def make_design_matrices(onsets,
n_scans,
tr,
motion=None,
hrf_model='canonical with derivative',
drift_model='cosine',
orthogonalize=None):
design_matrices = []
for i, onset in enumerate(onsets):
if n_scans[i] == 0:
design_matrices.append(None)
onset = np.array(onset)
labels = onset[:, 0]
time = onset[:, 1].astype('float')
duration = onset[:, 2].astype('float')
amplitude = onset[:, 3].astype('float')
if duration.sum() == 0:
paradigm = EventRelatedParadigm(labels, time, amplitude)
else:
paradigm = BlockParadigm(labels, time, duration, amplitude)
frametimes = np.linspace(0, (n_scans[i] - 1) * tr, n_scans[i])
if motion is not None:
add_regs = np.array(motion[i]).astype('float')
add_reg_names = ['motion_%i' % r for r in range(add_regs.shape[1])]
design_matrix = make_dmtx(frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
add_regs=add_regs,
add_reg_names=add_reg_names)
else:
design_matrix = make_dmtx(frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model)
if orthogonalize is not None:
if 'derivative' in hrf_model:
raise Exception(
'Orthogonalization not supported with hrf derivative.')
orth = orthogonalize[i]
if orth is not None:
for x, y in orth:
x_ = design_matrix.matrix[:, x]
y_ = design_matrix.matrix[:, y]
z = orthogonalize_vectors(x_, y_)
design_matrix.matrix[:, x] = z
design_matrices.append(design_matrix.matrix)
return design_matrices
def make_design_matrices(onsets, n_scans, tr, motion=None,
hrf_model='canonical with derivative',
drift_model='cosine', orthogonalize=None):
design_matrices = []
for i, onset in enumerate(onsets):
if n_scans[i] == 0:
design_matrices.append(None)
onset = np.array(onset)
labels = onset[:, 0]
time = onset[:, 1].astype('float')
duration = onset[:, 2].astype('float')
amplitude = onset[:, 3].astype('float')
if duration.sum() == 0:
paradigm = EventRelatedParadigm(labels, time, amplitude)
else:
paradigm = BlockParadigm(labels, time, duration, amplitude)
frametimes = np.linspace(0, (n_scans[i] - 1) * tr, n_scans[i])
if motion is not None:
add_regs = np.array(motion[i]).astype('float')
add_reg_names = ['motion_%i' % r
for r in range(add_regs.shape[1])]
design_matrix = make_dmtx(
frametimes, paradigm, hrf_model=hrf_model,
drift_model=drift_model,
add_regs=add_regs, add_reg_names=add_reg_names)
else:
design_matrix = make_dmtx(
frametimes, paradigm, hrf_model=hrf_model,
drift_model=drift_model)
if orthogonalize is not None:
if 'derivative' in hrf_model:
raise Exception(
'Orthogonalization not supported with hrf derivative.')
orth = orthogonalize[i]
if orth is not None:
for x, y in orth:
x_ = design_matrix.matrix[:, x]
y_ = design_matrix.matrix[:, y]
z = orthogonalize_vectors(x_, y_)
design_matrix.matrix[:, x] = z
design_matrices.append(design_matrix.matrix)
return design_matrices
def make_design(folder_name):
files = [f for f in listdir(folder_name) if isfile(join(folder_name, f))]
design_files = []
for i, run_file in files:
name = "design-{}".format(i)
tr = 0.2
path = os.path.join(folder_name, run_file)
img = nib.load(path)
data = img.get_data()
n_scans = data.shape[-1]
frametimes = np.arange(0, n_scans * tr, tr)
y = make_dmtx(frametimes,
paradigm=None,
hrf_model='canonical',
drift_model='cosine',
hfcut=128,
drift_order=1,
fir_delays=[0],
add_regs=None,
add_reg_names=None,
min_onset=0)
np.savez(name, y.matrix)
design_files.append(name)
return design_files
def make_design_matrices(events, n_scans, tr, hrf_model="canonical", drift_model="cosine", motion=None, orth=None):
design_matrices = []
n_sessions = len(n_scans)
for i in range(n_sessions):
onsets = events[i][0][:, 0]
duration = events[i][0][:, 1]
amplitude = events[i][0][:, 2]
trials = events[i][1]
order = np.argsort(onsets)
# make a block or event paradigm depending on stimulus duration
if duration.sum() == 0:
paradigm = EventRelatedParadigm(trials[order], onsets[order], amplitude[order])
else:
paradigm = BlockParadigm(trials[order], onsets[order], duration[order], amplitude[order])
frametimes = np.linspace(0, (n_scans[i] - 1) * tr, n_scans[i])
if motion is not None:
add_regs = np.array(motion[i]).astype("float")
add_reg_names = ["motion_%i" % r for r in range(add_regs.shape[1])]
design_matrix = make_dmtx(
frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
add_regs=add_regs,
add_reg_names=add_reg_names,
)
else:
design_matrix = make_dmtx(frametimes, paradigm, hrf_model=hrf_model, drift_model=drift_model)
if orth is not None:
session_orth = orth[i]
if session_orth is not None:
for x, y in session_orth:
reg = orthogonalize_regressors(design_matrix.matrix[:, x], design_matrix.matrix[:, y])
design_matrix.matrix[:, x] = reg
design_matrices.append(design_matrix)
return design_matrices
def make_design_matrices(events, n_scans, tr, hrf_model='canonical',
drift_model='cosine', motion=None):
design_matrices = []
n_sessions = len(n_scans)
for i in range(n_sessions):
onsets = events[i][0][:, 0]
duration = events[i][0][:, 1]
amplitude = events[i][0][:, 2]
cond_id = events[i][1]
order = np.argsort(onsets)
# make a block or event paradigm depending on stimulus duration
if duration.sum() == 0:
paradigm = EventRelatedParadigm(cond_id[order],
onsets[order],
amplitude[order])
else:
paradigm = BlockParadigm(cond_id[order], onsets[order],
duration[order], amplitude[order])
frametimes = np.linspace(0, (n_scans[i] - 1) * tr, n_scans[i])
if motion is not None:
add_regs = np.array(motion[i]).astype('float')
add_reg_names = ['motion_%i' % r
for r in range(add_regs.shape[1])]
design_matrix = make_dmtx(
frametimes, paradigm, hrf_model=hrf_model,
drift_model=drift_model,
add_regs=add_regs, add_reg_names=add_reg_names)
else:
design_matrix = make_dmtx(
frametimes, paradigm, hrf_model=hrf_model,
drift_model=drift_model)
design_matrices.append(design_matrix.matrix)
return design_matrices
def make_dmtx_from_timing_files(timing_files,
condition_ids=None,
frametimes=None,
n_scans=None,
tr=None,
add_regs_file=None,
add_reg_names=None,
**make_dmtx_kwargs):
# make paradigm
paradigm = make_paradigm_from_timing_files(timing_files,
condition_ids=condition_ids)
# make frametimes
if frametimes is None:
assert not n_scans is None, ("frametimes not specified, especting a "
"value for n_scans")
assert not tr is None, ("frametimes not specified, especting a "
"value for tr")
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
else:
assert n_scans is None, ("frametimes specified, not especting a "
"value for n_scans")
assert tr is None, ("frametimes specified, not especting a "
"value for tr")
# load addition regressors from file
if not add_regs_file is None:
if isinstance(add_regs_file, np.ndarray):
add_regs = add_regs_file
else:
assert os.path.isfile(add_regs_file), (
"add_regs_file %s doesn't exist")
add_regs = np.loadtxt(add_regs_file)
assert add_regs.ndim == 2, (
"Bad add_regs_file: %s (must contain a 2D array, each column "
"representing the values of a single regressor)" % add_regs_file)
if add_reg_names is None:
add_reg_names = [
"R%i" % (col + 1) for col in xrange(add_regs.shape[-1])
]
else:
assert len(add_reg_names) == add_regs.shape[1], (
"Expecting %i regressor names, got %i" %
(add_regs.shape[1], len(add_reg_names)))
make_dmtx_kwargs["add_reg_names"] = add_reg_names
make_dmtx_kwargs["add_regs"] = add_regs
# make design matrix
design_matrix = make_dmtx(frametimes, paradigm, **make_dmtx_kwargs)
# return output
return design_matrix, paradigm, frametimes
def make_dmtx_from_timing_files(timing_files, condition_ids=None,
frametimes=None, n_scans=None, tr=None,
add_regs_file=None,
add_reg_names=None,
**make_dmtx_kwargs):
# make paradigm
paradigm = make_paradigm_from_timing_files(timing_files,
condition_ids=condition_ids)
# make frametimes
if frametimes is None:
assert not n_scans is None, ("frametimes not specified, especting a "
"value for n_scans")
assert not tr is None, ("frametimes not specified, especting a "
"value for tr")
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
else:
assert n_scans is None, ("frametimes specified, not especting a "
"value for n_scans")
assert tr is None, ("frametimes specified, not especting a "
"value for tr")
# load addition regressors from file
if not add_regs_file is None:
if isinstance(add_regs_file, np.ndarray):
add_regs = add_regs_file
else:
assert os.path.isfile(add_regs_file), (
"add_regs_file %s doesn't exist")
add_regs = np.loadtxt(add_regs_file)
assert add_regs.ndim == 2, (
"Bad add_regs_file: %s (must contain a 2D array, each column "
"representing the values of a single regressor)" % add_regs_file)
if add_reg_names is None:
add_reg_names = ["R%i" % (col + 1) for col in range(
add_regs.shape[-1])]
else:
assert len(add_reg_names) == add_regs.shape[1], (
"Expecting %i regressor names, got %i" % (
add_regs.shape[1], len(add_reg_names)))
make_dmtx_kwargs["add_reg_names"] = add_reg_names
make_dmtx_kwargs["add_regs"] = add_regs
# make design matrix
design_matrix = make_dmtx(frametimes, paradigm, **make_dmtx_kwargs)
# return output
return design_matrix, paradigm, frametimes
def preprocess_encoding(ds, events, c, mp=None, design_kwargs=None):
if isinstance(c, basestring):
c = [c]
from nipy.modalities.fmri.design_matrix import make_dmtx
if design_kwargs is None:
design_kwargs = {'hrf_model': 'canonical', 'drift_model': 'blank'}
des_dict, rds = make_designmat(ds,
events,
time_attr='time_coords',
condition_attr=c,
design_kwargs=design_kwargs,
regr_attrs=None)
if mp is not None:
des_dict['motion'] = make_dmtx(ds.sa['time_coords'].value,
paradigm=None,
add_regs=mp,
drift_model='blank')
des = make_parammat(des_dict, hrf='canonical', zscore=True)
return rds, des
def make_designmat(frametimes,
cond_ids,
onsets,
durations,
amplitudes=None,
design_kwargs=None,
constant=False,
logger=None):
"""
Creates design matrix from TSV columns
:param frametimes: time index (in s) of each TR
:param cond_ids: condition ids. each unique string will become a regressor
:param onsets: condition onsets
:param durations: durations of trials
:param amplitudes: amplitude of trials (default None)
:param design_kwargs: additional arguments(motion parameters, HRF, etc)
:param logger: logger instance
:return: design matrix instance
"""
if design_kwargs is None:
design_kwargs = {}
if "drift_model" not in design_kwargs.keys():
design_kwargs["drift_model"] = "blank"
from nipy.modalities.fmri.design_matrix import make_dmtx
from nipy.modalities.fmri.experimental_paradigm import BlockParadigm
write_to_logger("Creating design matrix...", logger)
paradigm = BlockParadigm(con_id=cond_ids,
onset=onsets,
duration=durations,
amplitude=amplitudes)
dm = make_dmtx(frametimes, paradigm, **design_kwargs)
if constant is False:
import numpy as np
dm.matrix = np.delete(dm.matrix, dm.names.index("constant"), axis=1)
dm.names = dm.names.remove("constant")
return dm
def _preprocess_and_analysis_subject(subject_data,
do_normalize=False,
fwhm=0.,
slicer='z',
cut_coords=6,
threshold=3.,
cluster_th=15
):
"""
Preprocesses the subject and then fits (mass-univariate) GLM thereupon.
"""
# sanitize run_ids:
# Sub14/BOLD/Run_02/fMR09029-0004-00010-000010-01.nii is garbage,
# for example
run_ids = range(9)
if subject_data['subject_id'] == "Sub14":
run_ids = [0] + range(2, 9)
subject_data['func'] = [subject_data['func'][0]] + subject_data[
'func'][2:]
subject_data['session_id'] = [subject_data['session_id'][0]
] + subject_data['session_id'][2:]
# sanitize subject output dir
if not 'output_dir' in subject_data:
subject_data['output_dir'] = os.path.join(
output_dir, subject_data['subject_id'])
# preprocess the data
subject_data = do_subject_preproc(SubjectData(**subject_data),
do_realign=True,
do_coreg=True,
do_report=False,
do_cv_tc=False
)
assert not subject_data.anat is None
# norm
if do_normalize:
subject_data = nipype_do_subject_preproc(
subject_data,
do_realign=False,
do_coreg=False,
do_segment=True,
do_normalize=True,
func_write_voxel_sizes=[3, 3, 3],
anat_write_voxel_sizes=[2, 2, 2],
fwhm=fwhm,
hardlink_output=False,
do_report=False
)
# chronometry
stats_start_time = pretty_time()
# to-be merged lists, one item per run
paradigms = []
frametimes_list = []
design_matrices = [] # one
list_of_contrast_dicts = [] # one dict per run
n_scans = []
for run_id in run_ids:
_n_scans = len(subject_data.func[run_id])
n_scans.append(_n_scans)
# make paradigm
paradigm = make_paradigm(getattr(subject_data, 'timing')[run_id])
# make design matrix
tr = 2.
