def test_unmask_list(random_state=42):
rng = np.random.RandomState(random_state)
shape = (3, 4, 5)
affine = np.eye(4)
mask_data = (rng.rand(*shape) < .5)
mask_img = Nifti1Image(mask_data.astype(np.uint8), affine)
a = unmask(mask_data[mask_data], mask_img)
b = unmask(mask_data[mask_data].tolist(), mask_img) # shouldn't crash
assert_array_equal(a.get_data(), b.get_data())
def _generate_report(self):
""" Generates the visual report """
from niworkflows.viz.utils import plot_registration
NIWORKFLOWS_LOG.info('Generating visual report')
anat = load_img(self._anat_file)
contour_nii = load_img(self._contour) if self._contour is not None else None
if self._mask_file:
anat = unmask(apply_mask(anat, self._mask_file), self._mask_file)
mask_nii = load_img(self._mask_file)
else:
mask_nii = threshold_img(anat, 1e-3)
n_cuts = 7
if not self._mask_file and contour_nii:
cuts = cuts_from_bbox(contour_nii, cuts=n_cuts)
else:
cuts = cuts_from_bbox(mask_nii, cuts=n_cuts)
# Call composer
compose_view(
plot_registration(anat, 'fixed-image',
estimate_brightness=True,
cuts=cuts,
contour=contour_nii,
compress=self.inputs.compress_report),
[],
out_file=self._out_report
)
def _generate_report(self):
""" Generates the visual report """
from niworkflows.viz.utils import plot_registration
NIWORKFLOWS_LOG.info('Generating visual report')
anat = load_img(self._anat_file)
contour_nii = load_img(
self._contour) if self._contour is not None else None
if self._mask_file:
anat = unmask(apply_mask(anat, self._mask_file), self._mask_file)
mask_nii = load_img(self._mask_file)
else:
mask_nii = threshold_img(anat, 1e-3)
n_cuts = 7
if not self._mask_file and contour_nii:
cuts = cuts_from_bbox(contour_nii, cuts=n_cuts)
else:
cuts = cuts_from_bbox(mask_nii, cuts=n_cuts)
# Call composer
compose_view(plot_registration(anat,
'fixed-image',
estimate_brightness=True,
cuts=cuts,
contour=contour_nii,
compress=self.inputs.compress_report),
[],
out_file=self._out_report)
def _run_fwe_permutation(self, params):
"""
Run a single random permutation of a dataset. Does the shared work
between vFWE and cFWE.
"""
iter_df, iter_ijk, conn, z_thresh = params
iter_ijk = np.squeeze(iter_ijk)
iter_df[['i', 'j', 'k']] = iter_ijk
ale_values = self._compute_ale(iter_df)
_, z_values = self._ale_to_p(ale_values)
iter_max_value = np.max(ale_values)
# Begin cluster-extent thresholding by thresholding matrix at cluster-
# defining voxel-level threshold
iter_z_map = unmask(z_values, self.mask)
vthresh_iter_z_map = iter_z_map.get_data()
vthresh_iter_z_map[vthresh_iter_z_map < z_thresh] = 0
labeled_matrix = ndimage.measurements.label(vthresh_iter_z_map, conn)[0]
clust_sizes = [np.sum(labeled_matrix == val) for val in np.unique(labeled_matrix)]
if len(clust_sizes) == 1:
iter_max_cluster = 0
else:
clust_sizes = clust_sizes[1:] # First cluster is zeros in matrix
iter_max_cluster = np.max(clust_sizes)
return iter_max_value, iter_max_cluster
def _perm(self, params):
iter_ijk, iter_df, weight_vec, conn = params
iter_ijk = np.squeeze(iter_ijk)
iter_df[['i', 'j', 'k']] = iter_ijk
k_est = self.kernel_estimator(iter_df, self.mask)
iter_ma_maps = k_est.transform(self.ids, **self.kernel_arguments)
iter_ma_maps = apply_mask(iter_ma_maps, self.mask)
iter_ma_maps *= weight_vec
iter_of_map = np.sum(iter_ma_maps, axis=0)
iter_max_value = np.max(iter_of_map)
iter_of_map = unmask(iter_of_map, self.mask)
vthresh_iter_of_map = iter_of_map.get_data().copy()
vthresh_iter_of_map[vthresh_iter_of_map < self.voxel_thresh] = 0
labeled_matrix = ndimage.measurements.label(vthresh_iter_of_map,
conn)[0]
clust_sizes = [
np.sum(labeled_matrix == val) for val in np.unique(labeled_matrix)
]
clust_sizes = clust_sizes[1:] # First cluster is zeros in matrix
if clust_sizes:
iter_max_cluster = np.max(clust_sizes)
else:
iter_max_cluster = 0
return iter_max_value, iter_max_cluster
def _run_fwe_permutation(self, params):
iter_ijk, iter_df, conn, voxel_thresh = params
iter_ijk = np.squeeze(iter_ijk)
iter_df[['i', 'j', 'k']] = iter_ijk
iter_ma_maps = self.kernel_estimator.transform(iter_df,
mask=self.mask,
masked=True)
iter_ma_maps *= self.weight_vec
iter_of_map = np.sum(iter_ma_maps, axis=0)
iter_max_value = np.max(iter_of_map)
iter_of_map = unmask(iter_of_map, self.mask)
vthresh_iter_of_map = iter_of_map.get_data().copy()
vthresh_iter_of_map[vthresh_iter_of_map < voxel_thresh] = 0
labeled_matrix = ndimage.measurements.label(vthresh_iter_of_map,
conn)[0]
clust_sizes = [
np.sum(labeled_matrix == val) for val in np.unique(labeled_matrix)
]
clust_sizes = clust_sizes[1:] # First cluster is zeros in matrix
if clust_sizes:
iter_max_cluster = np.max(clust_sizes)
else:
iter_max_cluster = 0
return iter_max_value, iter_max_cluster
def compute_tsnr(self, run=None, mean_only=False, std_only=False):
""" Computes tsnr (or mean/std) image of the (mean) functional data. """
self.logger.info("Computing TSNR.")
if mean_only and std_only:
raise ValueError("Cannot return mean only and std only!")
if run is None:
n_runs = len(self.preproc['func_ts'])
else:
n_runs = 1
stat = np.zeros((n_runs, self.preproc['func_ts'][0].shape[-1]))
for run in range(n_runs):
func = self.preproc['func_ts'][run]
if mean_only:
this_stat = func.mean(axis=0)
elif std_only:
this_stat = func.std(axis=0)
else:
this_stat = func.mean(axis=0) / func.std(axis=0)
this_stat[np.isnan(this_stat)] = 0
stat[run, :] = this_stat
mean_stat = stat.mean(axis=0)
if self.mask is not None:
mean_stat = masking.unmask(mean_stat, self.mask)
return mean_stat
def scramble_img(img, mask_img, random_state=None):
'''Shuffles the voxel values within a Niimg-like object
img: Niimg-like object
Input image where the voxels should be randomly shuffled.
mask_img: Niimg-like object
A mask which masks the data to brain space
random_state: int, RandomState instance or None, optional, default=None
If int, random_state is the seed used by the random number generator;
If RandomState instance, random_state is the random number generator;
If None, the random number generator is the RandomState instance used by np.random.
Used when shuffle == True.
