def get_bids(bids_dir, subject):
from bidso.find import find_in_bids
return (
'sub-' + subject,
str(
find_in_bids(bids_dir,
subject=subject,
modality='T1w',
extension='.nii.gz')),
str(
find_in_bids(bids_dir,
subject=subject,
modality='bold',
extension='.nii.gz')),
str(
find_in_bids(bids_dir,
subject=subject,
modality='ieeg',
extension='.eeg')),
str(
find_in_bids(bids_dir,
subject=subject,
modality='electrodes',
extension='.tsv')),
)
def test_find_in_bids_01():
found = find_in_bids(filename, subject='bert', session='day01', run='1',
extension='.nii.gz', upwards=True)
assert found.name == 'sub-bert_ses-day01_task-motor_run-1_bold.nii.gz'
with warns(UserWarning):
find_in_bids(filename, subject='bert', useless='xxx', task='motor',
modality='channels', upwards=True)
def xmain(analysis_dir,
freesurfer_dir,
output_dir,
modality='compare',
surface='white',
surf_fwhm=0):
"""
map feat values on freesurfer surface',
Parameters
----------
analysis_dir : path
freesurfer_dir : path
output_dir : path
modality : str
"compare"
surface : str
"white", "pial"
surf_fwhm : float
FWHM
"""
p_all = []
surfs = []
for in_vol_file in find_in_bids(analysis_dir,
generator=True,
extension='.nii.gz',
modality=modality):
in_vol = file_Core(in_vol_file)
feat_path = find_in_bids(analysis_dir,
subject=in_vol.subject,
extension='.feat')
for hemi in ('lh', 'rh'):
p, out_surf = vol2surf(in_vol, feat_path, freesurfer_dir, hemi,
surface, surf_fwhm)
p_all.append(p)
surfs.append(out_surf)
# wait for all processes to run
[p.wait() for p in p_all]
[check_subprocess(p) for p in p_all]
[info['mri_nonan'].unlink() for info in surfs]
img_dir = output_dir / SURF_DIR
rmtree(img_dir, ignore_errors=True)
img_dir.mkdir(exist_ok=True, parents=True)
for one_surf in surfs:
plot_surf(img_dir, freesurfer_dir, one_surf, surface)
def main(analysis_dir, bands=[], method="5", noparallel=False):
"""
extract timefrequency after bandpass
Parameters
----------
analysis_dir : path
bands : str
write down frequency bands as 70-90,90-110 (no spaces)
method : str
"1", "2", "3", "4", "5"
noparallel : bool
if it should run serially (i.e. not parallely, mostly for debugging)
"""
# convert str "70-90,90-110" to [[70, 90], [90, 110]]
bands = [[float(f) for f in b.split('-')] for b in bands.split(',')]
args = []
for ieeg_file in find_in_bids(analysis_dir,
modality='ieegproc',
extension='.pkl',
generator=True):
args.append((ieeg_file, bands, method))
if noparallel:
for arg in args:
save_frequency(*arg)
else:
with Pool() as p:
p.starmap(save_frequency, args)
def xmain(bids_dir, freesurfer_dir, acquisition='clinical', noparallel=False):
"""
assign electrodes to brain regions',
Parameters
----------
bids_dir : path
freesurfer_dir : path
acquisition : str
acquisition type of the electrode files
noparallel : bool
if it should run serially (i.e. not parallely, mostly for debugging)
"""
args = []
for electrode_path in find_in_bids(bids_dir,
generator=True,
acquisition=acquisition,
modality='electrodes',
extension='.tsv'):
elec = Electrodes(electrode_path)
fs = Freesurfer(freesurfer_dir / ('sub-' + elec.subject))
args.append((elec, fs))
if noparallel:
for arg in args:
assign_regions(*arg)
else:
with Pool(processes=4) as p:
p.starmap(assign_regions, args)
def xmain(analysis_dir, freesurfer_dir):
"""
coreg feat with freesurfer
Parameters
----------
analysis_dir : path
freesurfer_dir : path
"""
for feat_path in find_in_bids(analysis_dir, generator=True, extension='.feat'):
lg.debug(f'Reading {feat_path}')
coreg_feat2freesurfer(feat_path, freesurfer_dir)
def xmain(analysis_dir,
method="analyzePRF",
task='bairprf',
input='ieegprocpsd',
noparallel=False):
"""
compute psd for two conditions
Parameters
----------
analysis_dir : path
method : str
"popeye" or "analyzePRF"
task : str
task to analyze
input : str
name of the modality of the preceding step
noparallel : bool
if it should run serially (i.e. not parallely, mostly for debugging)
"""
args = []
for prf_file in find_in_bids(analysis_dir,
task=task,
modality=input,
extension='.pkl',
generator=True):
if input.startswith('ieeg'):
funct = estimate_ieeg_prf
elif input.startswith('bold'):
funct = estimate_bold_prf
else:
raise ValueError(f'Unknown modality {input}')
args.append((funct, prf_file, method))
if noparallel:
for arg in args:
args[0](*arg[1:])
else:
with Pool() as p:
p.starmap(arg[0], arg[1:])
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_find_in_bids_06():
with raises(ValueError):
find_in_bids(BIDS_PATH, upwards=True, generator=True)
def test_find_in_bids_05():
with raises(FileNotFoundError):
find_in_bids(BIDS_PATH, subject='xxx')
with raises(StopIteration):
next(find_in_bids(BIDS_PATH, subject='xxx', generator=True))
def test_find_in_bids_04():
assert sum(1 for x in find_in_bids(BIDS_PATH, generator=True, subject='bert')) == 21
def test_find_in_bids_03():
with raises(FileNotFoundError):
find_in_bids(filename, upwards=True, subject='bert')