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
hfcut = 128.
frametimes = np.linspace(0, (_n_scans - 1) * tr, _n_scans)
design_matrix = make_dmtx(
frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
add_regs=np.loadtxt(getattr(subject_data,
'realignment_parameters')[run_id]),
add_reg_names=[
'Translation along x axis',
'Translation along yaxis',
'Translation along z axis',
'Rotation along x axis',
'Rotation along y axis',
'Rotation along z axis'
]
)
# import matplotlib.pyplot as plt
# design_matrix.show()
# plt.show()
paradigms.append(paradigm)
design_matrices.append(design_matrix)
frametimes_list.append(frametimes)
n_scans.append(_n_scans)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(
n_columns)[2 * i]
# more interesting contrasts"""
contrasts['Famous-Unfamiliar'] = contrasts[
'Famous'] - contrasts['Unfamiliar']
contrasts['Unfamiliar-Famous'] = -contrasts['Famous-Unfamiliar']
contrasts['Famous-Scrambled'] = contrasts[
'Famous'] - contrasts['Scrambled']
contrasts['Scrambled-Famous'] = -contrasts['Famous-Scrambled']
contrasts['Unfamiliar-Scrambled'] = contrasts[
'Unfamiliar'] - contrasts['Scrambled']
contrasts['Scrambled-Unfamiliar'] = -contrasts['Unfamiliar-Scrambled']
list_of_contrast_dicts.append(contrasts)
# importat maps
z_maps = {}
effects_maps = {}
# fit GLM
print('\r\nFitting a GLM (this takes time) ..')
fmri_glm = FMRILinearModel([nibabel.concat_images(sess_func)
for sess_func in subject_data.func],
[design_matrix.matrix
for design_matrix in design_matrices],
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
print "... done.\r\n"
# save computed mask
mask_path = os.path.join(subject_data.output_dir, "mask.nii.gz")
print "Saving mask image to %s ..." % mask_path
nibabel.save(fmri_glm.mask, mask_path)
print "... done.\r\n"
# replicate contrasts across runs
contrasts = dict((cid, [contrasts[cid]
for contrasts in list_of_contrast_dicts])
for cid, cval in contrasts.iteritems())
# compute effects
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, eff_map = fmri_glm.contrast(
contrast_val,
con_id=contrast_id,
output_z=True,
output_stat=False,
output_effects=True,
output_variance=False
)
# store stat maps to disk
for map_type, out_map in zip(['z', 'effects'], [z_map, eff_map]):
map_dir = os.path.join(
subject_data.output_dir, '%s_maps' % map_type)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
print "\t\tWriting %s ..." % map_path
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if map_type == 'z':
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
# remove repeated contrasts
contrasts = dict((cid, cval[0]) for cid, cval in contrasts.iteritems())
# do stats report
stats_report_filename = os.path.join(getattr(subject_data,
'reports_output_dir',
subject_data.output_dir),
"report_stats.html")
generate_subject_stats_report(
stats_report_filename,
contrasts,
z_maps,
fmri_glm.mask,
threshold=threshold,
cluster_th=cluster_th,
slicer=slicer,
cut_coords=cut_coords,
anat=nibabel.load(subject_data.anat).get_data(),
anat_affine=nibabel.load(subject_data.anat).get_affine(),
design_matrices=design_matrices,
subject_id=subject_data.subject_id,
start_time=stats_start_time,
title="GLM for subject %s" % subject_data.subject_id,
# additional ``kwargs`` for more informative report
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
drift_model=drift_model,
hrf_model=hrf_model,
paradigm=dict(("Run_%02i" % (run_id + 1), paradigms[run_id].__dict__)
for run_id in run_ids),
frametimes=dict(("Run_%02i" % (run_id + 1), frametimes_list[run_id])
for run_id in run_ids),
# fwhm=fwhm
)
ProgressReport().finish_dir(subject_data.output_dir)
print "\r\nStatistic report written to %s\r\n" % stats_report_filename
return contrasts, effects_maps, z_maps, mask_path
def do_subject_glm(subject_data):
"""FE analysis for a single subject."""
subject_id = subject_data['subject_id']
output_dir = subject_data["output_dir"]
func_files = subject_data['func']
anat = subject_data['anat']
onset_files = subject_data['onset']
tr = subject_data['TR']
time_units = subject_data['time_units'].lower()
assert time_units in ["seconds", "tr", "milliseconds"]
drift_model = subject_data['drift_model']
hrf_model = subject_data["hrf_model"]
hfcut = subject_data["hfcut"]
mem = Memory(os.path.join(output_dir, "cache"))
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if 0:
subject_data = mem.cache(do_subject_preproc)(dict(
func=func_files, anat=anat, output_dir=output_dir))
func_files = subject_data['func']
anat = subject_data['anat']
# reslice func images
func_files = [
mem.cache(reslice_vols)(sess_func,
target_affine=nibabel.load(
sess_func[0]).get_affine())
for sess_func in func_files
]
### GLM: loop on (session_bold, onse_file) pairs over the various sessions
design_matrices = []
for func_file, onset_file in zip(func_files, onset_files):
if isinstance(func_file, str):
bold = nibabel.load(func_file)
else:
if len(func_file) == 1:
func_file = func_file[0]
bold = nibabel.load(func_file)
assert len(bold.shape) == 4
n_scans = bold.shape[-1]
del bold
else:
n_scans = len(func_file)
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
conditions, onsets, durations, amplitudes = parse_onset_file(
onset_file)
if time_units == "tr":
onsets *= tr
durations *= tr
elif time_units in ["milliseconds"]:
onsets *= 1e-3
durations *= 1e-3
paradigm = BlockParadigm(con_id=conditions,
onset=onsets,
duration=durations,
amplitude=amplitudes)
design_matrices.append(
make_dmtx(frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
hfcut=hfcut))
# specify contrasts
n_columns = len(design_matrices[0].names)
contrasts = {}
for i in range(paradigm.n_conditions):
contrasts['%s' %
design_matrices[0].names[2 * i]] = np.eye(n_columns)[2 * i]
# effects of interest F-test
diff_contrasts = []
for i in range(paradigm.n_conditions - 1):
a = contrasts[design_matrices[0].names[2 * i]]
b = contrasts[design_matrices[0].names[2 * (i + 1)]]
diff_contrasts.append(a - b)
contrasts["diff"] = diff_contrasts
# fit GLM
print('Fitting a GLM (this takes time)...')
fmri_glm = FMRILinearModel([
nibabel.concat_images(sess_func, check_affines=False)
for sess_func in func_files
], [design_matrix.matrix for design_matrix in design_matrices],
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(output_dir, "mask.nii.gz")
print("Saving mask image %s" % mask_path)
nibabel.save(fmri_glm.mask, mask_path)
# compute contrasts
z_maps = {}
effects_maps = {}
for contrast_id, contrast_val in contrasts.items():
print("\tcontrast id: %s" % contrast_id)
if np.ndim(contrast_val) > 1:
contrast_type = "t"
else:
contrast_type = "F"
z_map, t_map, effects_map, var_map = fmri_glm.contrast(
[contrast_val] * len(func_files),
con_id=contrast_id,
contrast_type=contrast_type,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True)
# store stat maps to disk
for map_type, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, effects_map, var_map]):
map_dir = os.path.join(output_dir, '%s_maps' % map_type)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(map_dir, '%s.nii.gz' % contrast_id)
print("\t\tWriting %s ..." % map_path)
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if map_type == 'z':
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
return subject_id, anat, effects_maps, z_maps, contrasts, fmri_glm.mask
def do_subject_glm(subject_data):
"""FE analysis for a single subject."""
subject_id = subject_data['subject_id']
output_dir = subject_data["output_dir"]
func_files = subject_data['func']
anat = subject_data['anat']
onset_files = subject_data['onset']
# subject_id = os.path.basename(subject_dir)
# subject_output_dir = os.path.join(output_dir, subject_id)
mem = Memory(os.path.join(output_dir, "cache"))
if not os.path.exists(output_dir):
os.makedirs(output_dir)
# glob files: anat, session func files, session onset files
# anat = glob.glob(os.path.join(subject_dir, anat_wildcard))
# assert len(anat) == 1
# anat = anat[0]
# onset_files = sorted([glob.glob(os.path.join(subject_dir, session))[0]
# for session in session_onset_wildcards])
# func_files = sorted([sorted(glob.glob(os.path.join(subject_dir, session)))
# for session in session_func_wildcards])
### Preprocess data #######################################################
if 0:
subject_data = mem.cache(do_subject_preproc)(
dict(func=func_files, anat=anat, output_dir=output_dir))
func_files = subject_data['func']
anat = subject_data['anat']
# reslice func images
func_files = [mem.cache(reslice_vols)(
sess_func,
target_affine=nibabel.load(sess_func[0]).get_affine())
for sess_func in func_files]
### GLM: loop on (session_bold, onse_file) pairs over the various sessions
design_matrices = []
for session, (func_file, onset_file) in enumerate(zip(func_files,
onset_files)):
if isinstance(func_file, str):
bold = nibabel.load(func_file)
else:
if len(func_file) == 1:
func_file = func_file[0]
bold = nibabel.load(func_file)
assert len(bold.shape) == 4
n_scans = bold.shape[-1]
del bold
else:
n_scans = len(func_file)
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
conditions, onsets, durations, amplitudes = parse_onset_file(
onset_file)
onsets *= tr
durations *= tr
paradigm = BlockParadigm(con_id=conditions, onset=onsets,
duration=durations, amplitude=amplitudes)
design_matrices.append(make_dmtx(frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model,
hfcut=hfcut))
# specify contrasts
n_columns = len(design_matrices[0].names)
contrasts = {}
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrices[0].names[2 * i]
] = np.eye(n_columns)[2 * i]
# more interesting contrasts
contrasts['faces-scrambled'] = contrasts['faces'
] - contrasts['scrambled']
contrasts['scrambled-faces'] = -contrasts['faces-scrambled']
contrasts['effects_of_interest'] = contrasts['faces'
] + contrasts['scrambled']
# effects of interest F-test
diff_contrasts = []
for i in xrange(paradigm.n_conditions - 1):
a = contrasts[design_matrices[0].names[2 * i]]
b = contrasts[design_matrices[0].names[2 * (i + 1)]]
diff_contrasts.append(a - b)
contrasts["diff"] = diff_contrasts
# fit GLM
print 'Fitting a GLM (this takes time)...'
fmri_glm = FMRILinearModel([nibabel.concat_images(sess_func,
check_affines=False)
for sess_func in func_files],
[design_matrix.matrix
for design_matrix in design_matrices],
mask='compute'
)
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(output_dir, "mask.nii.gz")
print "Saving mask image %s" % mask_path
nibabel.save(fmri_glm.mask, mask_path)
# compute contrasts
z_maps = {}
effects_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
if np.ndim(contrast_val) > 1:
contrast_type = "t"
else:
contrast_type = "F"
z_map, t_map, effects_map, var_map = fmri_glm.contrast(
[contrast_val] * 2,
con_id=contrast_id,
contrast_type=contrast_type,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True
)
# store stat maps to disk
for map_type, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, effects_map, var_map]):
map_dir = os.path.join(
output_dir, '%s_maps' % map_type)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
print "\t\tWriting %s ..." % map_path
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if map_type == 'z':
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
return subject_id, anat, effects_maps, z_maps, contrasts, fmri_glm.mask
def load_glm_params(data_dir, model_id,
subject_ids=None,
hrf_model='canonical',
drift_model='cosine',
motion_params=None,
is_event_paradigm=True):
"""Load GLM parameters
XXX document this code!
"""
docs = []
study_id = os.path.split(data_dir)[-1]
tr = float(open(os.path.join(data_dir, 'scan_key.txt')).read().split()[1])
if subject_ids is None:
subject_dirs = sorted(glob.glob(os.path.join(data_dir, 'sub*')))
else:
subject_dirs = sorted([os.path.join(data_dir, subject_id)
for subject_id in subject_ids])
for subject_dir in subject_dirs:
params = {}
subject_id = os.path.split(subject_dir)[1]
params['study'] = study_id
params['subject'] = subject_id
# subjects models
model_dir = os.path.join(subject_dir, 'model', model_id)
session_dirs = sorted(glob.glob(
os.path.join(model_dir, 'onsets', '*')))
for i, session_dir in enumerate(session_dirs):
session_id = os.path.split(session_dir)[1]
img = nb.load(os.path.join(data_dir, subject_id, 'BOLD',
session_id, 'bold.nii.gz'))
n_scans = img.shape[-1]
params.setdefault('sessions', []).append(session_id)
params.setdefault('n_scans', []).append(n_scans)
onsets = None
cond_vect = None
cond_files = sorted(glob.glob(os.path.join(session_dir, 'cond*')))
for cond_file in cond_files:
cond_id = int(re.findall('cond(.*).txt',
os.path.split(cond_file)[1])[0])
# load paradigm
# replace whitespace characters by spaces before parsing
cond = open(cond_file, 'rb').read()
iterable = [
row.strip()
for row in re.sub('[\t\r\f\v]', ' ', cond).split('\n')]
reader = csv.reader(iterable, delimiter=' ')
rows = list(reader)
if onsets is None:
onsets = [float(row[0]) for row in rows if row != []]
cond_vect = [cond_id] * len(rows)
else:
onsets += [float(row[0]) for row in rows if row != []]
cond_vect += [cond_id] * len(rows)
onsets = np.array(onsets)
cond_vect = np.array(cond_vect)
order = np.argsort(onsets)
if is_event_paradigm:
paradigm = EventRelatedParadigm(
cond_vect[order], onsets[order])
else:
paradigm = BlockParadigm(cond_vect[order], onsets[order])
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
if motion_params is None or not subject_id in motion_params:
design_matrix = make_dmtx(
frametimes, paradigm, hrf_model=hrf_model,
drift_model=drift_model)
else:
add_regs = motion_params[subject_id][i]
add_reg_names = ['motion_%i' % r
for r in range(add_regs.shape[1])]
design_matrix = make_dmtx(
frametimes, paradigm, hrf_model=hrf_model,
drift_model=drift_model,
add_regs=add_regs, add_reg_names=add_reg_names)
# plot and save dmat
ax = design_matrix.show()
ax.set_position([.05, .25, .9, .65])
ax.set_title('Design matrix (%s, %s)' % (subject_id,
session_id))
dmat_outfile = os.path.join(session_dir, 'design_matrix.png')
print "Saving design matrix %s" % dmat_outfile
pl.savefig(dmat_outfile)
params.setdefault('design_matrices', []).append(
design_matrix.matrix)
docs.append(params)
# study model
n_regressors = [dm.shape[-1] for dm in params['design_matrices']]
model_dir = os.path.join(data_dir, 'models', model_id)
# replace whitespace characters by spaces before parsing
con = open(os.path.join(model_dir, 'task_contrasts.txt'), 'rb').read()
iterable = [row.strip()
for row in re.sub('[\t\r\f\v]', ' ', con).split('\n')]
reader = csv.reader(iterable, delimiter=' ')
# reader = csv.reader(contrasts_file, delimiter=' ')
contrasts = {}
shift = 0
for row in reader:
if row != []:
for n_regressor in n_regressors:
if row[0].startswith('task'): # file format varies
shift = 1
contrast_id = row[0 + shift]
# append zeros to contrasts for the confounds
contrast = np.hstack(
[np.array(row[1 + shift:]).astype('float'),
np.zeros(n_regressor - len(row[1 + shift:]))])
contrasts.setdefault(contrast_id, []).append(contrast)
for doc in docs:
doc['contrasts'] = contrasts
return docs
def execute_spm_auditory_glm(data, reg_motion=False):
reg_motion = reg_motion and 'realignment_parameters' in data
tr = 7.