'''
rng = check_random_state(random_state)
# mask image to MNI152 template
img_data = apply_mask(img, mask_img).flatten()
n_voxels = img_data.shape[0]
# shuffle data
img_data_scrambled = rng.choice(img_data, n_voxels, replace=False)
# transform back to image
img_scrambled = unmask(img_data_scrambled, mask_img)
return img_scrambled
def array_to_mni_map(array, fname, data_path, mask, threshold=None, **kwargs):
'''Transforms array to mni space and saves it as mni map
IN:
array - ndarray, array of statistics in group sapce to transform to mni space
fname - string, name under which to save the mni map
data_path - string, path to Forrest Gump directory
mask - string, filename of the mask to unmask array.
threshold - float, optional, threshold for mni map'''
from nipype.interfaces import fsl
import os
from nilearn.masking import unmask
if threshold is not None:
array[np.abs(array) < threshold] = 0
unmasked = unmask(array, mask)
unmasked.to_filename(fname)
flirt = fsl.ApplyXFM()
flirt.inputs.in_file = fname
flirt.inputs.out_file = fname
flirt.inputs.padding_size = 0
flirt.inputs.interp = 'nearestneighbour'
flirt.inputs.reference = os.path.join(data_path, 'templates',
'grpbold7Tp1', 'in_mni',
'brain_12dof.nii.gz')
flirt.inputs.in_matrix_file = os.path.join(data_path, 'templates',
'grpbold7Tp1', 'xfm',
'tmpl2mni_12dof.mat')
flirt.run()
def fit(self,
target_mask,
method='min_distance',
r=5,
n_exps=50,
n_parcels=2):
"""
Run MAPBOT parcellation.
Parameters
----------
region_name : :obj:`str`
Name of region for parcellation.
n_parcels : :obj:`int`, optional
Number of parcels to generate for ROI. If array_like, each parcel
number will be evaluated and results for all will be returned.
Default is 2.
"""
if not isinstance(n_parcels):
n_parcels = [n_parcels]
# Step 1: Build correlation matrix
target_data = apply_mask(target_mask, self.mask)
target_map = unmask(target_data, self.mask)
target_data = target_map.get_data()
mask_idx = np.vstack(np.where(target_data))
n_voxels = mask_idx.shape[1]
voxel_arr = np.zeros((n_voxels, np.sum(self.mask)))
del voxel_arr # currently unused
ijk = self.coordinates[['i', 'j', 'k']].values
temp_df = self.coordinates.copy()
term_df = pd.DataFrame(columns=self.tfidf_df.columns,
index=range(n_voxels))
for i_voxel in range(n_voxels):
voxel = mask_idx[:, i_voxel]
temp_df['distance'] = cdist(ijk, voxel)
if method == 'min_studies':
# number of studies
temp_df2 = temp_df.groupby('id')[['distance']].min()
temp_df2 = temp_df2.sort_values(by='distance')
sel_ids = temp_df2.iloc[:n_exps].index.values
elif method == 'min_distance':
# minimum distance
temp_df2 = temp_df.groupby('id')[['distance']].min()
sel_ids = temp_df2.loc[temp_df2['distance'] < r].index.values
# Build DT matrix
voxel_df = self.tfidf_df.loc[self.tfidf_df.index.isin(sel_ids)]
term_df.loc[i_voxel] = voxel_df.mean(axis=0)
values = term_df.values
d = np.dot(np.dot(values.T, values), np.ones((values.shape[0], 1)))
values_prime = np.dot(values, d**-.5)
for i_parc in n_parcels:
model = NMF(n_components=i_parc, init='nndsvd', random_state=0)
W = model.fit_transform(values_prime)
H = model.components_
del W, H # not sure what's next
def _run_interface(self, runtime):
ext = '.nii.gz' if self.inputs.compress else '.nii'
flat_mask = apply_mask(self.inputs.image, self.inputs.mask)
masked_image = unmask(flat_mask, self.inputs.mask)
self._results['masked_t2s'] = fname_presuffix(
self.inputs.image, suffix='_masked' + ext, newpath=runtime.cwd, use_ext=False)
masked_image.to_filename(self._results['masked_t2s'])
return runtime
def _run_interface(self, runtime):
ext = '.nii.gz' if self.inputs.compress else '.nii'
flat_mask = apply_mask(self.inputs.image, self.inputs.mask)
masked_image = unmask(flat_mask, self.inputs.mask)
self._results['masked_t2s'] = fname_presuffix(
self.inputs.image, suffix='_masked' + ext, newpath=runtime.cwd, use_ext=False)
masked_image.to_filename(self._results['masked_t2s'])
return runtime
def compute_TSNR(in_file, highpass=True, motion_corr=False):
""" Computes temporal signal-to-noise ratio (TSNR) for
a functional MRI file preprocessed with FMRIPREP.
Parameters
----------
in_file : str
Path to functional MRI file
highpass : bool
Whether to highpass the data (using the cosine basis
set in the *confounds.tsv file)
motion_corr : bool
Whether to include the six motion parameters from
motion correction in the confound regression step.
Returns
-------
out_file : str
Path to TSNR file
"""
base_dir = op.dirname(in_file)
base_file = op.basename(in_file)
if 'preproc' not in base_file:
raise ValueError("In_file should be a preprocessed file!")
# Mask BOLD file
mask = op.join(base_dir,
base_file.split('preproc')[0] + 'brain_mask.nii.gz')
bold_masked = masking.apply_mask(in_file, mask)
# Get confounds and regress out of data
if highpass or motion_corr:
conf = op.join(
base_dir,
base_file.split('space')[0] + 'desc-confounds_regressors.tsv')
conf_df = pd.read_csv(conf, sep='\t')
conf_vars = []
if highpass:
conf_vars.extend(
[col for col in conf_df.columns if 'cosine' in col])
if motion_corr:
conf_vars.extend(
['trans_x', 'trans_y', 'trans_z', 'rot_x', 'rot_y', 'rot_z'])
conf_df = conf_df.loc[:, conf_vars]
conf_values = np.c_[np.ones(conf_df.shape[0]), conf_df.values]
conf_params = np.linalg.lstsq(conf_values, bold_masked, rcond=-1)[0]
bold_masked = bold_masked - conf_values[:, 1:].dot(conf_params[1:, :])
# Compute tsnr
tsnr = bold_masked.mean(axis=0) / bold_masked.std(axis=0)
tsnr_img = masking.unmask(tsnr, mask)
out_file = in_file.replace('.nii.gz', '_TSNR.nii.gz')
tsnr_img.to_filename(out_file)
return out_file
def _generate_report(self):
""" Generates the visual report """
from niworkflows.viz.utils import plot_registration
NIWORKFLOWS_LOG.info('Generating visual report')
fixed_image_nii = load_img(self._fixed_image)
moving_image_nii = load_img(self._moving_image)
contour_nii = load_img(
self._contour) if self._contour is not None else None
if self._fixed_image_mask:
fixed_image_nii = unmask(
apply_mask(fixed_image_nii, self._fixed_image_mask),
self._fixed_image_mask)
