Update threshold in config file
context["postprocessing"]["binarize_prediction"] = {"thr": thr}
save_config_file(context, log_directory)
if command == 'train':
return best_training_dice, best_training_loss, best_validation_dice, best_validation_loss
if command == 'test':
# LOAD DATASET
ds_test = imed_loader.load_dataset(**{
**loader_params,
**{
'data_list': test_lst,
'transforms_params': transformation_dict,
'dataset_type': 'testing',
'requires_undo': True
}
},
device=device,
cuda_available=cuda_available)
metric_fns = imed_metrics.get_metric_fns(ds_test.task)
if 'film_layers' in model_params and any(model_params['film_layers']):
clustering_path = os.path.join(log_directory,
"clustering_models.joblib")
metadata_clustering_models = joblib.load(clustering_path)
ohe_path = os.path.join(log_directory, "one_hot_encoder.joblib")
one_hot_encoder = joblib.load(ohe_path)
ds_test = imed_film.normalize_metadata(ds_test,
metadata_clustering_models,
context["debugging"],
model_params['metadata'])
model_params.update({
"film_onehotencoder":
one_hot_encoder,
"n_metadata":
len([ll for l in one_hot_encoder.categories_ for ll in l])
})
# RUN INFERENCE
pred_metrics = imed_testing.test(
model_params=model_params,
dataset_test=ds_test,
testing_params=testing_params,
log_directory=log_directory,
device=device,
cuda_available=cuda_available,
metric_fns=metric_fns,
postprocessing=context['postprocessing'])
# RUN EVALUATION
df_results = imed_evaluation.evaluate(
bids_path=loader_params['bids_path'],
log_directory=log_directory,
target_suffix=loader_params["target_suffix"],
eval_params=context["evaluation_parameters"])
return df_results, pred_metrics
if command == 'segment':
bids_ds = bids.BIDS(context["loader_parameters"]["bids_path"])
df = bids_ds.participants.content
subj_lst = df['participant_id'].tolist()
bids_subjects = [
s for s in bids_ds.get_subjects()
if s.record["subject_id"] in subj_lst
]
# Add postprocessing to packaged model
path_model = os.path.join(context['log_directory'],
context['model_name'])
path_model_config = os.path.join(path_model,
context['model_name'] + ".json")
model_config = imed_config_manager.load_json(path_model_config)
model_config['postprocessing'] = context['postprocessing']
with open(path_model_config, 'w') as fp:
json.dump(model_config, fp, indent=4)
options = None
for subject in bids_subjects:
if context['loader_parameters']['multichannel']:
fname_img = []
provided_contrasts = []
contrasts = context['loader_parameters']['contrast_params'][
'testing']
# Keep contrast order
for c in contrasts:
for s in bids_subjects:
if subject.record['subject_id'] == s.record[
'subject_id'] and s.record['modality'] == c:
provided_contrasts.append(c)
fname_img.append(s.record['absolute_path'])
bids_subjects.remove(s)
if len(fname_img) != len(contrasts):
logger.warning(
"Missing contrast for subject {}. {} were provided but {} are required. Skipping "
"subject.".format(subject.record['subject_id'],
provided_contrasts, contrasts))
continue
else:
fname_img = [subject.record['absolute_path']]
if 'film_layers' in model_params and any(
model_params['film_layers']) and model_params['metadata']:
subj_id = subject.record['subject_id']
metadata = df[df['participant_id'] == subj_id][
model_params['metadata']].values[0]
options = {'metadata': metadata}
pred_list, target_list = imed_inference.segment_volume(
path_model,
fname_images=fname_img,
gpu_number=context['gpu'],
options=options)
pred_path = os.path.join(context['log_directory'], "pred_masks")
if not os.path.exists(pred_path):
os.makedirs(pred_path)
for pred, target in zip(pred_list, target_list):
filename = subject.record['subject_id'] + "_" + subject.record['modality'] + target + "_pred" + \
".nii.gz"
nib.save(pred, os.path.join(pred_path, filename))
#print(taffine)
break
buf = np.zeros(tshape, dtype=ttype)
# now create dyn image file to store all subtypes in one lesion file
i = 0
for tissu in tissues:
if tissu in masks[lesi]:
print(tissu)
print(lesi)
d = masks[lesi][tissu].get_data()
if tissu == 'edema':
d[d != 0] = 1
else:
if tissu == 'enh':
d[d != 0] = 2
else:
if tissu == 'necrosis':
d[d != 0] = 3
print "---> lesion ", lesi, "-", tissu, ": ", np.unique(
d)
buf[:, :, :, i] = d
i += 1
# flesion = os.path.basename(masks[lesion][tissue].get_filename()).split('_')[0]
# mlesion = os.path.basename(masks[lesion][tissue].get_filename()).split('_')[1]
flesion = '{}_{}_mask_lesion-{}'.format(s, model,
lesi) + '.nii.gz'
f = os.path.join(path, s, model, flesion)
print f
ni.save(ni.Nifti1Image(buf, affine=taffine), f)