n_scans = 96
_duration = 6
epoch_duration = _duration * tr
conditions = ['rest', 'active'] * 8
duration = epoch_duration * np.ones(len(conditions))
onset = np.linspace(0, (len(conditions) - 1) * epoch_duration,
len(conditions))
paradigm = BlockParadigm(con_id=conditions, onset=onset, duration=duration)
hfcut = 2 * 2 * epoch_duration
# construct design matrix
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
add_reg_names = None
add_regs = None
if reg_motion:
add_reg_names = ['tx', 'ty', 'tz', 'rx', 'ry', 'rz']
add_regs = data['realignment_parameters'][0]
if isinstance(add_regs, basestring):
add_regs = np.loadtxt(add_regs)
design_matrix = make_dmtx(frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
add_reg_names=add_reg_names,
add_regs=add_regs)
# plot and save design matrix
ax = design_matrix.show()
ax.set_position([.05, .25, .9, .65])
ax.set_title('Design matrix')
dmat_outfile = os.path.join(data['output_dir'],
'design_matrix.png')
pl.savefig(dmat_outfile, bbox_inches="tight", dpi=200)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# more interesting contrasts"""
contrasts['active-rest'] = contrasts['active'] - contrasts['rest']
# fit GLM
print('\r\nFitting a GLM (this takes time)...')
fmri_glm = FMRILinearModel(load_4D_img(data['func'][0]),
design_matrix.matrix,
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(data['output_dir'], "mask.nii.gz")
print "Saving mask image %s..." % mask_path
nibabel.save(fmri_glm.mask, mask_path)
# compute bg unto which activation will be projected
anat_img = load_vol(data['anat'])
anat = anat_img.get_data()
if anat.ndim == 4:
anat = anat[..., 0]
anat_affine = anat_img.get_affine()
print "Computing contrasts..."
z_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, t_map, eff_map, var_map = fmri_glm.contrast(
contrasts[contrast_id],
con_id=contrast_id,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True,
)
# store stat maps to disk
for dtype, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, eff_map, var_map]):
map_dir = os.path.join(
data['output_dir'], '%s_maps' % dtype)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if contrast_id == 'active-rest' and dtype == "z":
z_maps[contrast_id] = map_path
print "\t\t%s map: %s" % (dtype, map_path)
print
# do stats report
stats_report_filename = os.path.join(data['reports_output_dir'],
"report_stats.html")
contrasts = dict((contrast_id, contrasts[contrast_id])
for contrast_id in z_maps.keys())
generate_subject_stats_report(
stats_report_filename,
contrasts,
z_maps,
fmri_glm.mask,
design_matrices=[design_matrix],
subject_id=data['subject_id'],
anat=anat,
anat_affine=anat_affine,
cluster_th=50, # we're only interested in this 'large' clusters
# additional ``kwargs`` for more informative report
paradigm=paradigm.__dict__,
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
frametimes=frametimes,
drift_model=drift_model,
hrf_model=hrf_model,
)
ProgressReport().finish_dir(data['output_dir'])
print "\r\nStatistic report written to %s\r\n" % stats_report_filename
n_scans = 128
tr = 2.4
# paradigm
frametimes = np.linspace(0.5 * tr, (n_scans - .5) * tr, n_scans)
fmri_data = nibabel.load('s12069_swaloc1_corr.nii.gz')
########################################
# Design matrix
########################################
paradigm = load_paradigm_from_csv_file('localizer_paradigm.csv')['0']
design_matrix = make_dmtx(frametimes,
paradigm,
hrf_model='canonical with derivative',
drift_model="cosine",
hfcut=128)
#########################################
# Specify the contrasts
#########################################
# simplest ones
contrasts = {}
n_columns = len(design_matrix.names)
for i in range(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# Our contrast of interest
reading_vs_visual = contrasts["phrasevideo"] - contrasts["damier_H"]
def do_subject_glm(subject_data):
"""FE analysis for a single subject."""
subject_id = subject_data['subject_id']
output_dir = subject_data["output_dir"]
func_files = subject_data['func']
anat = subject_data['anat']
onset_files = subject_data['onset']
# subject_id = os.path.basename(subject_dir)
# subject_output_dir = os.path.join(output_dir, subject_id)
mem = Memory(os.path.join(output_dir, "cache"))
if not os.path.exists(output_dir):
os.makedirs(output_dir)
# glob files: anat, session func files, session onset files
# anat = glob.glob(os.path.join(subject_dir, anat_wildcard))
# assert len(anat) == 1
# anat = anat[0]
# onset_files = sorted([glob.glob(os.path.join(subject_dir, session))[0]
# for session in session_onset_wildcards])
# func_files = sorted([sorted(glob.glob(os.path.join(subject_dir, session)))
# for session in session_func_wildcards])
### Preprocess data #######################################################
if 0:
subject_data = mem.cache(do_subject_preproc)(
dict(func=func_files, anat=anat, output_dir=output_dir))
func_files = subject_data['func']
anat = subject_data['anat']
# reslice func images
func_files = [mem.cache(reslice_vols)(
sess_func,
target_affine=nibabel.load(sess_func[0]).get_affine())
for sess_func in func_files]
### GLM: loop on (session_bold, onse_file) pairs over the various sessions
design_matrices = []
for session, (func_file, onset_file) in enumerate(zip(func_files,
onset_files)):
if isinstance(func_file, str):
bold = nibabel.load(func_file)
else:
if len(func_file) == 1:
func_file = func_file[0]
bold = nibabel.load(func_file)
assert len(bold.shape) == 4
n_scans = bold.shape[-1]
del bold
else:
n_scans = len(func_file)
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
conditions, onsets, durations, amplitudes = parse_onset_file(
onset_file)
onsets *= tr
durations *= tr
paradigm = BlockParadigm(con_id=conditions, onset=onsets,
duration=durations, amplitude=amplitudes)
design_matrices.append(make_dmtx(frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model,
hfcut=hfcut))
# specify contrasts
n_columns = len(design_matrices[0].names)
contrasts = {}
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrices[0].names[2 * i]
] = np.eye(n_columns)[2 * i]
# more interesting contrasts
contrasts['faces-scrambled'] = contrasts['faces'
] - contrasts['scrambled']
contrasts['scrambled-faces'] = -contrasts['faces-scrambled']
contrasts['effects_of_interest'] = contrasts['faces'
] + contrasts['scrambled']
# effects of interest F-test
diff_contrasts = []
for i in xrange(paradigm.n_conditions - 1):
a = contrasts[design_matrices[0].names[2 * i]]
b = contrasts[design_matrices[0].names[2 * (i + 1)]]
diff_contrasts.append(a - b)
contrasts["diff"] = diff_contrasts
# fit GLM
print 'Fitting a GLM (this takes time)...'
fmri_glm = FMRILinearModel([nibabel.concat_images(sess_func,
check_affines=False)
for sess_func in func_files],
[design_matrix.matrix
for design_matrix in design_matrices],
mask='compute'
)
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(output_dir, "mask.nii.gz")
print "Saving mask image %s" % mask_path
nibabel.save(fmri_glm.mask, mask_path)
# compute contrasts
z_maps = {}
effects_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
if np.ndim(contrast_val) > 1:
contrast_type = "t"
else:
contrast_type = "F"
z_map, t_map, effects_map, var_map = fmri_glm.contrast(
[contrast_val] * 2,
con_id=contrast_id,
contrast_type=contrast_type,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True
)
# store stat maps to disk
for map_type, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, effects_map, var_map]):
map_dir = os.path.join(
output_dir, '%s_maps' % map_type)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
print "\t\tWriting %s ..." % map_path
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if map_type == 'z':
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
return subject_id, anat, effects_maps, z_maps, contrasts, fmri_glm.mask
mask_array = load(mask_file).get_data()
m = np.where(mask_array > 0)
pyhrf.verbose(1, 'Mask: shape=%s, nb vox in mask=%d'
%(str(mask_array.shape), mask_array.sum()))
# BOLD data
fmri_image = load(bold_file)
#pyhrf.verbose(1, 'BOLD shape : %s' %str(fmri_image.get_shape()))
Y = fmri_image.get_data()[m[0],m[1],m[2],:]
n_scans = Y.shape[1]
pyhrf.verbose(1, 'Loaded BOLD: nvox=%d, nscans=%d' %Y.shape)
# Design matrix
frametimes = np.linspace(0, (n_scans-1)*tr, n_scans)
design_matrix = dm.make_dmtx(frametimes, paradigm,
hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
fir_delays=fir_delays)
ns, nr = design_matrix.matrix.shape
pyhrf.verbose(2, 'Design matrix built with %d regressors:' %nr)
for rn in design_matrix.names:
pyhrf.verbose(2, ' - %s' %rn)
cdesign_matrix = xndarray(design_matrix.matrix,
axes_names=['time','regressor'],
axes_domains={'time':np.arange(ns)*tr,
'regressor':design_matrix.names})
cdesign_matrix.save(op.join(output_dir, 'design_matrix.nii'))
import cPickle
f = open(op.join(output_dir, 'design_matrix.pck'), 'w')
def execute_spm_multimodal_fmri_glm(data, reg_motion=False):
reg_motion = reg_motion and 'realignment_parameters' in data
# experimental paradigm meta-params
stats_start_time = time.ctime()
tr = 2.
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
hfcut = 128.
# make design matrices
design_matrices = []
for x in xrange(2):
n_scans = data['func'][x].shape[-1]
timing = scipy.io.loadmat(data['trials_ses%i' % (x + 1)],
squeeze_me=True, struct_as_record=False)
faces_onsets = timing['onsets'][0].ravel()
scrambled_onsets = timing['onsets'][1].ravel()
onsets = np.hstack((faces_onsets, scrambled_onsets))
onsets *= tr # because onsets were reporting in 'scans' units
conditions = ['faces'] * len(faces_onsets) + ['scrambled'] * len(
scrambled_onsets)
paradigm = EventRelatedParadigm(conditions, onsets)
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
add_reg_names = None
add_regs = None
if reg_motion:
add_reg_names = ['tx', 'ty', 'tz', 'rx', 'ry', 'rz']
add_regs = np.loadtxt(data['realignment_parameters'][x])
if isinstance(add_regs):
add_regs = np.loadtxt(add_regs)
design_matrix = make_dmtx(
frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
add_reg_names=add_reg_names,
add_regs=add_regs
)
design_matrices.append(design_matrix)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# more interesting contrasts
contrasts['faces-scrambled'] = contrasts['faces'] - contrasts['scrambled']
contrasts['scrambled-faces'] = contrasts['scrambled'] - contrasts['faces']
contrasts['effects_of_interest'] = contrasts[
'faces'] + contrasts['scrambled']
# we've thesame contrasts over sessions, so let's replicate
contrasts = dict((contrast_id, [contrast_val] * 2)
for contrast_id, contrast_val in contrasts.iteritems())
# fit GLM
print('\r\nFitting a GLM (this takes time)...')
fmri_glm = FMRILinearModel([load_4D_img(sess_func)
for sess_func in data['func']],
[dmat.matrix for dmat in design_matrices],
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(data['output_dir'], "mask.nii.gz")
print "Saving mask image %s" % mask_path
nibabel.save(fmri_glm.mask, mask_path)
# compute bg unto which activation will be projected
anat_img = load_vol(data['anat'])
anat = anat_img.get_data()
if anat.ndim == 4:
anat = anat[..., 0]
anat_affine = anat_img.get_affine()
print "Computing contrasts .."
z_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, t_map, eff_map, var_map = fmri_glm.contrast(
contrast_val,
con_id=contrast_id,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True,
)
# store stat maps to disk
for dtype, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, eff_map, var_map]):
map_dir = os.path.join(
data['output_dir'], '%s_maps' % dtype)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if dtype == 'z':
z_maps[contrast_id] = map_path
print "\t\t%s map: %s" % (dtype, map_path)
# do stats report
data['stats_report_filename'] = os.path.join(data['reports_output_dir'],
"report_stats.html")
contrasts = dict((contrast_id, contrasts[contrast_id])
for contrast_id in z_maps.keys())
generate_subject_stats_report(
data['stats_report_filename'],
contrasts,
z_maps,
fmri_glm.mask,
anat=anat,
anat_affine=anat_affine,
design_matrices=design_matrices,
subject_id=data['subject_id'],
cluster_th=15, # we're only interested in this 'large' clusters
start_time=stats_start_time,
# additional ``kwargs`` for more informative report
paradigm=paradigm.__dict__,
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
frametimes=frametimes,
drift_model=drift_model,
hrf_model=hrf_model,
)
ProgressReport().finish_dir(data['reports_output_dir'])
print "\r\nStatistic report written to %s\r\n" % data[
'stats_report_filename']
return data
def execute_spm_auditory_glm(data, reg_motion=False):
reg_motion = reg_motion and 'realignment_parameters' in data
tr = 7.
n_scans = 96
_duration = 6
epoch_duration = _duration * tr
conditions = ['rest', 'active'] * 8
duration = epoch_duration * np.ones(len(conditions))
onset = np.linspace(0, (len(conditions) - 1) * epoch_duration,
len(conditions))
paradigm = BlockParadigm(con_id=conditions, onset=onset, duration=duration)
hfcut = 2 * 2 * epoch_duration
# construct design matrix
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
add_reg_names = None
add_regs = None
if reg_motion:
add_reg_names = ['tx', 'ty', 'tz', 'rx', 'ry', 'rz']
add_regs = data['realignment_parameters'][0]
if isinstance(add_regs, basestring):
add_regs = np.loadtxt(add_regs)
design_matrix = make_dmtx(frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
add_reg_names=add_reg_names,
add_regs=add_regs)
# plot and save design matrix
ax = design_matrix.show()
ax.set_position([.05, .25, .9, .65])
ax.set_title('Design matrix')
dmat_outfile = os.path.join(data['output_dir'],
'design_matrix.png')
pl.savefig(dmat_outfile, bbox_inches="tight", dpi=200)
pl.close()
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# more interesting contrasts"""
contrasts['active-rest'] = contrasts['active'] - contrasts['rest']
# fit GLM
print('\r\nFitting a GLM (this takes time)...')
fmri_glm = FMRILinearModel(load_4D_img(data['func'][0]),
design_matrix.matrix,
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(data['output_dir'], "mask.nii.gz")
print "Saving mask image %s..." % mask_path
nibabel.save(fmri_glm.mask, mask_path)
# compute bg unto which activation will be projected
anat_img = load_vol(data['anat'])
anat = anat_img.get_data()
if anat.ndim == 4:
anat = anat[..., 0]
anat_affine = anat_img.get_affine()
print "Computing contrasts..."