# since the moving image is already in the fixed image space we
# should apply the same mask
moving_image_nii = unmask(
apply_mask(moving_image_nii, self._fixed_image_mask),
self._fixed_image_mask)
mask_nii = load_img(self._fixed_image_mask)
else:
mask_nii = threshold_img(fixed_image_nii, 1e-3)
n_cuts = 7
if not self._fixed_image_mask and contour_nii:
cuts = cuts_from_bbox(contour_nii, cuts=n_cuts)
else:
cuts = cuts_from_bbox(mask_nii, cuts=n_cuts)
# Call composer
compose_view(plot_registration(fixed_image_nii,
'fixed-image',
estimate_brightness=True,
cuts=cuts,
label=self._fixed_image_label,
contour=contour_nii,
compress=self.inputs.compress_report),
plot_registration(moving_image_nii,
'moving-image',
estimate_brightness=True,
cuts=cuts,
label=self._moving_image_label,
contour=contour_nii,
compress=self.inputs.compress_report),
out_file=self._out_report)
def preprocess_and_tmp_save_fmri(data_path,
task,
subj,
model,
tmp_path,
group_mask=None):
'''
Generator for preprocessed fMRI runs from one subject of Forrest Gump
aligns to group template
run-wise linear de-trending and z-scoring
IN:
data_path - string, path pointing to the Forrest Gump directory
task - string, which part of the Forrest Gump dataset to load
subj - int, subject to pre-process
tmp_path - string, path to save the dataset temporarily to
OUT:
preprocessed fMRI samples per run'''
from nipype.interfaces import fsl
dhandle = mvpa.OpenFMRIDataset(data_path)
flavor = 'dico_bold7Tp1_to_subjbold7Tp1'
if group_mask is None:
group_mask = os.path.join(data_path, 'sub{0:03d}'.format(subj),
'templates', 'bold7Tp1', 'in_grpbold7Tp1',
'brain_mask.nii.gz')
mask_fname = os.path.join(data_path, 'sub{0:03d}'.format(subj),
'templates', 'bold7Tp1', 'brain_mask.nii.gz')
for run_id in dhandle.get_task_bold_run_ids(task)[subj]:
run_ds = dhandle.get_bold_run_dataset(subj,
task,
run_id,
chunks=run_id - 1,
mask=mask_fname,
flavor=flavor)
filename = 'brain_subj_{}_run_{}.nii.gz'.format(subj, run_id)
tmp_file = os.path.join(tmp_path, filename)
save(unmask(run_ds.samples.astype('float32'), mask_fname), tmp_file)
warp = fsl.ApplyWarp()
warp.inputs.in_file = tmp_file
warp.inputs.out_file = os.path.join(tmp_path, 'group_' + filename)
warp.inputs.ref_file = os.path.join(data_path, 'templates',
'grpbold7Tp1', 'brain.nii.gz')
warp.inputs.field_file = os.path.join(data_path,
'sub{0:03d}'.format(subj),
'templates', 'bold7Tp1',
'in_grpbold7Tp1',
'subj2tmpl_warp.nii.gz')
warp.inputs.interp = 'nn'
warp.run()
os.remove(tmp_file)
run_ds = mvpa.fmri_dataset(os.path.join(tmp_path, 'group_' + filename),
mask=group_mask,
chunks=run_id - 1)
mvpa.poly_detrend(run_ds, polyord=1)
mvpa.zscore(run_ds)
os.remove(os.path.join(tmp_path, 'group_' + filename))
yield run_ds.samples.astype('float32')
def save_map_whole(subj, scores, threshold=None, model='logBSC_H200'):
'''Saves brainmap as nifti file'''
subj_mask = '/home/data/psyinf/forrest_gump/anondata/sub{0:03}'.format(subj) + '/templates/bold7Tp1/brain_mask.nii.gz'
if threshold is not None:
scores[scores<threshold] = 0
unmasked = unmask(scores, subj_mask)
unmasked.to_filename(
spenc_dir+'MaThe/maps/model_{}_subj_'.format(model)+\
'{}_map.nii.gz'.format(subj))
def save_map_avg_whole(scores, threshold=None, model='logBSC_H200'):
'''Saves brainmap as nifti file'''
mask = spenc_dir + 'brainmask_group_template.nii.gz'
if threshold is not None:
scores[scores<threshold] = 0
unmasked = unmask(scores, mask)
unmasked.to_filename(
spenc_dir+'MaThe/maps/model_{}_'.format(model)+\
'whole_avg_map.nii.gz')
def save_map_avg(subj, scores, threshold=0.0, model='logBSC_H200'):
'''Saves brainmap as nifti file'''
mask = spenc_dir+'temporal_lobe_mask_grp_7T_test.nii.gz'
if threshold is not None:
scores[scores<threshold] = 0
unmasked = unmask(scores, mask)
unmasked.to_filename(
spenc_dir+'MaThe/maps/model_avg_{}_subj_'.format(model)+\
'{}_map.nii.gz'.format(subj))
def unmask_img(d, mask):
"""
Unmasks matrix d according to mask
:param d: numpy array (2D)
:param mask: mask
:param logger: logger instance
:return: image file
"""
return masking.unmask(d, mask)
def _generate_report(self):
""" Generates the visual report """
from niworkflows.viz.utils import plot_registration
NIWORKFLOWS_LOG.info('Generating visual report')
fixed_image_nii = load_img(self._fixed_image)
moving_image_nii = load_img(self._moving_image)
contour_nii = load_img(self._contour) if self._contour is not None else None
if self._fixed_image_mask:
fixed_image_nii = unmask(apply_mask(fixed_image_nii,
self._fixed_image_mask),
self._fixed_image_mask)
# since the moving image is already in the fixed image space we
# should apply the same mask
moving_image_nii = unmask(apply_mask(moving_image_nii,
self._fixed_image_mask),
self._fixed_image_mask)
mask_nii = load_img(self._fixed_image_mask)
else:
mask_nii = threshold_img(fixed_image_nii, 1e-3)
n_cuts = 7
if not self._fixed_image_mask and contour_nii:
cuts = cuts_from_bbox(contour_nii, cuts=n_cuts)
else:
cuts = cuts_from_bbox(mask_nii, cuts=n_cuts)
# Call composer
compose_view(
plot_registration(fixed_image_nii, 'fixed-image',
estimate_brightness=True,
cuts=cuts,
label=self._fixed_image_label,
contour=contour_nii,
compress=self.inputs.compress_report),
plot_registration(moving_image_nii, 'moving-image',
estimate_brightness=True,
cuts=cuts,
label=self._moving_image_label,
contour=contour_nii,
compress=self.inputs.compress_report),
out_file=self._out_report
)
def main(file=None, mask=True, figure=False, out_dir=None):
""" Computes the median temporal signal-to-noise ratio (TSNR) of
a 4D fMRI file (similar to what MRIQC does).
Parameters
----------
file : str or None
If str, refers to the path of a 4D nifti file. If None,
a default file is loaded.
mask : bool
Whether to mask the file (using Nilearn)
figure : bool
If False, only prints out the median TSNR value. If True,
it will write out a figure with voxel-wise TSNR values.
out_dir : str
Directory to save TSNR figure to. If None, the same directory
as `file` will be used.
"""
if file is None:
print("WARNING: you did not specify a file! Exiting ...")
