def write_bids(data, filename, markers=[]):
write_brainvision(data, filename, markers)
_write_ieeg_json(
replace_extension(filename, '.json'))
_write_ieeg_channels(
replace_underscore(filename, 'channels.tsv'), data)
_write_ieeg_events(
replace_underscore(filename, 'events.tsv'), markers)
def simulate_ieeg(root, ieeg_task, elec):
bids_mkdir(root, ieeg_task)
chan_names = [x['name'] for x in elec]
ieeg_file = ieeg_task.get_filename(root)
create_ieeg_data(ieeg_file, chan_names)
create_ieeg_info(replace_extension(ieeg_file, '.json'))
create_channels(replace_underscore(ieeg_file, 'channels.tsv'), elec)
create_events(replace_underscore(ieeg_file, 'events.tsv'))
return iEEG(ieeg_file)
def compute_corr_ecog_fmri(fmri_file, ecog_file, output_dir, PVALUE):
output_dir.mkdir(exist_ok=True, parents=True)
fmri_tsv = read_tsv(fmri_file)
ecog_tsv = read_tsv(ecog_file)
fmri_tsv = select_channels(fmri_tsv, ecog_tsv)
kernel_sizes = fmri_tsv.dtype.names[1:]
results_tsv = output_dir / replace_underscore(ecog_file.stem,
'bold_r2.tsv')
with results_tsv.open('w') as f:
f.write('Kernel\tRsquared\tSlope\tIntercept\n')
for kernel in kernel_sizes:
try:
r2, slope, intercept = compute_rsquared(
ecog_tsv['measure'], fmri_tsv[kernel], ecog_tsv['pvalue'],
PVALUE)
except Exception:
r2 = slope = intercept = NaN
f.write(f'{float(kernel):.2f}\t{r2}\t{slope}\t{intercept}\n')
return results_tsv, fmri_file, ecog_file
def calc_fmri_at_elec(measure_nii, electrodes_file, distance, kernels,
graymatter, output_dir):
"""
Calculate the (weighted) average of fMRI values at electrode locations
"""
electrodes = Electrodes(electrodes_file)
img = nload(str(measure_nii))
mri = img.get_data()
mri[mri == 0] = NaN
labels = electrodes.electrodes.get(map_lambda=lambda x: x['name'])
chan_xyz = array(electrodes.get_xyz())
nd = array(list(ndindex(mri.shape)))
ndi = from_mrifile_to_chan(img, nd)
if graymatter:
gm_mri = nload(str(graymatter)).get_data().astype(bool)
mri[~gm_mri] = NaN
lg.debug(
f'Computing fMRI values for {measure_nii.name} at {len(labels)} electrodes and {len(kernels)} "{distance}" kernels'
)
fmri_vals, n_voxels = compute_kernels(kernels, chan_xyz, mri, ndi,
distance)
fmri_vals_tsv = output_dir / replace_underscore(measure_nii.name,
'compare.tsv')
n_voxels_tsv = output_dir / replace_underscore(measure_nii.name,
'nvoxels.tsv')
with fmri_vals_tsv.open('w') as f:
f.write('channel\t' + '\t'.join(str(one_k)
for one_k in kernels) + '\n')
for one_label, val_at_elec in zip(labels, fmri_vals):
f.write(one_label + '\t' +
'\t'.join(str(one_val) for one_val in val_at_elec) + '\n')
with n_voxels_tsv.open('w') as f:
f.write('channel\t' + '\t'.join(str(one_k)
for one_k in kernels) + '\n')
for one_label, val_at_elec in zip(labels, n_voxels):
f.write(one_label + '\t' +
'\t'.join(str(one_val) for one_val in val_at_elec) + '\n')
return fmri_vals_tsv, n_voxels_tsv
def simulate_bold_prf(bids_dir, task_prf):
prf_file = task_prf.get_filename(bids_dir)
prf_file.parent.mkdir(exist_ok=True, parents=True)
bars = generate_bars()
stimulus = generate_stimulus(bars)
model = generate_model(stimulus, spm_hrf)
X = -2
Y = 2
SIGMA = 2
BETA = 1
BASELINE = 0
dat = model.generate_prediction(X, Y, SIGMA, BETA, BASELINE)
create_bold(prf_file, task_prf.task, 11143, dat)
tsv_file = replace_underscore(prf_file, 'events.tsv')
create_prf_events(tsv_file, bars.shape[2], TR)
def simulate_bold(root, task_fmri):
bids_mkdir(root, task_fmri)
fmri_file = task_fmri.get_filename(root)
SHIFT = 3
x = r_[ones(SHIFT),
ones(16) * 5,
ones(16),
ones(16) * 5,
ones(16),
ones(16) * 5,
ones(16 - SHIFT)]
create_bold(fmri_file, task_fmri.task, 11129, x)
create_events(replace_underscore(fmri_file, 'events.tsv'))
return Task(fmri_file)
def prepare_design(func, anat, output_dir):
"""You should set remove_unnecessary_outputs to False, otherwise it removes