z_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, t_map, eff_map, var_map = fmri_glm.contrast(
contrasts[contrast_id],
con_id=contrast_id,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True,
)
# store stat maps to disk
for dtype, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, eff_map, var_map]):
map_dir = os.path.join(
data['output_dir'], '%s_maps' % dtype)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if contrast_id == 'active-rest' and dtype == "z":
z_maps[contrast_id] = map_path
print "\t\t%s map: %s" % (dtype, map_path)
print
# do stats report
stats_report_filename = os.path.join(data['reports_output_dir'],
"report_stats.html")
contrasts = dict((contrast_id, contrasts[contrast_id])
for contrast_id in z_maps.keys())
generate_subject_stats_report(
stats_report_filename,
contrasts,
z_maps,
fmri_glm.mask,
design_matrices=[design_matrix],
subject_id=data['subject_id'],
anat=anat,
anat_affine=anat_affine,
cluster_th=50, # we're only interested in this 'large' clusters
# additional ``kwargs`` for more informative report
paradigm=paradigm.__dict__,
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
frametimes=frametimes,
drift_model=drift_model,
hrf_model=hrf_model,
)
ProgressReport().finish_dir(data['output_dir'])
print "\r\nStatistic report written to %s\r\n" % stats_report_filename
def do_subject_glm(subject_data):
"""FE analysis for a single subject."""
subject_id = subject_data['subject_id']
output_dir = subject_data["output_dir"]
func_files = subject_data['func']
anat = subject_data['anat']
onset_files = subject_data['onset']
tr = subject_data['TR']
time_units = subject_data['time_units'].lower()
assert time_units in ["seconds", "tr", "milliseconds"]
drift_model = subject_data['drift_model']
hrf_model = subject_data["hrf_model"]
hfcut = subject_data["hfcut"]
mem = Memory(os.path.join(output_dir, "cache"))
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if 0:
subject_data = mem.cache(do_subject_preproc)(
dict(func=func_files, anat=anat, output_dir=output_dir))
func_files = subject_data['func']
anat = subject_data['anat']
# reslice func images
func_files = [mem.cache(reslice_vols)(
sess_func, target_affine=nibabel.load(sess_func[0]).get_affine())
for sess_func in func_files]
### GLM: loop on (session_bold, onse_file) pairs over the various sessions
design_matrices = []
for func_file, onset_file in zip(func_files, onset_files):
if isinstance(func_file, str):
bold = nibabel.load(func_file)
else:
if len(func_file) == 1:
func_file = func_file[0]
bold = nibabel.load(func_file)
assert len(bold.shape) == 4
n_scans = bold.shape[-1]
del bold
else:
n_scans = len(func_file)
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
conditions, onsets, durations, amplitudes = parse_onset_file(
onset_file)
if time_units == "tr":
onsets *= tr
durations *= tr
elif time_units in ["milliseconds"]:
onsets *= 1e-3
durations *= 1e-3
paradigm = BlockParadigm(con_id=conditions, onset=onsets,
duration=durations, amplitude=amplitudes)
design_matrices.append(make_dmtx(
frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut))
# specify contrasts
n_columns = len(design_matrices[0].names)
contrasts = {}
for i in range(paradigm.n_conditions):
contrasts['%s' % design_matrices[0].names[2 * i]
] = np.eye(n_columns)[2 * i]
# effects of interest F-test
diff_contrasts = []
for i in range(paradigm.n_conditions - 1):
a = contrasts[design_matrices[0].names[2 * i]]
b = contrasts[design_matrices[0].names[2 * (i + 1)]]
diff_contrasts.append(a - b)
contrasts["diff"] = diff_contrasts
# fit GLM
print('Fitting a GLM (this takes time)...')
fmri_glm = FMRILinearModel([nibabel.concat_images(sess_func,
check_affines=False)
for sess_func in func_files],
[design_matrix.matrix
for design_matrix in design_matrices],
mask='compute'
)
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(output_dir, "mask.nii.gz")
print("Saving mask image %s" % mask_path)
nibabel.save(fmri_glm.mask, mask_path)
# compute contrasts
z_maps = {}
effects_maps = {}
for contrast_id, contrast_val in contrasts.items():
print("\tcontrast id: %s" % contrast_id)
if np.ndim(contrast_val) > 1:
contrast_type = "t"
else:
contrast_type = "F"
z_map, t_map, effects_map, var_map = fmri_glm.contrast(
[contrast_val] * len(func_files),
con_id=contrast_id,
contrast_type=contrast_type,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True
)
# store stat maps to disk
for map_type, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, effects_map, var_map]):
map_dir = os.path.join(
output_dir, '%s_maps' % map_type)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
print("\t\tWriting %s ..." % map_path)
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if map_type == 'z':
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
return subject_id, anat, effects_maps, z_maps, contrasts, fmri_glm.mask
# timing
n_scans = 128
tr = 2.4
# paradigm
frametimes = np.linspace(0.5 * tr, (n_scans - .5) * tr, n_scans)
fmri_data = nibabel.load('s12069_swaloc1_corr.nii.gz')
########################################
# Design matrix
########################################
paradigm = load_paradigm_from_csv_file('localizer_paradigm.csv')['0']
design_matrix = make_dmtx(frametimes, paradigm,
hrf_model='canonical with derivative',
drift_model="cosine", hfcut=128)
#########################################
# Specify the contrasts
#########################################
# simplest ones
contrasts = {}
n_columns = len(design_matrix.names)
for i in range(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# Our contrast of interest
reading_vs_visual = contrasts["phrasevideo"] - contrasts["damier_H"]
squeeze_me=True, struct_as_record=False)
faces_onsets = timing['onsets'][0].ravel()
scrambled_onsets = timing['onsets'][1].ravel()
onsets = np.hstack((faces_onsets, scrambled_onsets))
onsets *= tr # because onsets were reporting in 'scans' units
conditions = ['faces'] * len(faces_onsets) + ['scrambled'] * len(
scrambled_onsets)
paradigm = EventRelatedParadigm(conditions, onsets)
# build design matrix
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
design_matrix = make_dmtx(
frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
add_reg_names=['tx', 'ty', 'tz', 'rx', 'ry', 'rz'],
add_regs=np.loadtxt(subject_data.realignment_parameters[x])
)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]
] = np.eye(n_columns)[2 * i]
# more interesting contrasts
contrasts['faces-scrambled'] = contrasts['faces'
] - contrasts['scrambled']
contrasts['scrambled-faces'] = -contrasts['faces-scrambled']
def _fit_hrf_event_model(ds,
events,
time_attr,
condition_attr='targets',
design_kwargs=None,
glmfit_kwargs=None,
regr_attrs=None):
if externals.exists('nipy', raise_=True):
from nipy.modalities.fmri.design_matrix import make_dmtx
from mvpa2.mappers.glm import NiPyGLMMapper
# Decide/device condition attribute on which GLM will actually be done
if isinstance(condition_attr, basestring):
# must be a list/tuple/array for the logic below
condition_attr = [condition_attr]
glm_condition_attr = 'regressor_names' # actual regressors
glm_condition_attr_map = dict([(con, dict()) for con in condition_attr]) #
# to map back to original conditions
events = copy.deepcopy(events) # since we are modifying in place
for event in events:
if glm_condition_attr in event:
raise ValueError("Event %s already has %s defined. Should not "
"happen. Choose another name if defined it" %
(event, glm_condition_attr))
compound_label = event[glm_condition_attr] = \
'glm_label_' + '+'.join(
str(event[con]) for con in condition_attr)
# and mapping back to original values, without str()
# for each condition:
for con in condition_attr:
glm_condition_attr_map[con][compound_label] = event[con]
evvars = _events2dict(events)
add_paradigm_kwargs = {}
if 'amplitude' in evvars:
add_paradigm_kwargs['amplitude'] = evvars['amplitude']
# create paradigm
if 'duration' in evvars:
from nipy.modalities.fmri.experimental_paradigm import BlockParadigm
# NiPy considers everything with a duration as a block paradigm
paradigm = BlockParadigm(con_id=evvars[glm_condition_attr],
onset=evvars['onset'],
duration=evvars['duration'],
**add_paradigm_kwargs)
else:
from nipy.modalities.fmri.experimental_paradigm \
import EventRelatedParadigm
paradigm = EventRelatedParadigm(con_id=evvars[glm_condition_attr],
onset=evvars['onset'],
**add_paradigm_kwargs)
# create design matrix -- all kinds of fancy additional regr can be
# auto-generated
if design_kwargs is None:
design_kwargs = {}
if not regr_attrs is None:
names = []
regrs = []
for attr in regr_attrs:
names.append(attr)
regrs.append(ds.sa[attr].value)
if len(regrs) < 2:
regrs = [regrs]
regrs = np.hstack(regrs).T
if 'add_regs' in design_kwargs:
design_kwargs['add_regs'] = np.hstack(
(design_kwargs['add_regs'], regrs))
else:
design_kwargs['add_regs'] = regrs
if 'add_reg_names' in design_kwargs:
design_kwargs['add_reg_names'].extend(names)
else:
design_kwargs['add_reg_names'] = names
design_matrix = make_dmtx(ds.sa[time_attr].value, paradigm,
**design_kwargs)
# push design into source dataset
glm_regs = [(reg, design_matrix.matrix[:, i])
for i, reg in enumerate(design_matrix.names)]
# GLM
glm = NiPyGLMMapper([],
glmfit_kwargs=glmfit_kwargs,
add_regs=glm_regs,
return_design=True,
return_model=True,
space=glm_condition_attr)
model_params = glm(ds)
# some regressors might be corresponding not to original condition_attr
# so let's separate them out
regressor_names = model_params.sa[glm_condition_attr].value
condition_regressors = np.array(
[v in glm_condition_attr_map.values()[0] for v in regressor_names])
assert (condition_regressors.dtype == np.bool)
if not np.all(condition_regressors):
# some regressors do not correspond to conditions and would need
# to be taken into a separate dataset
model_params.a['add_regs'] = model_params[~condition_regressors]
# then we process the rest
model_params = model_params[condition_regressors]
regressor_names = model_params.sa[glm_condition_attr].value
# now define proper condition sa's
for con, con_map in glm_condition_attr_map.iteritems():
model_params.sa[con] = [con_map[v] for v in regressor_names]
model_params.sa.pop(glm_condition_attr) # remove generated one
return model_params
from numpy import array from nipy.modalities.fmri.design_matrix import make_dmtx from nipy.modalities.fmri.experimental_paradigm import EventRelatedParadigm # Specify an event-related paradigm conditions = ['smile', 'smile', 'listen', 'listen', 'read', 'read'] onsets = [30, 70, 10, 90, 40, 60] # onset time in s. paradigm = EventRelatedParadigm(conditions, onsets) # provide frametimes and compute the design matrix frametimes = array(range(0, 100)) # time of the scans X = make_dmtx(frametimes, paradigm, drift_model='polynomial', drift_order=3) X.show()
def fit_event_hrf_model(
ds, events, time_attr, condition_attr='targets', design_kwargs=None,
glmfit_kwargs=None, regr_attrs=None, return_model=False):
"""Fit a GLM with HRF regressor and yield a dataset with model parameters
A univariate GLM is fitted for each feature and model parameters are
returned as samples. Model parameters are returned for each regressor in
the design matrix. Using functionality from NiPy, design matrices can be
generated from event definitions with a variety of customizations (HRF
model, confound regressors, ...).
Events need to be specified as a list of dictionaries
(see:class:`~mvpa2.misc.support.Event`) for a helper class. Each dictionary
contains all relevant attributes to describe an event.
HRF event model details
-----------------------
The event specifications are used to generate a design matrix for all
present conditions. In addition to the mandatory ``onset`` information
each event definition needs to include a label in order to associate
individual events to conditions (the design matrix will contain at least
one regressor for each condition). The name of this label attribute must
be specified too (see ``condition_attr`` argument).
NiPy is used to generate the actual design matrix. It is required to
specify a dataset sample attribute that contains time stamps for all input
data samples (see ``time_attr``). NiPy operation could be customized (see
``design_kwargs`` argument). Additional regressors from sample attributes
of the input dataset can be included in the design matrix (see
``regr_attrs``).
The actual GLM fit is also performed by NiPy and can be fully customized
(see ``glmfit_kwargs``).
Parameters
----------
ds : Dataset
The samples of this input dataset have to be in whatever ascending order.
events : list
Each event definition has to specify ``onset`` and ``duration``. All
other attributes will be passed on to the sample attributes collection of
the returned dataset.
time_attr : str
Attribute with dataset sample time stamps.
Its values will be treated as in-the-same-unit and are used to
determine corresponding samples from real-value onset and duration
definitions. For HRF modeling this argument is mandatory.
condition_attr : str
Name of the event attribute with the condition labels.
Can be a list of those (e.g. ['targets', 'chunks'] combination of which
would constitute a condition.
design_kwargs : dict
Arbitrary keyword arguments for NiPy's make_dmtx() used for design matrix
generation. Choose HRF model, confound regressors, etc.
glmfit_kwargs : dict
Arbitrary keyword arguments for NiPy's GeneralLinearModel.fit() used for
estimating model parameter. Choose fitting algorithm: OLS or AR1.
regr_attrs : list
List of dataset sample attribute names that shall be extracted from the
input dataset and used as additional regressors in the design matrix.
return_model : bool
Flag whether to included the fitted GLM model in the returned dataset.
For large input data this can be problematic, as the model may contain
the residuals (same size is input data), hence multiplies the memory
demand. Off by default.
Returns
-------
Dataset
One sample for each regressor/condition in the design matrix is returned.
The condition names are included as a sample attribute with the name
specified by the ``condition_attr`` argument. The actual design
regressors are included as ``regressors`` sample attribute. If enabled,
an instance with the fitted NiPy GLM results is included as a dataset
attribute ``model``, and can be used for computing contrasts subsequently.