sys.exit()
print(f"INFO: computing TSNR for {file}")
# Load in image and associated data
img = image.load_img(file)
# Apply mask
if mask:
print("INFO: computing EPI mask")
mask = masking.compute_epi_mask(img)
else:
# If no mask, at least remove zeros
nonzeros = (img.get_fdata().sum(axis=3) != 0).astype(int)
mask = nib.Nifti1Image(nonzeros, affine=img.affine)
img_2d = masking.apply_mask(img, mask)
# Compute TSNR
tsnr = np.mean(img_2d, axis=0) / np.std(img_2d, axis=0)
print(f"INFO: median TSNR = {np.median(tsnr):.3f}")
if figure:
# Recreate 3D nifti + plot with Nilearn
tsnr_img = masking.unmask(tsnr, mask_img=mask)
plotting.plot_epi(tsnr_img)
# Save to disk
if out_dir is None: # set dir if necessary
out_dir = os.path.dirname(file)
f_name = os.path.basename(file).replace('.nii.gz', '_tsnr.png')
f_out = os.path.join(out_dir, f_name)
print(f"INFO: Saving figure to {f_out}")
plt.savefig(f_out)
def save_map(subj, scores, threshold=0.0, model='logBSC_H200'):
'''Saves brainmap as nifti file'''
subj_mask = spenc_dir+'temporal_lobe_mask_brain'+\
'_subj{0:02}bold.nii.gz'.format(subj)
if threshold is not None:
scores[scores<threshold] = 0
unmasked = unmask(scores, subj_mask)
unmasked.to_filename(
spenc_dir+'MaThe/maps/model_{}_subj_'.format(model)+\
'{}_map.nii.gz'.format(subj))
def inverse_transform(self, X):
self._check_fitted()
img = masking.unmask(X, self.mask_img_)
# Be robust again memmapping that will create read-only arrays in
# internal structures of the header: remove the memmaped array
try:
img._header._structarr = np.array(img._header._structarr).copy()
except:
pass
return img
def inverse_transform(self, X):
self._check_fitted()
img = masking.unmask(X, self.mask_img_)
# Be robust again memmapping that will create read-only arrays in
# internal structures of the header: remove the memmaped array
try:
img._header._structarr = np.array(img._header._structarr).copy()
except:
pass
return img
def from_array_to_nifti(self, nii_output_filename, array, mask_img):
"""
Convert an array to a nitfi image and save it
:param nii_output_filename:
:param array: Dask array, shape(n_voxels)
:param mask_img:
:return:
"""
img_3D = unmask(array, mask_img, order='F')
nb.save(img_3D, nii_output_filename)
def unmaskImg(d, mask, logger=None):
"""
Unmasks matrix d according to mask
:param d: numpy array (2D)
:param mask: mask
:param logger: logger instance
:return: image file
"""
from nilearn.masking import unmask
write_to_logger("unmasking image...", logger)
return unmask(d, mask)
def from_array_to_vol(self, array, nii_output_filename, mask_img):
"""
Convert an array to a volume
:param array:
:param nii_output_filename:
:param mask_img:
:return:
"""
img_3D = unmask(array, mask_img, order='F')
nb.save(img_3D, nii_output_filename)
def save_stability_maps(self, darr_stab_maps_medoid, network_label, path_maps, mask_img, subject=''):
if os.path.exists(path_maps) == False:
os.makedirs(path_maps)
for idx_state in range(darr_stab_maps_medoid.shape[0]):
nii_output_filename = os.path.join(path_maps,
'map_' + subject + '_net' + str(network_label) + '_state' + str(
idx_state)[0])
img_3D = unmask(darr_stab_maps_medoid[idx_state, :], mask_img, order='F')
nb.save(img_3D, nii_output_filename)
def compute_TSNR(in_file, highpass=True, motion_corr=False):
""" Computes temporal signal-to-noise ratio (TSNR) for
a functional MRI file preprocessed with FMRIPREP.
Parameters
----------
in_file : str
Path to functional MRI file
highpass : bool
Whether to highpass the data (using the cosine basis
set in the *confounds.tsv file)
motion_corr : bool
Whether to include the six motion parameters from
motion correction in the confound regression step.
Returns
-------
out_file : str
Path to TSNR file
"""
base_dir = op.dirname(in_file)
base_file = op.basename(in_file)
if 'preproc' not in base_file:
raise ValueError("In_file should be a preprocessed file!")
# Mask BOLD file
mask = op.join(base_dir, base_file.split('preproc')[0] + 'brain_mask.nii.gz')
bold_masked = masking.apply_mask(in_file, mask)
# Get confounds and regress out of data
if highpass or motion_corr:
conf = op.join(base_dir, base_file.split('space')[0] + 'desc-confounds_regressors.tsv')
conf_df = pd.read_csv(conf, sep='\t')
conf_vars = []
if highpass:
conf_vars.extend([col for col in conf_df.columns if 'cosine' in col])
if motion_corr:
conf_vars.extend(['trans_x', 'trans_y', 'trans_z', 'rot_x', 'rot_y', 'rot_z'])
conf_df = conf_df.loc[:, conf_vars]
conf_values = np.c_[np.ones(conf_df.shape[0]), conf_df.values]
conf_params = np.linalg.lstsq(conf_values, bold_masked, rcond=-1)[0]
bold_masked = bold_masked - conf_values[:, 1:].dot(conf_params[1:, :])
# Compute tsnr
tsnr = bold_masked.mean(axis=0) / bold_masked.std(axis=0)
tsnr_img = masking.unmask(tsnr, mask)
out_file = in_file.replace('.nii.gz', '_TSNR.nii.gz')
tsnr_img.to_filename(out_file)
return out_file
def plot_highest_score_bold_predicted_vs_actual(path_predicted, path_actual, arg_highscore, save_path, mask_path):
print('Plotting', save_path)
from scipy.stats import zscore
x, y, z, fold = arg_highscore
# bold = []
# for i in range(6):
# # bold.append(joblib.load(path_actual.format(i))[:-1])
# bold.append(joblib.load(path_actual.format(i)))
# bold = np.concatenate(bold) # (time, voxel)
bold = joblib.load(path_actual.format(fold))
masks = joblib.load(mask_path)
bold = unmask(bold, masks[fold])
# bold_predicted = nib.load(path_predicted)
# bold_predicted = []
# for i in range(6):
# # bold_actual.append(joblib.load(path_predicted.format(i))[:-1])
# bold_predicted.append(joblib.load(path_predicted.format(i)))
# bold_predicted = np.concatenate(bold_predicted) # (time, voxel)
bold_predicted = joblib.load(path_predicted.format(fold))
bold_predicted = unmask(bold_predicted, masks[fold])
# print(bold_predicted.shape)
# print(bold.shape)
bold_predicted_high = bold_predicted.dataobj[x, y, z]
bold_predicted_high = zscore(bold_predicted_high)
bold_high = bold.dataobj[x, y, z]
bold_high = zscore(bold_high)
plt.plot(bold_predicted_high, label='Predicted bold')
plt.plot(bold_high, label='Actual bold')
plt.legend()
plt.xlabel('Volume')
plt.ylabel('Zscore')
r, prob = product_moment_corr(bold_predicted_high.reshape(-1, 1), bold_high.reshape(-1, 1))
plt.title('Predicted vs actual bold, voxel %s, r=%.4f, p=%.4f' % (str(arg_highscore), r, prob))
plt.savefig(save_path)
# plt.show()
plt.close()
def plot_subj_ko(subj, scores, threshold=0.01, coords=None):
'''plots subject scoremap using nilearn and returns display object'''
subj_mask = './masks/template_mask_thick.nii.gz'
background_img = os.path.join(DATA_DIR, 'templates', 'grpbold7Tp1', 'brain.nii.gz')
scores = scores.copy()
scores[scores<threshold] = 0.0
unmasked = unmask(scores, subj_mask)
