def __init__(self, contrasts={'dummy_contrast_example':'3*audio-video/3'},
contrast_test_baseline=0.0,
hrf_model='Canonical', drift_model='Cosine', hfcut=128.,
residuals_model='spherical',fit_method='ols',
outputPrefix='glm_', rescale_results=False,
rescale_factor_file='', fir_delays=[0]):
FMRIAnalyser.__init__(self, outputPrefix)
xmlio.XMLable2.__init__(self)
self.hrf_model = hrf_model
self.drift_model = drift_model
self.fir_delays = fir_delays
self.hfcut = hfcut
self.residuals_model = residuals_model
self.fit_method = fit_method
self.contrasts = contrasts
self.contrasts.pop('dummy_contrast_example',None)
self.con_bl = contrast_test_baseline
self.rescale_results = rescale_results
if rescale_factor_file != '':
self.rescale_factor = xndarray.load(rescale_factor_file).data
else:
self.rescale_factor = None
def __init__(self,
contrasts={'dummy_contrast_example': '3*audio-video/3'},
contrast_test_baseline=0.0,
hrf_model='Canonical',
drift_model='Cosine',
hfcut=128.,
residuals_model='spherical',
fit_method='ols',
outputPrefix='glm_',
rescale_results=False,
rescale_factor_file=None,
fir_delays=[0],
output_fit=False):
xmlio.XmlInitable.__init__(self)
FMRIAnalyser.__init__(self, outputPrefix)
self.output_fit = output_fit
self.hrf_model = hrf_model
self.drift_model = drift_model
self.fir_delays = fir_delays
self.hfcut = hfcut
self.residuals_model = residuals_model
self.fit_method = fit_method
self.contrasts = contrasts
self.contrasts.pop('dummy_contrast_example', None)
self.con_bl = contrast_test_baseline
self.rescale_results = rescale_results
if rescale_factor_file is not None:
self.rescale_factor = xndarray.load(rescale_factor_file).data
else:
self.rescale_factor = None
def handle_mask(self, mask_file, bold_files, tr, onsets, durations, output_dir, mesh_file=None):
if mesh_file is None: # Volumic
if self.force_input_parcellation:
if not op.exists(mask_file):
raise IOError("Input parcellation is forced but " "mask file %s not found" % mask_file)
else:
# TODO: check if n-ary
return mask_file
FMRIAnalyser.handle_mask(self, mask_file, bold_files, onsets, durations, mesh_file)
mask, mask_obj = read_volume(mask_file)
roi_ids = np.unique(mask)
if len(roi_ids) <= 2:
glm_output_dir = op.join(output_dir, "GLM")
if not op.exists(glm_output_dir):
os.makedirs(glm_output_dir)
return glm_parcellation(bold_file, tr)
def handle_mask(self, mask_file, bold_files, tr,
onsets, durations, output_dir, mesh_file=None):
if mesh_file is None: # Volumic
if self.force_input_parcellation:
if not op.exists(mask_file):
raise IOError("Input parcellation is forced but "
"mask file %s not found" % mask_file)
else:
# TODO: check if n-ary
return mask_file
FMRIAnalyser.handle_mask(self, mask_file, bold_files, onsets,
durations, mesh_file)
mask, mask_obj = read_volume(mask_file)
roi_ids = np.unique(mask)
if len(roi_ids) <= 2:
glm_output_dir = op.join(output_dir, 'GLM')
if not op.exists(glm_output_dir):
os.makedirs(glm_output_dir)
return glm_parcellation(bold_file, tr)
def __init__(self, HrfEstimator=RFIREstim(), outputPrefix='hrf_'):
xmlio.XmlInitable.__init__(self)
FMRIAnalyser.__init__(self, outputPrefix='rfir_')
self.hEstimator = HrfEstimator
def __init__(self, HrfEstimator=RFIREstim(), outputPrefix='hrf_'):
xmlio.XmlInitable.__init__(self)
FMRIAnalyser.__init__(self, outputPrefix='rfir_')
self.hEstimator = HrfEstimator
def __init__(self, outputPrefix="glm_"):
FMRIAnalyser.__init__(self, outputPrefix)
def __init__(self, HrfEstimator=RFIREstim(), outputPrefix="hrf_"):
FMRIAnalyser.__init__(self, outputPrefix="rfir_")
xmlio.XMLable2.__init__(self)
self.hEstimator = HrfEstimator
def __init__(self, outputPrefix='jde_', pass_error=True):
FMRIAnalyser.__init__(self, outputPrefix, pass_error=pass_error)
def __init__(self, outputPrefix='glm_'):
FMRIAnalyser.__init__(self, outputPrefix)
def __init__(self, outputPrefix='jde_', pass_error=True):
FMRIAnalyser.__init__(self, outputPrefix, pass_error=pass_error)
def __init__(self, outputPrefix='glm_'):
FMRIAnalyser.__init__(self, outputPrefix)