the events.tsv file
"""
task = Task(func)
events_fsl = output_dir / task.events.filename.name
_write_events(task.events.filename, events_fsl)
# collect info
img = niload(str(task.filename))
n_vols = img.header.get_data_shape()[3]
tr = img.header['pixdim'][4] # Not sure it it's reliable
with DESIGN_TEMPLATE.open('r') as f:
design = f.read()
feat_dir = output_dir / replace_extension(
Path(task.filename).name, '.feat')
design_values = {
'XXX_OUTPUTDIR': str(feat_dir),
'XXX_NPTS': str(n_vols),
'XXX_TR': str(tr),
'XXX_FEAT_FILE': str(task.filename),
'XXX_HIGHRES_FILE': str(anat),
'XXX_EV1': 'active',
'XXX_TSVFILE': str(events_fsl),
}
for pattern, value in design_values.items():
design = design.replace(pattern, value)
subj_design = output_dir / replace_underscore(
Path(task.filename).name, 'design.fsf')
with subj_design.open('w') as f:
f.write(design)
return subj_design
def vol2surf(in_vol, feat_path, freesurfer_dir, hemi, surface, surf_fwhm):
out_surf = replace_underscore(in_vol.filename,
in_vol.modality + 'surf' + hemi + '.mgh')
mri_nonan = mri_nan2zero(in_vol.filename)
cmd = [
'mri_vol2surf',
'--src',
str(mri_nonan),
'--srcreg',
str(feat_path / 'reg/freesurfer/anat2exf.register.dat'),
'--trgsubject',
'sub-' + in_vol.subject, # freesurfer subject
'--hemi',
hemi,
'--out',
str(out_surf),
'--surf',
surface,
'--surf-fwhm',
str(surf_fwhm),
]
p = Popen(cmd,
env={
**ENVIRON, 'SUBJECTS_DIR': str(freesurfer_dir)
},
stdout=PIPE,
stderr=PIPE)
info = {
"surf": out_surf,
"hemi": hemi,
"subject": 'sub-' + in_vol.subject,
"mri_nonan": mri_nonan,
}
return p, info
def assign_regions(elec, freesurfer):
bids_dir = find_root(elec.filename)
elec.acquisition += 'regions'
tsv_electrodes = elec.get_filename(bids_dir)
with tsv_electrodes.open('w') as f:
f.write('name\tx\ty\tz\ttype\tsize\tmaterial\tregion\n'
) # TODO: region is not in BEP010
for _tsv in elec.electrodes.tsv:
xyz = array([float(_tsv['x']), float(_tsv['y']), float(_tsv['z'])])
region = freesurfer.find_brain_region(
xyz, exclude_regions=('White', 'WM', 'Unknown'))[0]
f.write(
f'{_tsv["name"]}\t{_tsv["x"]}\t{_tsv["y"]}\t{_tsv["z"]}\t{_tsv["type"]}\t{_tsv["size"]}\t{_tsv["material"]}\t{region}\n'
)
elec.coordframe.json[
'iEEGCoordinateProcessingDescription'] += '; Assign brain regions' # TODO: better description + remove None
new_json = replace_underscore(tsv_electrodes, 'coordsystem.json')
with new_json.open('w') as f:
dump(elec.coordframe.json, f, indent=2)
return Electrodes(tsv_electrodes)
def simulate_electrodes(root, elec_obj, electrodes_file=None):
bids_mkdir(root, elec_obj)
if electrodes_file is None:
electrodes_file = data_elec
output_file = elec_obj.get_filename(root)
copyfile(electrodes_file, output_file)
coordsystem_file = replace_underscore(output_file, 'coordsystem.json')
COORDSYSTEM = {
"iEEGCoordinateSystem": 'T1w',
"iEEGCoordinateUnits": 'mm',
"iEEGCoordinateProcessingDescription": "none",
"IntendedFor":
"/sub-bert/ses-day01/anat/sub-bert_ses-day01_acq-wholebrain_T1w.nii.gz",
"AssociatedImageCoordinateSystem": "T1w",
"AssociatedImageCoordinateUnits": "mm",
}
with coordsystem_file.open('w') as f:
dump(COORDSYSTEM, f, indent=' ')
return Electrodes(output_file)
def simulate_ieeg_prf(bids_dir, task_prf):
prf_file = task_prf.get_filename(bids_dir)
bars = generate_bars()
stimulus = generate_stimulus(bars)
model = generate_model(stimulus, nohrf)
dat = generate_population_data(model, N_CHAN)
chan = _make_chan_name(n_chan=N_CHAN)
data = Data(data=dat,
s_freq=S_FREQ,
chan=chan,
time=arange(dat[0].shape[0]) / S_FREQ)
data.start_time = fake_time
data.export(prf_file, 'bids')
tsv_file = replace_underscore(prf_file, 'events.tsv')
create_prf_events(tsv_file, bars.shape[2], DUR)
stimuli_dir = bids_dir / 'stimuli'
stimuli_dir.mkdir(exist_ok=True, parents=True)