unmasked = threshold_img(unmasked, 0.001)
display = plot_stat_map(
unmasked, cut_coords=coords, bg_img=background_img,
symmetric_cbar=False,
title='metric per voxel', dim=-1, aspect=1.25,
threshold=0.001, draw_cross=False)
fig = plt.gcf()
fig.set_size_inches(12, 4)
return display
def plot_diff_avg(scores, threshold=0.01, coords=None, cross=False, **kwargs):
'''plots subject scoremap using nilearn and returns display object'''
mask = spenc_dir+'temporal_lobe_mask_grp_7T_test.nii.gz'
background_img = '/home/data/psyinf/forrest_gump/anondata/templates/' + \
'grpbold7Tp1/brain.nii.gz'
scores = scores.copy()
scores[np.abs(scores)<threshold] = 0.0
unmasked = unmask(scores, mask)
unmasked = threshold_img(unmasked, 0.001)
display = plot_stat_map(
unmasked, cut_coords=coords, bg_img=background_img,
title='metric per voxel', dim=-1, aspect=1.25,
threshold=0.001, draw_cross=cross, **kwargs)
fig = plt.gcf()
fig.set_size_inches(12, 4)
return display
def plot_subj(subj, scores, threshold=0.01, coords=None):
'''plots subject scoremap using nilearn and returns display object'''
subj_mask = spenc_dir+'temporal_lobe_mask_brain_subj{0:02}bold.nii.gz'.format(subj)
background_img = '/home/data/psyinf/forrest_gump/anondata/sub{0:03}/'.format(subj)+\
'templates/bold7Tp1/brain.nii.gz'
scores = scores.copy()
scores[scores<threshold] = 0.0
unmasked = unmask(scores, subj_mask)
unmasked = threshold_img(unmasked, 0.001)
display = plot_stat_map(
unmasked, cut_coords=coords, bg_img=background_img,
symmetric_cbar=False,
title='metric per voxel', dim=-1, aspect=1.25,
threshold=0.001, draw_cross=False)
fig = plt.gcf()
fig.set_size_inches(12, 4)
return display
def swap_img_data(img, mask_img, absolute_values=True):
'''Swap data in a nifti image. User can choose to do swapping by taking
the real or absolute values in the image into account'''
img_data = apply_mask(img, mask_img)
if absolute_values == True:
map_dict = dict(
zip(sorted(set(img_data), key=abs),
sorted(set(img_data), key=abs, reverse=True)))
else:
map_dict = dict(
zip(sorted(set(img_data)), sorted(set(img_data), reverse=True)))
img_data_swapped = np.array([map_dict[x] for x in img_data])
img_swapped = unmask(img_data_swapped, mask_img)
return img_swapped
def load_data_whole(subj, model='logBSC_H200', metric='r'):
'''Loads data and returns them as an Encoding instance'''
fmri_data = np.hstack(
[joblib.load(('/home/data/scratch/mboos/prepro/'
'whole_fmri_subj_{}_split_{}.pkl').format(subj, i))
for i in xrange(10)]).astype('float32')
subj_mask_lobe = spenc_dir+'temporal_lobe_mask_brain_subj{0:02}bold.nii.gz'.format(subj)
subj_mask_brain = '/home/data/psyinf/forrest_gump/anondata/sub{0:03}'.format(subj) + '/templates/bold7Tp1/brain_mask.nii.gz'
img = unmask(fmri_data, mask_img=subj_mask_brain)
fmri_data = apply_mask(img, subj_mask_lobe)
model_preds = joblib.load(spenc_dir + ('MaThe/predictions/'
'{}_subj_{}_all.pkl').format(model, subj))
if metric in ('p', 'p_adj'):
scores_model = metric_functions['r'](model_preds, fmri_data)
else:
scores_model = metric_functions[metric](model_preds, fmri_data)
return Encoding(fmri_data, model_preds,
scores_model, metric=metric)
def plot_max_coefs(ridges_path, mask_path, arg_highscore, save_path):
mask = joblib.load(mask_path)
for fold in range(len(mask)):
filename = ridges_path.format(fold)
if not os.path.exists(filename):
continue
print('Plotting', save_path.format(fold))
ridges = joblib.load(filename)
# print(ridges.alpha_)
coefs = unmask(ridges.coef_.T, mask[fold])
max_coefs = coefs.dataobj[arg_highscore[:3]]
if use_mel_spec_features:
max_coefs = max_coefs.reshape((-1, n_mel))
n_lag_bins = max_coefs.shape[0]
# lagging_offset = 4.25
lagging_offset = 0.0
# lagging_offset = 4.0
x_ticks = (np.arange(n_lag_bins) * 0.025) + lagging_offset
# x_stride = 20
x_stride = 80
if use_mel_spec_features:
n_mel_stride = 4
plt.imshow(max_coefs.T, aspect='auto', origin='lower')
plt.ylabel('Mel frequency (Hz)')
plt.gca().set_yticks(np.arange(0, n_mel, n_mel_stride))
plt.gca().set_yticklabels(mel_frequencies[:n_mel:n_mel_stride])
cbar = plt.colorbar()
cbar.set_label('Ridge coefficient', rotation=270)
else:
plt.plot(max_coefs)
plt.ylabel('Ridge coefficient')
plt.xlabel('Time lag (s)')
plt.gca().set_xticks(np.arange(3, n_lag_bins, x_stride))
plt.gca().set_xticklabels(["%.1f" % tick for tick in x_ticks[3::x_stride]])
plt.tight_layout()
plt.savefig(save_path.format(fold) + '.svg')
plt.close()
def generate_nifti_4D(loc_volume, av_win, bm, smooth_f, fdir):
fun_data = np.zeros((bm.shape[0], bm.shape[1], bm.shape[2], t_size))
for iv, (xv, yv, zv) in enumerate(loc_volume):
# Put the time average of the functional data over a time window av_win long
fun_data[xv, yv, zv, :] = np.average(fun[iv, :].reshape((-1, av_win)),
axis=1)
fun_img = nib.Nifti2Image(fun_data, affine=bm.affine)
# Apply smoothing
fun_img = smooth_img(fun_img, smooth_f)
# Apply bm mask
fun_img = unmask(apply_mask(fun_img, bm), bm)
fout = fdir + 'T{:03d}_S{:02d}.nii.gz'.format(av_win, smooth_f)
print('Nifti saved in {}'.format(fout))
nib.save(fun_img, fout)
return fun_img
def compute_fxe_contrast(self, contrast_def, stat_type='t', run=None, output_type='z_score'):
""" Computes a fixed effect across multiple runs. """
self.logger.info(f"Computing contrast: {contrast_def} for task {self.task} ...")
if self.glm is None:
raise ValueError("GLM has not been run yet!")
if run is None:
results = self.glm['results']
labels = self.glm['labels']
dms = self.glm['dms']
design_info = DesignInfo(dms[0].columns.tolist())
else:
results = self.glm['results'][run]
labels = self.glm['labels'][run]
dms = self.glm['dms'][run]
design_info = DesignInfo(dms.columns.tolist())
if isinstance(contrast_def, (np.ndarray, str)):
con_vals = [contrast_def]
elif isinstance(contrast_def, (list, tuple)):
con_vals = contrast_def
else:
raise ValueError('contrast_def must be an array or str or list of'
' (array or str)')
for cidx, con in enumerate(con_vals):
if not isinstance(con, np.ndarray):
con_vals[cidx] = design_info.linear_constraint(con).coefs
if run is None:
contrast = _fixed_effect_contrast(labels, results, con_vals, stat_type)
else:
contrast = compute_contrast(labels, results, con_vals, stat_type)
values = getattr(contrast, output_type)()
if self.mask is not None:
return masking.unmask(values, self.mask)
else:
return values
def visualize(self, statmap, space='fsnative', threshold=0, hemi='R', mask=None, **plot_args):
""" Visualizes a statmap on an image/surface background. """
if 'fs' in space and isinstance(statmap, nib.Nifti1Image):
raise ValueError("Statmap is an image, but space is fs* something ...")
bg = 'surface' if 'fs' in space else 'volume'
self.logger.info(f"Visualizing statmap on {bg} ...")