"""
if externals.exists('nipy', raise_=True):
from nipy.modalities.fmri.design_matrix import make_dmtx
from mvpa2.mappers.glm import NiPyGLMMapper
# Decide/device condition attribute on which GLM will actually be done
if isinstance(condition_attr, basestring):
# must be a list/tuple/array for the logic below
condition_attr = [condition_attr]
glm_condition_attr = 'regressor_names' # actual regressors
glm_condition_attr_map = dict([(con, dict()) for con in condition_attr]) #
# to map back to original conditions
events = copy.deepcopy(events) # since we are modifying in place
for event in events:
if glm_condition_attr in event:
raise ValueError("Event %s already has %s defined. Should not "
"happen. Choose another name if defined it"
% (event, glm_condition_attr))
compound_label = event[glm_condition_attr] = \
'glm_label_' + '+'.join(
str(event[con]) for con in condition_attr)
# and mapping back to original values, without str()
# for each condition:
for con in condition_attr:
glm_condition_attr_map[con][compound_label] = event[con]
evvars = _events2dict(events)
add_paradigm_kwargs = {}
if 'amplitude' in evvars:
add_paradigm_kwargs['amplitude'] = evvars['amplitude']
# create paradigm
if 'duration' in evvars:
from nipy.modalities.fmri.experimental_paradigm import BlockParadigm
# NiPy considers everything with a duration as a block paradigm
paradigm = BlockParadigm(
con_id=evvars[glm_condition_attr],
onset=evvars['onset'],
duration=evvars['duration'],
**add_paradigm_kwargs)
else:
from nipy.modalities.fmri.experimental_paradigm \
import EventRelatedParadigm
paradigm = EventRelatedParadigm(
con_id=evvars[glm_condition_attr],
onset=evvars['onset'],
**add_paradigm_kwargs)
# create design matrix -- all kinds of fancy additional regr can be
# auto-generated
if design_kwargs is None:
design_kwargs = {}
if not regr_attrs is None:
names = []
regrs = []
for attr in regr_attrs:
regr = ds.sa[attr].value
# add rudimentary dimension for easy hstacking later on
if regr.ndim < 2:
regr = regr[:, np.newaxis]
if regr.shape[1] == 1:
names.append(attr)
else:
# add one per each column of the regressor
for i in xrange(regr.shape[1]):
names.append("%s.%d" % (attr, i))
regrs.append(regr)
regrs = np.hstack(regrs)
if 'add_regs' in design_kwargs:
design_kwargs['add_regs'] = np.hstack((design_kwargs['add_regs'],
regrs))
else:
design_kwargs['add_regs'] = regrs
if 'add_reg_names' in design_kwargs:
design_kwargs['add_reg_names'].extend(names)
else:
design_kwargs['add_reg_names'] = names
design_matrix = make_dmtx(ds.sa[time_attr].value,
paradigm,
**design_kwargs)
# push design into source dataset
glm_regs = [
(reg, design_matrix.matrix[:, i])
for i, reg in enumerate(design_matrix.names)]
# GLM
glm = NiPyGLMMapper([], glmfit_kwargs=glmfit_kwargs,
add_regs=glm_regs,
return_design=True, return_model=return_model,
space=glm_condition_attr)
model_params = glm(ds)
# some regressors might be corresponding not to original condition_attr
# so let's separate them out
regressor_names = model_params.sa[glm_condition_attr].value
condition_regressors = np.array([v in glm_condition_attr_map.values()[0]
for v in regressor_names])
assert(condition_regressors.dtype == np.bool)
if not np.all(condition_regressors):
# some regressors do not correspond to conditions and would need
# to be taken into a separate dataset
model_params.a['add_regs'] = model_params[~condition_regressors]
# then we process the rest
model_params = model_params[condition_regressors]
regressor_names = model_params.sa[glm_condition_attr].value
# now define proper condition sa's
for con, con_map in glm_condition_attr_map.iteritems():
model_params.sa[con] = [con_map[v] for v in regressor_names]
model_params.sa.pop(glm_condition_attr) # remove generated one
return model_params
def runsub(sub, thisContrast, thisContrastStr, testContrast,
filterLen, filterOrd, write=False, debug=False,
alphas=1, roi='grayMatter'):
thisSub = {sub: subList[sub]}
mc_params = lmvpa.loadmotionparams(paths, thisSub)
beta_events = lmvpa.loadevents(paths, thisSub)
dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi, c='trial_type')
thisDS = dsdict[sub]
# savitsky golay filtering
sg.sg_filter(thisDS, filterLen, filterOrd)
# gallant group zscores before regression.
# zscore w.r.t. rest trials
# zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
# zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
zscore(thisDS, chunks_attr='chunks')
# kay method: leave out a model run, use it to fit an HRF for each voxel
# huth method: essentially use FIR
# mumford method: deconvolution with canonical HRF
# get timing data from timing files
rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub], contrasts) # adding features
# we can model out motion and just not use those betas.
# Ridge
if isinstance(thisContrast, basestring):
thisContrast = [thisContrast]
desX, rds = lmvpa.make_designmat(rds, events, time_attr='time_coords', condition_attr=thisContrast,
design_kwargs={'hrf_model': 'canonical', 'drift_model': 'blank'},
regr_attrs=None)
# 'add_regs': mc_params[sub]
desX['motion'] = make_dmtx(rds.sa['time_coords'].value, paradigm=None, add_regs=mc_params[sub], drift_model='blank')
des = lmvpa.make_parammat(desX, hrf='canonical', zscore=True)
# split by language and pictures
lidx = thisDS.chunks < thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
pidx = thisDS.chunks >= thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
ldes = cp.copy(des)
pdes = cp.copy(des)
ldes.matrix = ldes.matrix[lidx]
pdes.matrix = pdes.matrix[pidx]
covarmat = None
mus = None
lwts, _, lres, lceil = bsr.bootstrap_ridge(ds=rds[lidx], des=ldes, chunklen=1, nchunks=1,
cov0=None, mu0=None, part_attr='chunks', mode='test',
alphas=[alphas[0]], single_alpha=True, normalpha=False,
nboots=1, corrmin=.2, singcutoff=1e-10, joined=None,
use_corr=True)
print 'language ' + str(np.mean(lres))
pwts, _, pres, pceil = bsr.bootstrap_ridge(ds=rds[pidx], des=pdes, chunklen=1, nchunks=1,
cov0=None, mu0=None, part_attr='chunks', mode='test',
alphas=[alphas[1]], single_alpha=True, normalpha=False,
nboots=1, corrmin=.2, singcutoff=1e-10, joined=None,
use_corr=True)
# pictures within
print 'pictures: ' + str(np.mean(pres))
if write:
map2nifti(thisDS, dataset.vstack([lres, pres])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_corrs.nii.gz'))
map2nifti(thisDS, dataset.vstack([lwts, pwts])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_wts.nii.gz'))
map2nifti(thisDS, dataset.vstack([lceil, pceil])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_ceiling.nii.gz'))
for t in testContrast:
tstr = '+'.join(t)
lcorr = lmvpa.testmodel(wts=lwts, des=ldes, ds=rds[lidx], tc=cp.copy(t), use_corr=True)
pcorr = lmvpa.testmodel(wts=pwts, des=pdes, ds=rds[pidx], tc=cp.copy(t), use_corr=True)
if write:
map2nifti(thisDS, dataset.vstack([lcorr, pcorr])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + tstr +
'_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_test_corrs.nii.gz'))
del lres, pres, lwts, pwts, lceil, pceil
crossSet = thisDS.copy()
crossSet.chunks[lidx] = 1
crossSet.chunks[pidx] = 2
# cwts, cres, cceil = bsr.ridge(rds[pidx], pdes, mu0=mus, cov0=covarmat,
# part_attr='chunks', mode='test', alphas=alphas[0], single_alpha=True,
# normalpha=False, corrmin=.2, singcutoff=1e-10, joined=None,
# use_corr=True)
cwts, _, cres, cceil = bsr.bootstrap_ridge(ds=crossSet, des=des, chunklen=1, nchunks=1,
cov0=None, mu0=None, part_attr='chunks', mode='test',
alphas=[alphas[2]], single_alpha=True, normalpha=False,
nboots=1, corrmin=.2, singcutoff=1e-10, joined=None,
use_corr=True)
for t in testContrast:
tstr = '+'.join(t)
ccorr = lmvpa.testmodel(wts=cwts, des=des, ds=crossSet, tc=cp.copy(t), use_corr=True)
if write:
map2nifti(thisDS, ccorr[0]) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + tstr +
'_P2L_ridge_alpha_' + str(alphas[2]) + '_test_corr.nii.gz'))
map2nifti(thisDS, ccorr[1]) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + tstr +
'_L2P_ridge_alpha_' + str(alphas[2]) + '_test_corr.nii.gz'))
print 'cross: ' + str(np.mean(cres))
if write:
map2nifti(thisDS, cres[0]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_P2L_ridge_alpha_' + str(alphas[2]) + '_corr.nii.gz'))
map2nifti(thisDS, cres[1]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_L2P_ridge_alpha_' + str(alphas[2]) + '_corr.nii.gz'))
map2nifti(thisDS, cwts[cwts.chunks==1]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_P2L_ridge_alpha_' + str(alphas[2]) + '_wts.nii.gz'))
map2nifti(thisDS, cwts[cwts.chunks==2]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_L2P_ridge_alpha' + str(alphas[2]) + '_wts.nii.gz'))
map2nifti(thisDS, cceil[0]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_P2L_ridge_alpha_' + str(alphas[2]) + '_ceiling.nii.gz'))
map2nifti(thisDS, cceil[1]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_L2P_ridge_alpha_' + str(alphas[2]) + '_ceiling.nii.gz'))
del cres, cwts, cceil
def execute_spm_multimodal_fmri_glm(data, reg_motion=False):
reg_motion = reg_motion and 'realignment_parameters' in data
# experimental paradigm meta-params
stats_start_time = time.ctime()
tr = 2.
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
hfcut = 128.
# make design matrices
design_matrices = []
for x in xrange(2):
n_scans = data['func'][x].shape[-1]
timing = scipy.io.loadmat(data['trials_ses%i' % (x + 1)],
squeeze_me=True, struct_as_record=False)
faces_onsets = timing['onsets'][0].ravel()
scrambled_onsets = timing['onsets'][1].ravel()
onsets = np.hstack((faces_onsets, scrambled_onsets))
onsets *= tr # because onsets were reporting in 'scans' units
conditions = ['faces'] * len(faces_onsets) + ['scrambled'] * len(
scrambled_onsets)
paradigm = EventRelatedParadigm(conditions, onsets)
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
add_reg_names = None
add_regs = None
if reg_motion:
add_reg_names = ['tx', 'ty', 'tz', 'rx', 'ry', 'rz']
add_regs = np.loadtxt(data['realignment_parameters'][x])
if isinstance(add_regs):
add_regs = np.loadtxt(add_regs)
design_matrix = make_dmtx(
frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
add_reg_names=add_reg_names,
add_regs=add_regs
)
design_matrices.append(design_matrix)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# more interesting contrasts
contrasts['faces-scrambled'] = contrasts['faces'] - contrasts['scrambled']
contrasts['scrambled-faces'] = contrasts['scrambled'] - contrasts['faces']
contrasts['effects_of_interest'] = contrasts[
'faces'] + contrasts['scrambled']
# we've thesame contrasts over sessions, so let's replicate
contrasts = dict((contrast_id, [contrast_val] * 2)
for contrast_id, contrast_val in contrasts.iteritems())
# fit GLM
print('\r\nFitting a GLM (this takes time)...')
fmri_glm = FMRILinearModel([load_4D_img(sess_func)
for sess_func in data['func']],
[dmat.matrix for dmat in design_matrices],
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(data['output_dir'], "mask.nii.gz")
print "Saving mask image %s" % mask_path
nibabel.save(fmri_glm.mask, mask_path)
# compute bg unto which activation will be projected
anat_img = load_vol(data['anat'])
anat = anat_img.get_data()
if anat.ndim == 4:
anat = anat[..., 0]
anat_affine = anat_img.get_affine()
print "Computing contrasts .."
z_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, t_map, eff_map, var_map = fmri_glm.contrast(
contrast_val,
con_id=contrast_id,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True,
)
# store stat maps to disk
for dtype, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, eff_map, var_map]):
map_dir = os.path.join(
data['output_dir'], '%s_maps' % dtype)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s.nii.gz' % contrast_id)
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if dtype == 'z':
z_maps[contrast_id] = map_path
print "\t\t%s map: %s" % (dtype, map_path)
# do stats report
data['stats_report_filename'] = os.path.join(data['reports_output_dir'],
"report_stats.html")
contrasts = dict((contrast_id, contrasts[contrast_id])
for contrast_id in z_maps.keys())
generate_subject_stats_report(
data['stats_report_filename'],
contrasts,
z_maps,
fmri_glm.mask,
anat=anat,
anat_affine=anat_affine,
design_matrices=design_matrices,
subject_id=data['subject_id'],
cluster_th=15, # we're only interested in this 'large' clusters
start_time=stats_start_time,
# additional ``kwargs`` for more informative report
paradigm=paradigm.__dict__,
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
frametimes=frametimes,
drift_model=drift_model,
hrf_model=hrf_model,
)
ProgressReport().finish_dir(data['reports_output_dir'])
print "\r\nStatistic report written to %s\r\n" % data[
'stats_report_filename']
return data
_duration = 6
epoch_duration = _duration * tr
conditions = ['rest', 'active'] * 8
duration = epoch_duration * np.ones(len(conditions))
onset = np.linspace(0, (len(conditions) - 1) * epoch_duration, len(conditions))
paradigm = BlockParadigm(con_id=conditions, onset=onset, duration=duration)
hfcut = 2 * 2 * epoch_duration
# construct design matrix
nscans = len(subject_data.func[0])
frametimes = np.linspace(0, (nscans - 1) * tr, nscans)
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
design_matrix = make_dmtx(frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
hfcut=hfcut)
# plot and save design matrix
ax = design_matrix.show()
ax.set_position([.05, .25, .9, .65])
ax.set_title('Design matrix')
dmat_outfile = os.path.join(subject_data.output_dir, 'design_matrix.png')
pl.savefig(dmat_outfile, bbox_inches="tight", dpi=200)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
def make_designmat(ds,
eorig,
time_attr='time_coords',
condition_attr='targets',
design_kwargs=None,
regr_attrs=None):
# make glm regressors for all attributes. so loop through condition_attr and add them all...
import copy
from nipy.modalities.fmri.design_matrix import make_dmtx
import numpy as np
# Decide/device condition attribute on which GLM will actually be done
if isinstance(condition_attr, basestring):
# must be a list/tuple/array for the logic below
condition_attr = [condition_attr]
e = copy.deepcopy(eorig) # since we are modifying in place
glm_condition_attrs = []
for i, con in enumerate(condition_attr):
glm_condition_attr = 'regressors_' + str(con)
glm_condition_attrs.append(glm_condition_attr)
for ei in e:
if glm_condition_attr in ei:
raise ValueError(
"Event %s already has %s defined. Should not "
"happen. Choose another name if defined it" %
(ei, glm_condition_attr))
ei[glm_condition_attr] = \
'glm_label_' + str(con) + '_' + '+'.join(str(ei[c]) for c in [con])
evvars = events2dict(e)
add_paradigm_kwargs = {}
if 'amplitude' in evvars:
add_paradigm_kwargs['amplitude'] = evvars['amplitude']
if design_kwargs is None:
design_kwargs = {}
if regr_attrs is not None:
names = []
regrs = []
for attr in regr_attrs:
regr = ds.sa[attr].value
# add rudimentary dimension for easy hstacking later on
if regr.ndim < 2:
regr = regr[:, np.newaxis]
if regr.shape[1] == 1:
names.append(attr)
else:
# add one per each column of the regressor
for i in xrange(regr.shape[1]):
names.append("%s.%d" % (attr, i))
regrs.append(regr)
regrs = np.hstack(regrs)
if 'add_regs' in design_kwargs:
design_kwargs['add_regs'] = np.hstack(
(design_kwargs['add_regs'], regrs))
else:
design_kwargs['add_regs'] = regrs
if 'add_reg_names' in design_kwargs:
design_kwargs['add_reg_names'].extend(names)
else:
design_kwargs['add_reg_names'] = names
X = {}
for ci, con in enumerate(condition_attr):
# create paradigm
if 'duration' in evvars:
from nipy.modalities.fmri.experimental_paradigm import BlockParadigm
# NiPy considers everything with a duration as a block paradigm
paradigm = BlockParadigm(con_id=evvars[glm_condition_attrs[ci]],
onset=evvars['onset'],
duration=evvars['duration'],
**add_paradigm_kwargs)
else:
from nipy.modalities.fmri.experimental_paradigm \
import EventRelatedParadigm
paradigm = EventRelatedParadigm(
con_id=evvars[glm_condition_attrs[ci]],
onset=evvars['onset'],
**add_paradigm_kwargs)
X[con] = make_dmtx(ds.sa[time_attr].value,
paradigm=paradigm,
**design_kwargs)
for i, reg in enumerate(X[con].names):
ds.sa[reg] = X[con].matrix[:, i]
if con in ds.sa.keys():
ds.sa.pop(con)
for reg in ds.sa.keys():
if str(con) + '0' in reg:
ds.sa['glm_label_probe'] = ds.sa.pop(reg)
# concatenate X... add chunk regressors...
# if 'chunks' in ds.sa.keys():
# for i in ds.sa['chunks'].unique:
# ds.sa['glm_label_chunks' + str(i)] = np.array(ds.sa['chunks'].value == i, dtype=np.int)
return X, ds
def _preprocess_and_analysis_subject(subject_data,
slicer='z',
cut_coords=6,
threshold=3.,
cluster_th=15,
**preproc_params):
"""
Preprocesses the subject and then fits (mass-univariate) GLM thereup.