bar_file = stimuli_dir / STIM_FILE
save(bar_file, bars)
def xmain(bids_dir,
analysis_dir,
freesurfer_dir,
output_dir,
acquisition='clinical',
measure_modality="",
measure_column=""):
"""
plot electrodes onto the brain surface,
Parameters
----------
bids_dir : path
analysis_dir : path
freesurfer_dir : path
output_dir : path
acquisition : str
acquisition type of the electrode files
measure_modality : str
modality
measure_column : str
column
"""
img_dir = output_dir / ELECSURF_DIR
rmtree(img_dir, ignore_errors=True)
img_dir.mkdir(exist_ok=True, parents=True)
for electrode_path in find_in_bids(bids_dir,
generator=True,
acquisition=acquisition,
modality='electrodes',
extension='.tsv'):
lg.debug(f'Reading electrodes from {electrode_path}')
elec = Electrodes(electrode_path)
fs = Freesurfer(freesurfer_dir / ('sub-' + elec.subject))
labels = None
if measure_modality != "":
try:
ecog_file = find_in_bids(analysis_dir,
subject=elec.subject,
modality=measure_modality,
extension='.tsv')
except FileNotFoundError as err:
lg.warning(err)
continue
lg.debug(f'Reading {measure_column} from {ecog_file}')
ecog_tsv = read_tsv(ecog_file)
labels = [x['name'] for x in elec.electrodes.tsv]
labels, vals = read_channels(ecog_tsv, labels, measure_column)
else:
vals = None
v = plot_electrodes(elec, fs, labels, vals)
png_file = img_dir / replace_underscore(elec.get_filename(),
'surfaceplot.png')
lg.debug(f'Saving electrode plot on {png_file}')
v.save(png_file)
v.close()
def test_replace_underscore():
assert replace_underscore('file_mod.txt', 'dat.txt') == 'file_dat.txt'
def project_electrodes(elec, freesurfer, analysis_dir):
elec.acquisition += 'projected'
bids_root = find_root(elec.filename)
tsv_electrodes = elec.get_filename(bids_root)
elec_realigned = {}
HEMI = {
'L': 'lh',
'R': 'rh',
}
groups = {x['group'] for x in elec.electrodes.tsv}
for group in groups:
print(group)
anat_dir = analysis_dir / ('sub-' + elec.subject) / 'anat'
anat_dir.mkdir(exist_ok=True, parents=True)
labels = [
x['name'] for x in elec.electrodes.tsv if x['group'] == group
]
hemi = [
x['hemisphere'] for x in elec.electrodes.tsv if x['group'] == group
][0]
elec_type = [
x['type'] for x in elec.electrodes.tsv if x['group'] == group
][0]
if not elec_type == 'surface':
print(f'not realigning {group} because its type is {elec_type}')
for _elec in elec.electrodes_tsv:
if _elec['group'] == group:
elec_realigned[_elec['label']] = (float(_elec['x']),
float(_elec['y']),
float(_elec['z']))
anat_file = anat_dir / (HEMI[hemi] + '.smooth')
if not anat_file.exists():
surf = getattr(freesurfer.read_brain('pial'), HEMI[hemi])
fill_surface(surf.surf_file, anat_file)
xyz = array([(float(x['x']), float(x['y']), float(x['z']))
for x in elec.electrodes.tsv if x['group'] == group])
xyz -= freesurfer.surface_ras_shift
xyz_realigned = snap_elec_to_surf(xyz, anat_file)
for label, xyz_ in zip(labels, xyz_realigned):
elec_realigned[label] = xyz_ + freesurfer.surface_ras_shift
with tsv_electrodes.open('w') as f:
f.write('name\tgroup\tx\ty\tz\tsize\ttype\tmaterial\themisphere\n')
for _elec in elec.electrodes.tsv:
label = _elec['name']
xyz = "\t".join(f'{x:f}' for x in elec_realigned[label])
one_chans = [x for x in elec.electrodes.tsv
if x['name'] == label][0]
group = one_chans['group']
elec_type = one_chans['type']
size = one_chans['size']
material = one_chans['material']
hemisphere = one_chans['hemisphere']
f.write(
f'{label}\t{group}\t{xyz}\t{size}\t{elec_type}\t{material}\t{hemisphere}\n'
)
elec.coordframe.json[
'iEEGCoordinateProcessingDescription'] += '; Dijkstra et al.' # TODO: better description + remove None
new_json = replace_underscore(tsv_electrodes, 'coordsystem.json')
with new_json.open('w') as f:
dump(elec.coordframe.json, f, indent=2)
return Electrodes(tsv_electrodes)