if 'fs' in space:
fs_base = op.dirname(self.fs_dir)
if space == 'fsnative':
fs_id = f'sub-{self.sub}'
else:
fs_id = space
return plotting.view_surf(
surf_mesh=op.join(fs_base, fs_id, 'surf', f'{hemi.lower()}h.inflated'),
surf_map=statmap,
bg_map=op.join(fs_base, fs_id, 'surf', f'{hemi.lower()}h.sulc'),
threshold=threshold,
**plot_args
)
else:
if mask is not None:
statmap = masking.unmask(statmap, mask)
if space == 'T1w':
bg = op.join(self.fp_dir, 'anat', f'sub-{self.sub}_desc-preproc_T1w.nii.gz')
else:
bg = 'MNI152'
return plotting.view_img(
stat_map_img=statmap,
bg_img=bg,
threshold=threshold,
**plot_args
)
def tmp_save_fmri(datapath, task, subj, model):
dhandle = mvpa.OpenFMRIDataset(datapath)
#mask_fname = os.path.join('/home','mboos','SpeechEncoding','temporal_lobe_mask_brain_subj' + str(subj) + 'bold.nii.gz')
flavor = 'dico_bold7Tp1_to_subjbold7Tp1'
group_brain_mask = '/home/mboos/SpeechEncoding/brainmask_group_template.nii.gz'
mask_fname = os.path.join(datapath, 'sub{0:03d}'.format(subj), 'templates', 'bold7Tp1', 'brain_mask.nii.gz')
#mask_fname = '/home/mboos/SpeechEncoding/masks/epi_subj_{}.nii.gz'.format(subj)
scratch_path = '/home/data/scratch/mboos/prepro/tmp/'
for run_id in dhandle.get_task_bold_run_ids(task)[subj]:
run_ds = dhandle.get_bold_run_dataset(subj,task,run_id,chunks=run_id-1,mask=mask_fname,flavor=flavor)
filename = 'whole_brain_subj_{}_run_{}.nii.gz'.format(subj, run_id)
tmp_path = scratch_path + filename
save(unmask(run_ds.samples.astype('float32'), mask_fname), tmp_path)
os.system('applywarp -i {0} -o {1} -r /home/data/psyinf/forrest_gump/anondata/templates/grpbold7Tp1/brain.nii.gz -w /home/data/psyinf/forrest_gump/anondata/sub{2:03}/templates/bold7Tp1/in_grpbold7Tp1/subj2tmpl_warp.nii.gz --interp=nn'.format(tmp_path, scratch_path+'group_'+filename,subj))
os.remove(tmp_path)
run_ds = mvpa.fmri_dataset(scratch_path+'group_'+filename, mask=group_brain_mask, chunks=run_id-1)
mvpa.poly_detrend(run_ds, polyord=1)
mvpa.zscore(run_ds)
joblib.dump(run_ds.samples.astype('float32'),
'/home/data/scratch/mboos/prepro/tmp/whole_brain_subj_{}_run_{}.pkl'.format(subj, run_id))
os.remove(scratch_path+'group_'+filename)
return run_ds.samples.shape[1]
def main(posterior_dir, args):
# Laod fixed effect posteriors
fixef = pd.read_csv(join(posterior_dir, 'POP.txt'), sep='\t')
# Load random effect posteriors
ROI_Intercept = pd.read_csv(join(posterior_dir, 'ROI_Intercept.txt'),
sep='\t')
VOX_Intercept = pd.read_csv(join(posterior_dir, 'VOX_Intercept.txt'),
sep='\t')
posteriors = combinePos(ROI_Intercept, VOX_Intercept)
posteriors = add_mean(posteriors, fixef, 'Intercept')
# Load the insula mask
mask = nil.image.load_img(args.mask)
roi_indx = np.unique(mask.get_data())[1:]
print('ROI indexes: ', roi_indx)
# P+ of every voxel is computed and rendered on a brain template for visualization
probMask = nil.image.new_img_like(mask, np.zeros_like(mask.get_data()))
for ii, n in enumerate(roi_indx):
n_vox = (mask.get_data() == n).sum()
roi_mask = getSubMask(n, mask)
print('ROI index:', n)
print('Num of voxels in data table:', n_vox)
print('Number of vox in the roi mask:',
(roi_mask.get_data() == 1).sum())
p_plus = []
for jj, m in enumerate(range(n_vox)):
vox = posteriors['roi{:02d}_{:03d}'.format(int(n), m)]
p_plus.append(np.mean(vox > 0))
rendered = unmask(p_plus, roi_mask)
probMask = nil.image.math_img("img1 + img2",
img1=probMask,
img2=rendered)
return probMask
def gen_lag_map(epi_img, brain_mask_img, gm_mask_img, lags):
print("...masking data...")
epi_gm_masked_data = masking.apply_mask(epi_img, gm_mask_img)
gm_mean_signal = np.mean(epi_gm_masked_data, axis=1)
epi_brain_masked_data = masking.apply_mask(epi_img, brain_mask_img).T
lag_index_correction = np.sum(np.array(lags) > 0)
xcorr_array = []
print("...calculating lags...")
for voxel in tqdm(epi_brain_masked_data, unit='voxel'):
vox_signal = voxel
vox_xcorr = xcorr_range(gm_mean_signal, vox_signal, lags)
xcorr_maxima = sci_signal.argrelmax(np.array(vox_xcorr), order=1)[0]
if len(xcorr_maxima) == 0:
interp_max = np.argmax(vox_xcorr) - lag_index_correction
elif len(xcorr_maxima) == 1:
interp_max = parabolic(vox_xcorr, xcorr_maxima[0])[0]
interp_max = interp_max - lag_index_correction
elif len(xcorr_maxima) > 1:
xpeak = xcorr_maxima[np.argmax(vox_xcorr[xcorr_maxima])]
interp_max = parabolic(vox_xcorr, xpeak)[0]
interp_max = interp_max - lag_index_correction
xcorr_array.append(interp_max)
return (masking.unmask(np.array(xcorr_array), brain_mask_img))
def generate_nifti_windows(fun, loc_volume, av_win, bm, smooth_f, fdir):
fun_img = {}
for e in ERPs:
fun_data = np.zeros((bm.shape[0], bm.shape[1], bm.shape[2]))
for iv, (xv, yv, zv) in enumerate(loc_volume):
# Put the time average of the functional data over a time window av_win long
fun_data[xv, yv, zv] = np.average(fun[iv,
ERPs[e][0][0]:ERPs[e][0][1]])
fun_img[e] = nib.Nifti2Image(fun_data, affine=bm.affine)
# Apply smoothing
fun_img[e] = smooth_img(fun_img[e], smooth_f)
# Apply bm mask
fun_img[e] = unmask(apply_mask(fun_img[e], bm), bm)
fout = out_dir + '{}_S{:02d}.nii.gz'.format(e, smooth_f)
print('Nifti saved in {}'.format(fout))
nib.save(fun_img[e], fout)
return fun_img
plt.ylabel('Explained variance')
plt.savefig(spenc_dir+'MaThe/plots/'+\
'{}_r2_subj_{}.svg'.format('_'.join(model_scores.keys()), subj))
plt.close()
# best voxels as a violin plot
sns.violinplot(pd.DataFrame(
{model:get_best_voxels(scores, voxel_limit)
for model, scores in model_scores.iteritems()}), cut=0)
plt.savefig(spenc_dir+'MaThe/plots/'+\
'{}_violin_subj_{}.svg'.format('_'.join(model_scores.keys()), subj))
plt.close()
subj_mask = spenc_dir+\
'temporal_lobe_mask_head_subj{0:02}bold.nii.gz'.format(subj)
background_img = '/home/data/psyinf/forrest_gump/anondata/sub{0:03}/'.format(subj)+\
'templates/bold7Tp1/head.nii.gz'
# plotting the statistical map on the brain
for model, scores in model_scores.iteritems():
unmasked = unmask(scores, subj_mask)
# thresholding
unmasked = threshold_img(unmasked, threshold)
display = plot_stat_map(
unmasked, bg_img=background_img, symmetric_cbar=False,
title='Explained variance per voxel ({})'.format(model),
vmax=max_r2, draw_cross=False)
plt.savefig(spenc_dir+'MaThe/plots/'+\
'{}_r2_map_subj_{}.svg'.format(model, subj))
plt.close()
def test_unmask():
# A delta in 3D
shape = (10, 20, 30, 40)
generator = np.random.RandomState(42)
data4D = generator.rand(*shape)
data3D = data4D[..., 0]
mask = generator.randint(2, size=shape[:3])
mask_img = Nifti1Image(mask, np.eye(4))
mask = mask.astype(bool)
masked4D = data4D[mask, :].T
unmasked4D = data4D.copy()
unmasked4D[-mask, :] = 0
masked3D = data3D[mask]
unmasked3D = data3D.copy()