"""
# sanitize run_ids:
# Sub14/BOLD/Run_02/fMR09029-0004-00010-000010-01.nii is garbage,
# for example
run_ids = range(9)
if subject_data['subject_id'] == "Sub14":
run_ids = [0] + range(2, 9)
subject_data['func'] = [subject_data['func'][0]
] + subject_data['func'][2:]
subject_data['session_id'] = [subject_data['session_id'][0]
] + subject_data['session_id'][2:]
# sanitize subject output dir
if not 'output_dir' in subject_data:
subject_data['output_dir'] = os.path.join(output_dir,
subject_data['subject_id'])
# preprocess the data
subject_data = do_subject_preproc(subject_data, **preproc_params)
# chronometry
stats_start_time = pretty_time()
# to-be merged lists, one item per run
paradigms = []
frametimes_list = []
design_matrices = [] # one
list_of_contrast_dicts = [] # one dict per run
n_scans = []
for run_id in run_ids:
_n_scans = len(subject_data.func[run_id])
n_scans.append(_n_scans)
# make paradigm
paradigm = make_paradigm(getattr(subject_data, 'timing')[run_id])
# make design matrix
tr = 2.
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
hfcut = 128.
frametimes = np.linspace(0, (_n_scans - 1) * tr, _n_scans)
design_matrix = make_dmtx(
frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
hfcut=hfcut,
add_regs=np.loadtxt(
getattr(subject_data, 'realignment_parameters')[run_id]),
add_reg_names=[
'Translation along x axis', 'Translation along yaxis',
'Translation along z axis', 'Rotation along x axis',
'Rotation along y axis', 'Rotation along z axis'
])
# import matplotlib.pyplot as plt
# design_matrix.show()
# plt.show()
paradigms.append(paradigm)
design_matrices.append(design_matrix)
frametimes_list.append(frametimes)
n_scans.append(_n_scans)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' %
design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# more interesting contrasts"""
contrasts['Famous-Unfamiliar'] = contrasts['Famous'] - contrasts[
'Unfamiliar']
contrasts['Unfamiliar-Famous'] = -contrasts['Famous-Unfamiliar']
contrasts[
'Famous-Scrambled'] = contrasts['Famous'] - contrasts['Scrambled']
contrasts['Scrambled-Famous'] = -contrasts['Famous-Scrambled']
contrasts['Unfamiliar-Scrambled'] = contrasts[
'Unfamiliar'] - contrasts['Scrambled']
contrasts['Scrambled-Unfamiliar'] = -contrasts['Unfamiliar-Scrambled']
list_of_contrast_dicts.append(contrasts)
# importat maps
z_maps = {}
effects_maps = {}
# fit GLM
print('\r\nFitting a GLM (this takes time) ..')
fmri_glm = FMRILinearModel(
[nibabel.concat_images(sess_func) for sess_func in subject_data.func],
[design_matrix.matrix for design_matrix in design_matrices],
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
print "... done.\r\n"
# save computed mask
mask_path = os.path.join(subject_data.output_dir, "mask.nii.gz")
print "Saving mask image to %s ..." % mask_path
nibabel.save(fmri_glm.mask, mask_path)
print "... done.\r\n"
# replicate contrasts across runs
contrasts = dict(
(cid, [contrasts[cid] for contrasts in list_of_contrast_dicts])
for cid, cval in contrasts.iteritems())
# compute effects
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, eff_map = fmri_glm.contrast(contrast_val,
con_id=contrast_id,
output_z=True,
output_stat=False,
output_effects=True,
output_variance=False)
# store stat maps to disk
for map_type, out_map in zip(['z', 'effects'], [z_map, eff_map]):
map_dir = os.path.join(subject_data.output_dir,
'%s_maps' % map_type)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(map_dir, '%s.nii.gz' % contrast_id)
print "\t\tWriting %s ..." % map_path
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if map_type == 'z':
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
# remove repeated contrasts
contrasts = dict((cid, cval[0]) for cid, cval in contrasts.iteritems())
# do stats report
stats_report_filename = os.path.join(
getattr(subject_data, 'reports_output_dir', subject_data.output_dir),
"report_stats.html")
generate_subject_stats_report(
stats_report_filename,
contrasts,
z_maps,
fmri_glm.mask,
threshold=threshold,
cluster_th=cluster_th,
slicer=slicer,
cut_coords=cut_coords,
design_matrices=design_matrices,
subject_id=subject_data.subject_id,
start_time=stats_start_time,
title="GLM for subject %s" % subject_data.subject_id,
# additional ``kwargs`` for more informative report
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
drift_model=drift_model,
hrf_model=hrf_model,
paradigm=dict(("Run_%02i" % (run_id + 1), paradigms[run_id])
for run_id in run_ids),
frametimes=dict(("Run_%02i" % (run_id + 1), frametimes_list[run_id])
for run_id in run_ids),
# fwhm=fwhm
)
ProgressReport().finish_dir(subject_data.output_dir)
print "\r\nStatistic report written to %s\r\n" % stats_report_filename
return contrasts, effects_maps, z_maps, mask_path
def first_level(subject_dic):
# experimental paradigm meta-params
stats_start_time = time.ctime()
tr = 2.4
drift_model = 'blank'
hrf_model = 'canonical' # hemodynamic reponse function
hfcut = 128.
n_scans = 128
# make design matrices
mask_images = []
design_matrices = []
fmri_files = subject_dic['func']
for x in xrange(len(fmri_files)):
paradigm = paradigm_contrasts.localizer_paradigm()
# build design matrix
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
design_matrix = make_dmtx(
frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
hfcut=hfcut,
)
design_matrices.append(design_matrix)
# Specify contrasts
contrasts = paradigm_contrasts.localizer_contrasts(design_matrix)
#create output directory
subject_session_output_dir = os.path.join(subject_dic['output_dir'],
'res_stats')
if not os.path.exists(subject_session_output_dir):
os.makedirs(subject_session_output_dir)
# Fit GLM
print 'Fitting a GLM (this takes time)...'
fmri_glm = FMRILinearModel(
fmri_files,
[design_matrix.matrix for design_matrix in design_matrices],
mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(subject_session_output_dir, "mask.nii.gz")
print "Saving mask image %s" % mask_path
nibabel.save(fmri_glm.mask, mask_path)
mask_images.append(mask_path)
# compute contrasts
z_maps = {}
effects_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, t_map, effects_map, var_map = fmri_glm.contrast(
[contrast_val] * 1,
con_id=contrast_id,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True)
# store stat maps to disk
for map_type, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, effects_map, var_map]):
map_dir = os.path.join(subject_session_output_dir,
'%s_maps' % map_type)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir,
'%s%s.nii.gz' % (subject_dic['subject_id'], contrast_id))
print "\t\tWriting %s ..." % map_path
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if map_type == 'z':
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
# do stats report
anat_img = nibabel.load(subject_dic['anat'])
stats_report_filename = os.path.join(subject_session_output_dir,
"report_stats.html")
generate_subject_stats_report(
stats_report_filename,
contrasts,
z_maps,
fmri_glm.mask,
threshold=2.3,
cluster_th=15,
anat=anat_img.get_data(),
anat_affine=anat_img.get_affine(),
design_matrices=design_matrix,
subject_id="sub001",
start_time=stats_start_time,
title="GLM for subject %s" % subject_dic['session_id'],
# additional ``kwargs`` for more informative report
paradigm=paradigm.__dict__,
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
frametimes=frametimes,
drift_model=drift_model,
hrf_model=hrf_model,
)
ProgressReport().finish_dir(subject_session_output_dir)
print "Statistic report written to %s\r\n" % stats_report_filename
return z_maps
fmri_series = [
os.path.join(fmri_dir, '%s_series_%s_lh_smooth5.gii' %
(subject, session)) for session in sessions]
elif side == 'right':
fmri_series = [
os.path.join(fmri_dir, '%s_series_%s_rh_smooth5.gii' %
(subject, session)) for session in sessions]
# compute the mask
if side == False:
mean_img = glob.glob(os.path.join(fmri_dir, 'mean*.nii'))[0]
mask_array = compute_mask_files(mean_img, epi_mask, True,
inf_threshold, sup_threshold)[0]
# get the contrasts
n_reg = make_dmtx(frametimes, add_regs=reg_matrix,
drift_model=drift_model, hfcut=hfcut).matrix.shape[1]
contrasts, all_reg = make_contrasts(sessions, n_reg)
contrast_obj = {}
for (sess, (session, fmri_data)) in enumerate(zip(
sessions, fmri_series)):
# create design matrices
reg = all_reg[2 * sess: 2 * sess + 2] # fixme
design_matrix = make_dmtx(
frametimes, add_regs=reg_matrix, add_reg_names=reg,
drift_model=drift_model, hfcut=hfcut)
# plot the design matrix
ax = design_matrix.show()
ax.set_position([.05, .25, .9, .65])
def first_level(subject_dic):
# experimental paradigm meta-params
stats_start_time = time.ctime()
tr = 2.4
drift_model = 'blank'
hrf_model = 'canonical' # hemodynamic reponse function
hfcut = 128.
n_scans = 128
# make design matrices
mask_images = []
design_matrices = []
fmri_files = subject_dic['func']
for x in xrange(len(fmri_files)):
paradigm = paradigm_contrasts.localizer_paradigm()
# build design matrix
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
design_matrix = make_dmtx(
frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
)
design_matrices.append(design_matrix)
# Specify contrasts
contrasts = paradigm_contrasts.localizer_contrasts(design_matrix)
#create output directory
subject_session_output_dir = os.path.join(subject_dic['output_dir'],
'res_stats')
if not os.path.exists(subject_session_output_dir):
os.makedirs(subject_session_output_dir)
# Fit GLM
print 'Fitting a GLM (this takes time)...'
fmri_glm = FMRILinearModel(fmri_files,
[design_matrix.matrix
for design_matrix in design_matrices],
mask='compute'
)
fmri_glm.fit(do_scaling=True, model='ar1')
# save computed mask
mask_path = os.path.join(subject_session_output_dir,
"mask.nii.gz")
print "Saving mask image %s" % mask_path
nibabel.save(fmri_glm.mask, mask_path)
mask_images.append(mask_path)
# compute contrasts
z_maps = {}
effects_maps = {}
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, t_map, effects_map, var_map = fmri_glm.contrast(
[contrast_val] * 1,
con_id=contrast_id,
output_z=True,
output_stat=True,
output_effects=True,
output_variance=True
)
# store stat maps to disk
for map_type, out_map in zip(['z', 't', 'effects', 'variance'],
[z_map, t_map, effects_map, var_map]):
map_dir = os.path.join(
subject_session_output_dir, '%s_maps' % map_type)
if not os.path.exists(map_dir):
os.makedirs(map_dir)
map_path = os.path.join(
map_dir, '%s%s.nii.gz' %(subject_dic['subject_id'], contrast_id))
print "\t\tWriting %s ..." % map_path
nibabel.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if map_type == 'z':
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
# do stats report
anat_img = nibabel.load(subject_dic['anat'])
stats_report_filename = os.path.join(subject_session_output_dir,
"report_stats.html")
generate_subject_stats_report(
stats_report_filename,
contrasts,
z_maps,
fmri_glm.mask,
threshold=2.3,
cluster_th=15,
anat=anat_img,
anat_affine=anat_img.get_affine(),
design_matrices=design_matrix,
subject_id="sub001",
start_time=stats_start_time,
title="GLM for subject %s" % subject_dic['session_id'],
# additional ``kwargs`` for more informative report
paradigm=paradigm.__dict__,
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
frametimes=frametimes,
drift_model=drift_model,
hrf_model=hrf_model,
)
ProgressReport().finish_dir(subject_session_output_dir)
print "Statistic report written to %s\r\n" % stats_report_filename
return z_maps
def glm_nipy(fmri_data,
contrasts=None,
hrf_model='Canonical',
drift_model='Cosine',
hfcut=128,
residuals_model='spherical',
fit_method='ols',
fir_delays=[0],
rescale_results=False,
rescale_factor=None):
"""
Perform a GLM analysis on fMRI data using the implementation of Nipy.
