def from_vol_files_rel(self, mask_file, paradigm_csv_file, bold_files,
tr, rel_conditions):
paradigm = Paradigm.from_csv(paradigm_csv_file)
durations = OrderedDict()
onsets = OrderedDict()
for i in xrange(len(rel_conditions)):
durations[rel_conditions[i]] = paradigm.stimDurations[
rel_conditions[i]]
onsets[rel_conditions[i]] = paradigm.stimOnsets[rel_conditions[i]]
m, mmo, mlf, b, ss = load_vol_bold_and_mask(bold_files, mask_file)
mask = m
mask_meta_obj = mmo
mask_loaded_from_file = mlf
bold = b
sessionScans = ss
fd = FmriData(onsets, bold, tr, sessionScans, mask,
stimDurations=durations, meta_obj=mask_meta_obj,
data_files=bold_files + [mask_file, paradigm_csv_file],
data_type='volume',
mask_loaded_from_file=mask_loaded_from_file)
fd.set_init(FmriData.from_vol_files, mask_file=mask_file,
paradigm_csv_file=paradigm_csv_file,
bold_files=bold_files, tr=tr)
return fd
def from_vol_files(self, mask_file=DEFAULT_MASK_VOL_FILE,
paradigm_csv_file=DEFAULT_PARADIGM_CSV,
bold_files=[DEFAULT_BOLD_VOL_FILE],
tr=DEFAULT_BOLD_VOL_TR, background_label=None,
paradigm_csv_delim=None):
paradigm = Paradigm.from_csv(paradigm_csv_file,
delim=paradigm_csv_delim)
durations = paradigm.stimDurations
onsets = paradigm.stimOnsets
m, mmo, mlf, b, ss = load_vol_bold_and_mask(bold_files, mask_file)
mask = m
mask_meta_obj = mmo
mask_loaded_from_file = mlf
bold = b
sessionScans = ss
fd = FmriData(onsets, bold, tr, sessionScans, mask,
stimDurations=durations, meta_obj=mask_meta_obj,
data_files=bold_files + [mask_file, paradigm_csv_file],
data_type='volume',
mask_loaded_from_file=mask_loaded_from_file,
backgroundLabel=background_label)
fd.set_init(FmriData.from_vol_files, mask_file=mask_file,
paradigm_csv_file=paradigm_csv_file,
bold_files=bold_files, tr=tr,
background_label=background_label,
paradigm_csv_delim=paradigm_csv_delim)
return fd
def from_surf_files(self,
paradigm_csv_file=DEFAULT_PARADIGM_CSV,
bold_files=None,
tr=DEFAULT_BOLD_SURF_TR,
mesh_file=DEFAULT_MESH_FILE,
mask_file=None):
"""Return FmriData representation from surf files"""
if bold_files is None:
bold_files = [DEFAULT_BOLD_SURF_FILE]
paradigm = Paradigm.from_csv(paradigm_csv_file)
durations = paradigm.stimDurations
onsets = paradigm.stimOnsets
mask, mask_meta_obj, _, bold, session_scans, graphs, edge_lengths = \
load_surf_bold_mask(bold_files, mesh_file, mask_file)
fmri_data = FmriData(onsets,
bold,
tr,
session_scans,
mask,
graphs,
stimDurations=durations,
meta_obj=mask_meta_obj,
data_files=bold_files + [mask_file, mesh_file],
data_type='surface',
edge_lengths=edge_lengths)
fmri_data.set_init(FmriData.from_surf_files,
paradigm_csv_file=paradigm_csv_file,
bold_files=bold_files,
tr=tr,
mesh_file=mesh_file,
mask_file=mask_file)
return fmri_data
def from_vol_files_rel(self, mask_file, paradigm_csv_file, bold_files, tr,
rel_conditions):
paradigm = Paradigm.from_csv(paradigm_csv_file)
durations = OrderedDict()
onsets = OrderedDict()
for i in xrange(len(rel_conditions)):
durations[rel_conditions[i]] = paradigm.stimDurations[
rel_conditions[i]]
onsets[rel_conditions[i]] = paradigm.stimOnsets[rel_conditions[i]]
m, mmo, mlf, b, ss = load_vol_bold_and_mask(bold_files, mask_file)
mask = m
mask_meta_obj = mmo
mask_loaded_from_file = mlf
bold = b
sessionScans = ss
fd = FmriData(onsets,
bold,
tr,
sessionScans,
mask,
stimDurations=durations,
meta_obj=mask_meta_obj,
data_files=bold_files + [mask_file, paradigm_csv_file],
data_type='volume',
mask_loaded_from_file=mask_loaded_from_file)
fd.set_init(FmriData.from_vol_files,
mask_file=mask_file,
paradigm_csv_file=paradigm_csv_file,
bold_files=bold_files,
tr=tr)
return fd
def from_vol_files(self,
mask_file=DEFAULT_MASK_VOL_FILE,
paradigm_csv_file=DEFAULT_PARADIGM_CSV,
bold_files=[DEFAULT_BOLD_VOL_FILE],
tr=DEFAULT_BOLD_VOL_TR,
background_label=None,
paradigm_csv_delim=None):
paradigm = Paradigm.from_csv(paradigm_csv_file,
delim=paradigm_csv_delim)
durations = paradigm.stimDurations
onsets = paradigm.stimOnsets
m, mmo, mlf, b, ss = load_vol_bold_and_mask(bold_files, mask_file)
mask = m
mask_meta_obj = mmo
mask_loaded_from_file = mlf
bold = b
sessionScans = ss
fd = FmriData(onsets,
bold,
tr,
sessionScans,
mask,
stimDurations=durations,
meta_obj=mask_meta_obj,
data_files=bold_files + [mask_file, paradigm_csv_file],
data_type='volume',
mask_loaded_from_file=mask_loaded_from_file,
backgroundLabel=background_label)
fd.set_init(FmriData.from_vol_files,
mask_file=mask_file,
paradigm_csv_file=paradigm_csv_file,
bold_files=bold_files,
tr=tr,
background_label=background_label,
paradigm_csv_delim=paradigm_csv_delim)
return fd
def from_surf_files(self, paradigm_csv_file=DEFAULT_PARADIGM_CSV,
bold_files=None, tr=DEFAULT_BOLD_SURF_TR,
mesh_file=DEFAULT_MESH_FILE, mask_file=None):
"""Return FmriData representation from surf files"""
if bold_files is None:
bold_files = [DEFAULT_BOLD_SURF_FILE]
paradigm = Paradigm.from_csv(paradigm_csv_file)
durations = paradigm.stimDurations
onsets = paradigm.stimOnsets
mask, mask_meta_obj, _, bold, session_scans, graphs, edge_lengths = \
load_surf_bold_mask(bold_files, mesh_file, mask_file)
fmri_data = FmriData(onsets, bold, tr, session_scans, mask, graphs,
stimDurations=durations, meta_obj=mask_meta_obj,
data_files=bold_files + [mask_file, mesh_file],
data_type='surface', edge_lengths=edge_lengths)
fmri_data.set_init(FmriData.from_surf_files,
paradigm_csv_file=paradigm_csv_file,
bold_files=bold_files, tr=tr, mesh_file=mesh_file,
mask_file=mask_file)
return fmri_data