unmasked3D[-mask] = 0
# 4D Test, test value ordering at the same time.
t = unmask(masked4D, mask_img, order="C").get_data()
assert_equal(t.ndim, 4)
assert_true(t.flags["C_CONTIGUOUS"])
assert_false(t.flags["F_CONTIGUOUS"])
assert_array_equal(t, unmasked4D)
t = unmask([masked4D], mask_img, order="F")
t = [t_.get_data() for t_ in t]
assert_true(isinstance(t, list))
assert_equal(t[0].ndim, 4)
assert_false(t[0].flags["C_CONTIGUOUS"])
assert_true(t[0].flags["F_CONTIGUOUS"])
assert_array_equal(t[0], unmasked4D)
# 3D Test - check both with Nifti1Image and file
for create_files in (False, True):
with write_tmp_imgs(mask_img, create_files=create_files) as filename:
t = unmask(masked3D, filename, order="C").get_data()
assert_equal(t.ndim, 3)
assert_true(t.flags["C_CONTIGUOUS"])
assert_false(t.flags["F_CONTIGUOUS"])
assert_array_equal(t, unmasked3D)
t = unmask([masked3D], filename, order="F")
t = [t_.get_data() for t_ in t]
assert_true(isinstance(t, list))
assert_equal(t[0].ndim, 3)
assert_false(t[0].flags["C_CONTIGUOUS"])
assert_true(t[0].flags["F_CONTIGUOUS"])
assert_array_equal(t[0], unmasked3D)
# Error test: shape
vec_1D = np.empty((500,), dtype=np.int)
assert_raises(TypeError, unmask, vec_1D, mask_img)
assert_raises(TypeError, unmask, [vec_1D], mask_img)
vec_2D = np.empty((500, 500), dtype=np.float64)
assert_raises(TypeError, unmask, vec_2D, mask_img)
assert_raises(TypeError, unmask, [vec_2D], mask_img)
# Error test: mask type
assert_raises_regex(TypeError, 'mask must be a boolean array',
_unmask_3d, vec_1D, mask.astype(np.int))
assert_raises_regex(TypeError, 'mask must be a boolean array',
_unmask_4d, vec_2D, mask.astype(np.float64))
# Transposed vector
transposed_vector = np.ones((np.sum(mask), 1), dtype=np.bool)
assert_raises_regex(TypeError, 'X must be of shape',
unmask, transposed_vector, mask_img)
def test_unmask():
# A delta in 3D
shape = (10, 20, 30, 40)
generator = np.random.RandomState(42)
data4D = generator.rand(*shape)
data3D = data4D[..., 0]
mask = generator.randint(2, size=shape[:3])
mask_img = Nifti1Image(mask, np.eye(4))
mask = mask.astype(bool)
masked4D = data4D[mask, :].T
unmasked4D = data4D.copy()
unmasked4D[np.logical_not(mask), :] = 0
masked3D = data3D[mask]
unmasked3D = data3D.copy()
unmasked3D[np.logical_not(mask)] = 0
# 4D Test, test value ordering at the same time.
t = get_data(unmask(masked4D, mask_img, order="C"))
assert_equal(t.ndim, 4)
assert_true(t.flags["C_CONTIGUOUS"])
assert_false(t.flags["F_CONTIGUOUS"])
assert_array_equal(t, unmasked4D)
t = unmask([masked4D], mask_img, order="F")
t = [get_data(t_) for t_ in t]
assert_true(isinstance(t, list))
assert_equal(t[0].ndim, 4)
assert_false(t[0].flags["C_CONTIGUOUS"])
assert_true(t[0].flags["F_CONTIGUOUS"])
assert_array_equal(t[0], unmasked4D)
# 3D Test - check both with Nifti1Image and file
for create_files in (False, True):
with write_tmp_imgs(mask_img, create_files=create_files) as filename:
t = get_data(unmask(masked3D, filename, order="C"))
assert_equal(t.ndim, 3)
assert_true(t.flags["C_CONTIGUOUS"])
assert_false(t.flags["F_CONTIGUOUS"])
assert_array_equal(t, unmasked3D)
t = unmask([masked3D], filename, order="F")
t = [get_data(t_) for t_ in t]
assert_true(isinstance(t, list))
assert_equal(t[0].ndim, 3)
assert_false(t[0].flags["C_CONTIGUOUS"])
assert_true(t[0].flags["F_CONTIGUOUS"])
assert_array_equal(t[0], unmasked3D)
# Error test: shape
vec_1D = np.empty((500, ), dtype=np.int)
assert_raises(TypeError, unmask, vec_1D, mask_img)
assert_raises(TypeError, unmask, [vec_1D], mask_img)
vec_2D = np.empty((500, 500), dtype=np.float64)
assert_raises(TypeError, unmask, vec_2D, mask_img)
assert_raises(TypeError, unmask, [vec_2D], mask_img)
# Error test: mask type
assert_raises_regex(TypeError, 'mask must be a boolean array', _unmask_3d,
vec_1D, mask.astype(np.int))
assert_raises_regex(TypeError, 'mask must be a boolean array', _unmask_4d,
vec_2D, mask.astype(np.float64))
# Transposed vector
transposed_vector = np.ones((np.sum(mask), 1), dtype=np.bool)
assert_raises_regex(TypeError, 'X must be of shape', unmask,
transposed_vector, mask_img)
dset.coordinates,
mask=dset.masker.mask_img,
n_topics=10,
n_regions=4,
symmetric=True,
)
model.fit(n_iters=100, loglikely_freq=20)
model.save("gclda_model.pkl.gz")