Args:
fmri_data (pyhrf.core.FmriData): the input fMRI data defining the
paradigm and the measured 3D+time signal.
contrasts (dict): keys are contrast labels and values are arithmetic
expressions involving regressor names. Valid names are:
* names of experimental conditions as defined in fmri_data
* constant
hrf_model: "Canonical", "Canonical with Derivative", "FIR"
residuals_model: "spherical", "ar1"
fit_method: "ols", "kalman" (If residuals_model is "ar1" then method
is set to "kalman" and this argument is ignored)
fir_delays: list of integers indicating the delay of each FIR coefficient
(in terms of scans). Eg if TR = 2s. and we want a FIR
duration of 20s.: fir_delays=range(10)
Returns:
(glm instance, design matrix, dict of contrasts of objects)
Examples:
>>> from pyhrf.core import FmriData
>>> from pyhrf.glm import glm_nipy
>>> g,dmtx,con = glm_nipy(FmriData.from_vol_ui())
>>> g,dmtx,con = glm_nipy(FmriData.from_vol_ui(), \
contrasts={'A-V':'audio-video'})
"""
paradigm = fmri_data.paradigm.to_nipy_paradigm()
# BOLD data
Y = fmri_data.bold.T
n_scans = Y.shape[1]
# Design matrix
frametimes = np.linspace(0, (n_scans - 1) * fmri_data.tr, n_scans)
design_matrix = dm.make_dmtx(frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
hfcut=hfcut,
fir_delays=fir_delays)
ns, nr = design_matrix.matrix.shape
logger.info('Design matrix built with %d regressors:', nr)
for rn in design_matrix.names:
logger.info(' - %s', rn)
# GLM fit
my_glm = glm.glm()
logger.info('Fit GLM - method: %s, residual model: %s', fit_method,
residuals_model)
my_glm.fit(Y.T,
design_matrix.matrix,
method=fit_method,
model=residuals_model)
from pyhrf.tools import map_dict
from pyhrf.paradigm import contrasts_to_spm_vec
if rescale_results:
if 1:
if rescale_results and rescale_factor is None:
# Rescale by the norm of each regressor in the design matrix
dm_reg_norms = (design_matrix.matrix**2).sum(0)**.5
logger.info(
'GLM results (beta and con effects) are '
'rescaled by reg norm. Weights: %s ', str(dm_reg_norms))
for ib in xrange(my_glm.beta.shape[0]):
my_glm.beta[ib] = my_glm.beta[ib] * dm_reg_norms[ib]
else:
logger.info('GLM results (beta and con effects) are '
'rescaled by input scale factor.')
# Use input rescale factors:
for ib in xrange(rescale_factor.shape[0]):
my_glm.beta[ib] = my_glm.beta[ib] * rescale_factor[ib]
# TOCHECK: nvbeta seems to be a covar matrix between reg
# -> we dont get position-specific variances ...
#my_glm.nvbeta[ib,:] = my_glm.nvbeta[ib,:] * rescale_factor[ib]**2
if contrasts is not None:
con_vectors = contrasts_to_spm_vec(design_matrix.names, contrasts)
# if rescale_results:
# for con_vec in con_vectors.itervalues():
# con_vec *= dm_reg_norms
contrast_result = map_dict(my_glm.contrast, con_vectors)
else:
contrast_result = None
return my_glm, design_matrix, contrast_result
# actually: not possible to compute PPM from glm results
# Should relaunch estimation with propoer model under SPM
# def PPMcalculus_glmWN(beta, var_beta, dm, threshold_value):
'''
img = nb.load(smooth_file)
#-----------------------------------------------------------------
# Construct a design matrix for each test
#-----------------------------------------------------------------
print(' Make design matrix...')
print(' Conditions:\n {}'.format(conditions))
print(' Amplitudes:\n {}'.format(amplitudes))
print(' Onsets:\n {}'.format(onsets))
print(' Durations:\n {}'.format(durations))
paradigm = BlockParadigm(con_id=conditions, onset=onsets,
duration=durations, amplitude=amplitudes)
frametimes = np.linspace(0, n_images-1, n_images)
if ntest < 3:
dmtx = make_dmtx(frametimes, paradigm, hrf_model='FIR',
drift_model='polynomial', drift_order=2, hfcut=np.inf)
else:
dmtx = make_dmtx(frametimes, paradigm, hrf_model='FIR', hfcut=np.inf)
design_matrix = dmtx.matrix
# Plot the design matrix
if plot_design_matrix:
fig1 = mp.figure(figsize=(10, 6))
dmtx.show()
mp.title(desc)
fig1_file = os.path.join(out_path, label + 'design_matrix_test' + \
str(ntest) + '.png')
mp.savefig(fig1_file)
#-----------------------------------------------------------------
# Mean-scale, de-mean and multiply data by 100
def glm_nipy(fmri_data, contrasts=None, hrf_model='Canonical',
drift_model='Cosine', hfcut=128,
residuals_model='spherical', fit_method='ols',
fir_delays=[0],
rescale_results=False, rescale_factor=None):
"""
Perform a GLM analysis on fMRI data using the implementation of Nipy.
Args:
fmri_data (pyhrf.core.FmriData): the input fMRI data defining the
paradigm and the measured 3D+time signal.
contrasts (dict): keys are contrast labels and values are arithmetic
expressions involving regressor names. Valid names are:
* names of experimental conditions as defined in fmri_data
* constant
hrf_model: "Canonical", "Canonical with Derivative", "FIR"
residuals_model: "spherical", "ar1"
fit_method: "ols", "kalman" (If residuals_model is "ar1" then method
is set to "kalman" and this argument is ignored)
fir_delays: list of integers indicating the delay of each FIR coefficient
(in terms of scans). Eg if TR = 2s. and we want a FIR
duration of 20s.: fir_delays=range(10)
Returns:
(glm instance, design matrix, dict of contrasts of objects)
Examples:
>>> from pyhrf.core import FmriData
>>> from pyhrf.glm import glm_nipy
>>> g,dmtx,con = glm_nipy(FmriData.from_vol_ui())
>>> g,dmtx,con = glm_nipy(FmriData.from_vol_ui(), \
contrasts={'A-V':'audio-video'})
"""
paradigm = fmri_data.paradigm.to_nipy_paradigm()
# BOLD data
Y = fmri_data.bold.T
n_scans = Y.shape[1]
# Design matrix
frametimes = np.linspace(0, (n_scans - 1) * fmri_data.tr, n_scans)
design_matrix = dm.make_dmtx(frametimes, paradigm,
hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
fir_delays=fir_delays)
ns, nr = design_matrix.matrix.shape
logger.info('Design matrix built with %d regressors:', nr)
for rn in design_matrix.names:
logger.info(' - %s', rn)
# GLM fit
my_glm = glm.glm()
logger.info('Fit GLM - method: %s, residual model: %s', fit_method,
residuals_model)
my_glm.fit(Y.T, design_matrix.matrix, method=fit_method,
model=residuals_model)
from pyhrf.tools import map_dict
from pyhrf.paradigm import contrasts_to_spm_vec
if rescale_results:
if 1:
if rescale_results and rescale_factor is None:
# Rescale by the norm of each regressor in the design matrix
dm_reg_norms = (design_matrix.matrix ** 2).sum(0) ** .5
logger.info('GLM results (beta and con effects) are '
'rescaled by reg norm. Weights: %s ',
str(dm_reg_norms))
for ib in xrange(my_glm.beta.shape[0]):
my_glm.beta[ib] = my_glm.beta[ib] * dm_reg_norms[ib]
else:
logger.info('GLM results (beta and con effects) are '
'rescaled by input scale factor.')
# Use input rescale factors:
for ib in xrange(rescale_factor.shape[0]):
my_glm.beta[ib] = my_glm.beta[ib] * rescale_factor[ib]
# TOCHECK: nvbeta seems to be a covar matrix between reg
# -> we dont get position-specific variances ...
#my_glm.nvbeta[ib,:] = my_glm.nvbeta[ib,:] * rescale_factor[ib]**2
if contrasts is not None:
con_vectors = contrasts_to_spm_vec(design_matrix.names, contrasts)
# if rescale_results:
# for con_vec in con_vectors.itervalues():
# con_vec *= dm_reg_norms
contrast_result = map_dict(my_glm.contrast, con_vectors)
else:
contrast_result = None
return my_glm, design_matrix, contrast_result
# actually: not possible to compute PPM from glm results
# Should relaunch estimation with propoer model under SPM
# def PPMcalculus_glmWN(beta, var_beta, dm, threshold_value):
'''
def runsub(sub, thisContrast, thisContrastStr,
filterLen, filterOrd,
paramEst, chunklen, alphas=np.logspace(0, 3, 20), debug=False, write=False, roi='grayMatter'):
thisSub = {sub: subList[sub]}
mc_params = lmvpa.loadmotionparams(paths, thisSub)
beta_events = lmvpa.loadevents(paths, thisSub)
dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi, c='trial_type')
thisDS = dsdict[sub]
# savitsky golay filtering
sg.sg_filter(thisDS, filterLen, filterOrd)
# gallant group zscores before regression.
# zscore w.r.t. rest trials
# zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
# zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
zscore(thisDS, chunks_attr='chunks')
# kay method: leave out a model run, use it to fit an HRF for each voxel
# huth method: essentially use FIR
# mumford method: deconvolution with canonical HRF
# refit events and regress...
# get timing data from timing files
# rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub])
rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub], contrasts) # adding features
# we can model out motion and just not use those betas.
# Ridge
if isinstance(thisContrast, basestring):
thisContrast = [thisContrast]
# instead of binarizing each one, make them parametric
desX, rds = lmvpa.make_designmat(rds, events, time_attr='time_coords', condition_attr=thisContrast,
design_kwargs={'hrf_model': 'canonical', 'drift_model': 'blank'},
regr_attrs=None)
# want to collapse ap and cr, but have anim separate
desX['motion'] = make_dmtx(rds.sa['time_coords'].value, paradigm=None, add_regs=mc_params[sub], drift_model='blank')
des = lmvpa.make_parammat(desX, hrf='canonical', zscore=True)
# set chunklen and nchunks
# split by language and pictures
lidx = thisDS.chunks < thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
pidx = thisDS.chunks >= thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
ldes = cp.copy(des)
pdes = cp.copy(des)
ldes.matrix = ldes.matrix[lidx]
pdes.matrix = pdes.matrix[pidx]
nchunks = int(len(thisDS)*paramEst / chunklen)
nboots=50
covarmat = None
mus = None
lwts, lalphas, lres, lceil = bsr.bootstrap_ridge(rds[lidx], ldes, chunklen=chunklen, nchunks=nchunks,
cov0=covarmat, mu0=mus, part_attr='chunks', mode='test',
alphas=alphas, single_alpha=True, normalpha=False,
nboots=nboots, corrmin=.2, singcutoff=1e-10, joined=None,
plot=debug, use_corr=True)
pwts, palphas, pres, pceil = bsr.bootstrap_ridge(rds[pidx], pdes, chunklen=chunklen, nchunks=nchunks,
part_attr='chunks', mode='test',
alphas=alphas, single_alpha=True, normalpha=False,
nboots=nboots, corrmin=.2, singcutoff=1e-10, joined=None,
plot=debug, use_corr=True)
print 'language ' + str(np.mean(lres))
# pictures within
print 'pictures: ' + str(np.mean(pres))
# need to change outstring
if write:
from mvpa2.base import dataset
map2nifti(thisDS, dataset.vstack([lres, pres])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_corrs.nii.gz'))
map2nifti(thisDS, dataset.vstack([lwts, pwts])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_weights.nii.gz'))
map2nifti(thisDS, dataset.vstack([lalphas, palphas])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_alphas.nii.gz'))
map2nifti(thisDS, dataset.vstack([lceil, pceil])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_ceiling.nii.gz'))
del lres, pres, lwts, pwts, lalphas, palphas, lceil, pceil
crossSet = thisDS.copy()
crossSet.chunks[lidx] = 1
crossSet.chunks[pidx] = 2
cwts, calphas, cres, cceil = bsr.bootstrap_ridge(crossSet, des, chunklen=chunklen, nchunks=nchunks,
part_attr='chunks', mode='test',
alphas=alphas, single_alpha=True, normalpha=False,
nboots=nboots, corrmin=.2, singcutoff=1e-10, joined=None,
use_corr=True)
print 'cross: ' + str(np.mean(cres))
if write:
map2nifti(thisDS, cres[0]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_ridge_corr.nii.gz'))
map2nifti(thisDS, cres[1]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_ridge_corr.nii.gz'))
map2nifti(thisDS, cwts[0]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_ridge_weights.nii.gz'))
map2nifti(thisDS, cwts[1]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_ridge_weights.nii.gz'))
map2nifti(thisDS, calphas[calphas.chunks==1]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_ridge_alphas.nii.gz'))
map2nifti(thisDS, calphas[calphas.chunks==2]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_ridge_alphas.nii.gz'))
map2nifti(thisDS, cceil[0]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_ridge_ceiling.nii.gz'))
map2nifti(thisDS, cceil[1]).to_filename(
os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_ridge_ceiling.nii.gz'))
del cres, cwts, calphas, cceil
empty_conditions.append(c)
elif len(conditions[c]) < 2:
pseudo_empty_conditions.append(c)
condition += [c]*len(conditions[c])
onset = np.hstack([onset, conditions[c]])
duration += [durations[c]]*len(conditions[c])
paradigm = BlockParadigm(con_id=condition,
onset=onset,
duration=duration)
frametimes = np.linspace(0, (N_SCANS-1)*TR/1000., num=N_SCANS)
design_mat = design_matrix.make_dmtx(frametimes, paradigm,
hrf_model='Canonical with derivative',
add_regs=regressors,
drift_model='Cosine',
hfcut=128)
# Fill empty conditions
for c in empty_conditions:
if c == 'anticip_missed_largewin':
ind = 6
elif c == 'feedback_missed_largewin':
ind = 18
elif c == 'anticip_missed_smallwin':
ind = 10
elif c == 'feedback_missed_smallwin':
ind = 20
elif c == 'anticip_missed_nowin':
def fit_event_hrf_model(ds,
events,
time_attr,
condition_attr='targets',
design_kwargs=None,
glmfit_kwargs=None,
regr_attrs=None,
return_model=False):
"""Fit a GLM with HRF regressor and yield a dataset with model parameters
A univariate GLM is fitted for each feature and model parameters are
returned as samples. Model parameters are returned for each regressor in
the design matrix. Using functionality from NiPy, design matrices can be
generated from event definitions with a variety of customizations (HRF
model, confound regressors, ...).
Events need to be specified as a list of dictionaries
(see:class:`~mvpa2.misc.support.Event`) for a helper class. Each dictionary
contains all relevant attributes to describe an event.
HRF event model details
-----------------------
The event specifications are used to generate a design matrix for all
present conditions. In addition to the mandatory ``onset`` information
each event definition needs to include a label in order to associate
individual events to conditions (the design matrix will contain at least
one regressor for each condition). The name of this label attribute must
be specified too (see ``condition_attr`` argument).