# Let's remove the model now that you know how to generate it.
os.remove("gclda_model.pkl.gz")
###############################################################################
# Look at topics
# -----------------------------------------------------------------------------
topic_img_4d = masking.unmask(model.p_voxel_g_topic_.T, model.mask)
for i_topic in range(5):
topic_img_3d = image.index_img(topic_img_4d, i_topic)
plotting.plot_stat_map(
topic_img_3d,
draw_cross=False,
colorbar=False,
annotate=False,
title=f"Topic {i_topic + 1}",
)
###############################################################################
# Generate a pseudo-statistic image from text
# -----------------------------------------------------------------------------
text = "dorsal anterior cingulate cortex"
encoded_img, _ = decode.encode.gclda_encode(model, text)
expl_var_pc[model] = pca.explained_variance_ratio_[:10]
fig = plt.figure(figsize=(6, 6))
filtered = pca.transform(model_preds[:, voxels_to_use])
PC_rep[model] = filtered
scatter = plt.scatter(filtered[:, 0], filtered[:, 1], cmap='YlGnBu',
c=logenergy, marker='o', alpha=0.3)
plt.xlabel('1st PC')
plt.ylabel('2nd PC')
plt.title('{0}, 1st PC r w/ log stim energy {1:.2f}'.format(model, corrcoef(filtered[:, 0], logenergy)[0,1]))
plt.savefig(spenc_dir+'MaThe/plots/feature_space/two_PCs_{}_subj_{}.svg'.format(model, subj))
plt.close()
subj_mask = spenc_dir + 'temporal_lobe_mask_head_subj{0:02}bold.nii.gz'.format(subj)
background_img = '/home/data/psyinf/forrest_gump/anondata/sub{0:03}/'.format(subj) + 'templates/bold7Tp1/head.nii.gz'
scores[scores<threshold] = 0
unmasked = unmask(scores, subj_mask)
unmasked = threshold_img(unmasked, threshold)
display = plot_stat_map(
unmasked, bg_img=background_img, symmetric_cbar=False, aspect=1.25,
vmax=max_r2, threshold=threshold, draw_cross=False, dim=-1.)
fig = plt.gcf()
fig.set_size_inches(12, 4)
plt.savefig(spenc_dir+'MaThe/plots/feature_space/PC_model_{}_subj_{}_pcnr_0.svg'.format(model, subj))
plt.close()
display = plot_stat_map(
unmasked, bg_img=background_img, symmetric_cbar=False, aspect=1.25,
vmax=max_r2, threshold=threshold, dim=-1.)
plt.savefig(spenc_dir+'MaThe/plots/feature_space/PC_model_{}_subj_{}_pcnr_0_cross.svg'.format(model, subj))
plt.close()
brain_mask = sys.argv[2]
gm_mask = sys.argv[3]
max_lag = int(sys.argv[4])
out_dir = sys.argv[5]
out_prefix = sys.argv[6]
smooth_kernel = sys.argv[7]
lags = range(-max_lag, max_lag+1)
brain_mask_img = nib.load(brain_mask)
brain_mask_data = brain_mask_img.get_data().astype(bool)
gm_mask_img = nib.load(gm_mask)
gm_mask_data = gm_mask_img.get_data().astype(bool)
epi_img = nib.load(epi)
epi_img_resampled = image.resample_img(epi_img, target_affine=brain_mask_img.get_affine(), target_shape=brain_mask_img.shape)
epi_data_resampled = epi_img_resampled.get_data()
lag_map_data = gen_lag_map(epi_data_resampled, brain_mask_data, gm_mask_data, lags)
lag_map_image = masking.unmask(lag_map_data, brain_mask_img)
lag_map_image_smoothed = image.smooth_img(lag_map_image, float(smooth_kernel))
nib.save(lag_map_image, os.path.join(out_dir, out_prefix+'_lag{}.nii.gz'.format(str(max_lag))))
nib.save(lag_map_image_smoothed, os.path.join(out_dir, out_prefix+'_lag{}_smoothed{}.nii.gz'.format(str(max_lag),smooth_kernel)))
def remove_mean(**kwargs):
default_conf = {
'subject': ['110929angque','110929anngio','111004edolat'],
'experiment':['memory', 'decision'],
'level': [1,3,5],
'ds_num' : [1,2,3,4,5] ,
'ds_type':['BETA'],
'file_pattern': \
"%s_%s_%s_MVPA_evidence_%s_balance_ds_%s_radius_3_searchlight_total_map.nii.gz",
'dir_pattern': "%s_%s_%s_MVPA_evidence_%s_balance_ds_%s" ,
"path": "/home/robbis/mount/fmri/memory/0_results/sl_k_3/",
"mask_dir": "/home/robbis/mount/fmri/data7/Carlo_MDM/"
}
from nilearn.masking import apply_mask, unmask
default_conf.update(kwargs)
dir_pattern = default_conf.pop("dir_pattern")
file_pattern = default_conf.pop("file_pattern")
path = default_conf.pop("path")
mask_dir = default_conf.pop("mask_dir")
key_dict = dict(zip(default_conf.keys(), range(len(default_conf.keys()))))
conf_product = itertools.product(*default_conf.values())
for elements in conf_product:
subject = elements[key_dict['subject']]
experiment = elements[key_dict['experiment']]
level = elements[key_dict['level']]
ds_num = elements[key_dict['ds_num']]
ds_type = elements[key_dict['ds_type']]
if experiment == 'memory' and ds_num > 1:
continue
file_path = os.path.join(path,
dir_pattern % (subject,
experiment,
ds_type,
level,
str(ds_num)),
file_pattern % (subject,
experiment,
ds_type,
level,
str(ds_num)),
)
img = ni.load(file_path)
mask_path = os.path.join(mask_dir,
subject,
"RESIDUALS_MVPA",
"brain_mask.nii.gz",
)
mask_img = ni.load(mask_path)
masked_data = apply_mask(img, mask_img)
mean_ = masked_data.mean()
demeaned_data = masked_data - mean_
demeaned_img = unmask(demeaned_data, mask_img)
save_pattern = file_pattern % (subject,
experiment,
ds_type,
level,
str(ds_num)
)
save_pattern_ = save_pattern[:-7]+"_demeaned.nii.gz"
save_path = os.path.join(path,
dir_pattern % (subject,
experiment,
ds_type,
level,
str(ds_num)),
save_pattern_
)
print subject, level, experiment, ds_num, mean_
ni.save(demeaned_img, save_path)
mean_img = unmask(masked_data.mean(0), mask_img)
save_pattern_ = save_pattern[:-7]+"_mean.nii.gz"
save_path = os.path.join(path,
dir_pattern % (subject,
experiment,
ds_type,
level,
str(ds_num)),
save_pattern_
)
ni.save(mean_img, save_path)
demeaned_mean = masked_data.mean(0) - masked_data.mean(0).mean()
demeaned_mean_img = unmask(demeaned_mean, mask_img)
save_pattern_ = save_pattern[:-7]+"_mean_demenead.nii.gz"
save_path = os.path.join(path,
dir_pattern % (subject,
experiment,
ds_type,
level,
str(ds_num)),
save_pattern_
)
ni.save(demeaned_mean_img, save_path)
model_argmax = np.argmax([model_scores[model]
for model in sorted(models)], axis=0)
sorted_score_list = np.sort([model_scores[model]
for model in sorted(models)],
axis=0)
model_diffs = sorted_score_list[-1] - sorted_score_list[-2]
diff_max = np.max(model_diffs)
for i, model in enumerate(sorted(models)):
model_curr_diff = np.zeros_like(model_diffs)
elements = np.logical_and(nonz_perf, model_argmax==i)
model_curr_diff[elements] = model_diffs[elements]
unmasked = unmask(model_curr_diff, subj_mask)
unmasked = threshold_img(unmasked, threshold)
if i == 0:
display = plot_stat_map(
unmasked, bg_img=background_img, symmetric_cbar=False,
title=' '.join(['{}:{}'.format(m,n) for m,n in zip(models, cmap_names)]),
threshold=threshold, cmap=cmap_cycle[i], vmax=diff_max, draw_cross=False,
display_mode='z', cut_coords=6, colorbar=False, dim=-.5)
else:
display.add_overlay(unmasked, cmap=cmap_cycle[i], threshold=threshold)
fig = plt.gcf()
fig.set_size_inches(16, 12)
plt.savefig(spenc_dir+'MaThe/plots/'+\
'diff_comparison_subj_{}_models_{}.svg'.format(subj, '_'.join(models)))