NiPy is used to generate the actual design matrix. It is required to
specify a dataset sample attribute that contains time stamps for all input
data samples (see ``time_attr``). NiPy operation could be customized (see
``design_kwargs`` argument). Additional regressors from sample attributes
of the input dataset can be included in the design matrix (see
``regr_attrs``).
The actual GLM fit is also performed by NiPy and can be fully customized
(see ``glmfit_kwargs``).
Parameters
----------
ds : Dataset
The samples of this input dataset have to be in whatever ascending order.
events : list
Each event definition has to specify ``onset`` and ``duration``. All
other attributes will be passed on to the sample attributes collection of
the returned dataset.
time_attr : str
Attribute with dataset sample time stamps.
Its values will be treated as in-the-same-unit and are used to
determine corresponding samples from real-value onset and duration
definitions. For HRF modeling this argument is mandatory.
condition_attr : str
Name of the event attribute with the condition labels.
Can be a list of those (e.g. ['targets', 'chunks'] combination of which
would constitute a condition.
design_kwargs : dict
Arbitrary keyword arguments for NiPy's make_dmtx() used for design matrix
generation. Choose HRF model, confound regressors, etc.
glmfit_kwargs : dict
Arbitrary keyword arguments for NiPy's GeneralLinearModel.fit() used for
estimating model parameter. Choose fitting algorithm: OLS or AR1.
regr_attrs : list
List of dataset sample attribute names that shall be extracted from the
input dataset and used as additional regressors in the design matrix.
return_model : bool
Flag whether to included the fitted GLM model in the returned dataset.
For large input data this can be problematic, as the model may contain
the residuals (same size is input data), hence multiplies the memory
demand. Off by default.
Returns
-------
Dataset
One sample for each regressor/condition in the design matrix is returned.
The condition names are included as a sample attribute with the name
specified by the ``condition_attr`` argument. The actual design
regressors are included as ``regressors`` sample attribute. If enabled,
an instance with the fitted NiPy GLM results is included as a dataset
attribute ``model``, and can be used for computing contrasts subsequently.
Examples
--------
The documentation also contains an :ref:`example script
<example_eventrelated>` showing a spatio-temporal analysis of fMRI data
that involves this function.
>>> from mvpa2.datasets import Dataset
>>> ds = Dataset(np.random.randn(10, 25))
>>> ds.sa['time_coords'] = np.linspace(0, 50, len(ds))
>>> events = [{'onset': 2, 'duration': 4, 'condition': 'one'},
... {'onset': 4, 'duration': 4, 'condition': 'two'}]
>>> hrf_estimates = fit_event_hrf_model(
... ds, events,
... time_attr='time_coords',
... condition_attr='condition',
... design_kwargs=dict(drift_model='blank'),
... glmfit_kwargs=dict(model='ols'),
... return_model=True)
>>> print hrf_estimates.sa.condition
['one' 'two']
>>> print hrf_estimates.shape
(2, 25)
>>> len(hrf_estimates.a.model.get_mse())
25
Additional regressors used in GLM modeling are also available in a
dataset attribute:
>>> print hrf_estimates.a.add_regs.sa.regressor_names
['constant']
"""
if externals.exists('nipy', raise_=True):
from nipy.modalities.fmri.design_matrix import make_dmtx
from mvpa2.mappers.glm import NiPyGLMMapper
# Decide/device condition attribute on which GLM will actually be done
if isinstance(condition_attr, str):
# must be a list/tuple/array for the logic below
condition_attr = [condition_attr]
glm_condition_attr = 'regressor_names' # actual regressors
glm_condition_attr_map = dict([(con, dict()) for con in condition_attr]) #
# to map back to original conditions
events = copy.deepcopy(events) # since we are modifying in place
for event in events:
if glm_condition_attr in event:
raise ValueError("Event %s already has %s defined. Should not "
"happen. Choose another name if defined it" %
(event, glm_condition_attr))
compound_label = event[glm_condition_attr] = \
'glm_label_' + '+'.join(
str(event[con]) for con in condition_attr)
# and mapping back to original values, without str()
# for each condition:
for con in condition_attr:
glm_condition_attr_map[con][compound_label] = event[con]
evvars = _events2dict(events)
add_paradigm_kwargs = {}
if 'amplitude' in evvars:
add_paradigm_kwargs['amplitude'] = evvars['amplitude']
# create paradigm
if 'duration' in evvars:
from nipy.modalities.fmri.experimental_paradigm import BlockParadigm
# NiPy considers everything with a duration as a block paradigm
paradigm = BlockParadigm(con_id=evvars[glm_condition_attr],
onset=evvars['onset'],
duration=evvars['duration'],
**add_paradigm_kwargs)
else:
from nipy.modalities.fmri.experimental_paradigm \
import EventRelatedParadigm
paradigm = EventRelatedParadigm(con_id=evvars[glm_condition_attr],
onset=evvars['onset'],
**add_paradigm_kwargs)
# create design matrix -- all kinds of fancy additional regr can be
# auto-generated
if design_kwargs is None:
design_kwargs = {}
if regr_attrs is not None:
names = []
regrs = []
for attr in regr_attrs:
regr = ds.sa[attr].value
# add rudimentary dimension for easy hstacking later on
if regr.ndim < 2:
regr = regr[:, np.newaxis]
if regr.shape[1] == 1:
names.append(attr)
else:
# add one per each column of the regressor
for i in range(regr.shape[1]):
names.append("%s.%d" % (attr, i))
regrs.append(regr)
regrs = np.hstack(regrs)
if 'add_regs' in design_kwargs:
design_kwargs['add_regs'] = np.hstack(
(design_kwargs['add_regs'], regrs))
else:
design_kwargs['add_regs'] = regrs
if 'add_reg_names' in design_kwargs:
design_kwargs['add_reg_names'].extend(names)
else:
design_kwargs['add_reg_names'] = names
design_matrix = make_dmtx(ds.sa[time_attr].value, paradigm,
**design_kwargs)
# push design into source dataset
glm_regs = [(reg, design_matrix.matrix[:, i])
for i, reg in enumerate(design_matrix.names)]
# GLM
glm = NiPyGLMMapper([],
glmfit_kwargs=glmfit_kwargs,
add_regs=glm_regs,
return_design=True,
return_model=return_model,
space=glm_condition_attr)
model_params = glm(ds)
# some regressors might be corresponding not to original condition_attr
# so let's separate them out
regressor_names = model_params.sa[glm_condition_attr].value
condition_regressors = np.array([
v in list(glm_condition_attr_map.values())[0] for v in regressor_names
])
assert (condition_regressors.dtype == np.bool)
if not np.all(condition_regressors):
# some regressors do not correspond to conditions and would need
# to be taken into a separate dataset
model_params.a['add_regs'] = model_params[~condition_regressors]
# then we process the rest
model_params = model_params[condition_regressors]
regressor_names = model_params.sa[glm_condition_attr].value
# now define proper condition sa's
for con, con_map in glm_condition_attr_map.items():
model_params.sa[con] = [con_map[v] for v in regressor_names]
model_params.sa.pop(glm_condition_attr) # remove generated one
return model_params
def _fit_hrf_event_model(
ds, events, time_attr, condition_attr="targets", design_kwargs=None, glmfit_kwargs=None, regr_attrs=None
):
if externals.exists("nipy", raise_=True):
from nipy.modalities.fmri.design_matrix import make_dmtx
from mvpa2.mappers.glm import NiPyGLMMapper
# Decide/device condition attribute on which GLM will actually be done
if isinstance(condition_attr, basestring):
# must be a list/tuple/array for the logic below
condition_attr = [condition_attr]
glm_condition_attr = "regressor_names" # actual regressors
glm_condition_attr_map = dict([(con, dict()) for con in condition_attr]) #
# to map back to original conditions
events = copy.deepcopy(events) # since we are modifying in place
for event in events:
if glm_condition_attr in event:
raise ValueError(
"Event %s already has %s defined. Should not "
"happen. Choose another name if defined it" % (event, glm_condition_attr)
)
compound_label = event[glm_condition_attr] = "glm_label_" + "+".join(str(event[con]) for con in condition_attr)
# and mapping back to original values, without str()
# for each condition:
for con in condition_attr:
glm_condition_attr_map[con][compound_label] = event[con]
evvars = _events2dict(events)
add_paradigm_kwargs = {}
if "amplitude" in evvars:
add_paradigm_kwargs["amplitude"] = evvars["amplitude"]
# create paradigm
if "duration" in evvars:
from nipy.modalities.fmri.experimental_paradigm import BlockParadigm
# NiPy considers everything with a duration as a block paradigm
paradigm = BlockParadigm(
con_id=evvars[glm_condition_attr], onset=evvars["onset"], duration=evvars["duration"], **add_paradigm_kwargs
)
else:
from nipy.modalities.fmri.experimental_paradigm import EventRelatedParadigm
paradigm = EventRelatedParadigm(con_id=evvars[glm_condition_attr], onset=evvars["onset"], **add_paradigm_kwargs)
# create design matrix -- all kinds of fancy additional regr can be
# auto-generated
if design_kwargs is None:
design_kwargs = {}
if not regr_attrs is None:
names = []
regrs = []
for attr in regr_attrs:
names.append(attr)
regrs.append(ds.sa[attr].value)
if len(regrs) < 2:
regrs = [regrs]
regrs = np.hstack(regrs).T
if "add_regs" in design_kwargs:
design_kwargs["add_regs"] = np.hstack((design_kwargs["add_regs"], regrs))
else:
design_kwargs["add_regs"] = regrs
if "add_reg_names" in design_kwargs:
design_kwargs["add_reg_names"].extend(names)
else:
design_kwargs["add_reg_names"] = names
design_matrix = make_dmtx(ds.sa[time_attr].value, paradigm, **design_kwargs)
# push design into source dataset
glm_regs = [(reg, design_matrix.matrix[:, i]) for i, reg in enumerate(design_matrix.names)]
# GLM
glm = NiPyGLMMapper(
[],
glmfit_kwargs=glmfit_kwargs,
add_regs=glm_regs,
return_design=True,
return_model=True,
space=glm_condition_attr,
)
model_params = glm(ds)
# some regressors might be corresponding not to original condition_attr
# so let's separate them out
regressor_names = model_params.sa[glm_condition_attr].value
condition_regressors = np.array([v in glm_condition_attr_map.values()[0] for v in regressor_names])
assert condition_regressors.dtype == np.bool
if not np.all(condition_regressors):
# some regressors do not correspond to conditions and would need
# to be taken into a separate dataset
model_params.a["add_regs"] = model_params[~condition_regressors]
# then we process the rest
model_params = model_params[condition_regressors]
regressor_names = model_params.sa[glm_condition_attr].value
# now define proper condition sa's
for con, con_map in glm_condition_attr_map.iteritems():
model_params.sa[con] = [con_map[v] for v in regressor_names]
model_params.sa.pop(glm_condition_attr) # remove generated one
return model_params
def preprocess_files(self, func_files, anat_files=None, verbose=1):
def get_beta_filepath(func_file, cond):
return func_file.replace('_bold.nii.gz', '_beta-%s.nii.gz' % cond)
beta_files = []
for fi, func_file in enumerate(func_files):
# Don't re-do preprocessing.
beta_mask = func_file.replace('_bold.nii.gz', '_beta*.nii.gz')
cond_file = func_file.replace('_bold.nii.gz', '_events.tsv')
cond_data = pd.read_csv(cond_file, sep='\t')
# Get condition info, to search if betas have been done.
conditions = cond_data['trial_type'].tolist()
all_conds = np.unique(conditions)
all_beta_files = [
get_beta_filepath(func_file, cond) for cond in all_conds
]
# All betas are done.
if np.all([os.path.exists(f) for f in all_beta_files]):
beta_files += all_beta_files
continue
if verbose >= 0:
print('Preprocessing file %d of %d' %
(fi + 1, len(func_files)))
# Need to do regression.
tr = cond_data['duration'].as_matrix().mean()
onsets = cond_data['onset'].tolist()
img = nibabel.load(func_file)
n_scans = img.shape[3]
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
# Create the design matrix
paradigm = EventRelatedParadigm(conditions, onsets)
design_mat = dm.make_dmtx(frametimes,
paradigm,
drift_model='cosine',
hfcut=n_scans,
hrf_model='canonical')
# Do the GLM
mask_img = compute_epi_mask(img)
fmri_glm = FMRILinearModel(img, design_mat.matrix, mask=mask_img)
fmri_glm.fit(do_scaling=True, model='ar1')
# Pull out the betas
beta_hat = fmri_glm.glms[0].get_beta(
) # Least-squares estimates of the beta
mask = fmri_glm.mask.get_data() > 0
# output beta images
dim = design_mat.matrix.shape[1]
beta_map = np.tile(mask.astype(np.float)[..., np.newaxis], dim)
beta_map[mask] = beta_hat.T
beta_image = nibabel.Nifti1Image(beta_map, fmri_glm.affine)
beta_image.get_header()['descrip'] = (
'Parameter estimates of the localizer dataset')
# Save beta images
for ci, cond in enumerate(np.unique(conditions)):
beta_cond_img = index_img(beta_image, ci)
beta_filepath = get_beta_filepath(func_file, cond)
nibabel.save(beta_cond_img, beta_filepath)
beta_files.append(beta_filepath)
return beta_files
nscans = 128
frametimes = np.linspace(0, (nscans - 1) * tr, nscans)
# experimental paradigm
conditions = ['c0', 'c0', 'c0', 'c1', 'c1', 'c1', 'c3', 'c3', 'c3']
onsets = [30, 70, 100, 10, 30, 90, 30, 40, 60]
hrf_model = 'canonical'
motion = np.cumsum(np.random.randn(128, 6), 0)
add_reg_names = ['tx', 'ty', 'tz', 'rx', 'ry', 'rz']
#event-related design matrix
paradigm = EventRelatedParadigm(conditions, onsets)
X1 = make_dmtx(frametimes,
paradigm,
drift_model='polynomial',
drift_order=3,
add_regs=motion,
add_reg_names=add_reg_names)
# block design matrix
duration = 7 * np.ones(9)
paradigm = BlockParadigm(con_id=conditions, onset=onsets, duration=duration)
X2 = make_dmtx(frametimes, paradigm, drift_model='polynomial', drift_order=3)
# FIR model
paradigm = EventRelatedParadigm(conditions, onsets)
hrf_model = 'FIR'
X3 = make_dmtx(frametimes,
paradigm,
hrf_model='fir',
def glm_nipy(fmri_data, contrasts=None, hrf_model='Canonical',
drift_model='Cosine', hfcut=128,
residuals_model='spherical', fit_method='ols',
fir_delays=[0],
rescale_results=False, rescale_factor=None):
"""
Perform a GLM analysis on fMRI data using the implementation of Nipy.
Args:
fmri_data (pyhrf.core.FmriData): the input fMRI data defining the
paradigm and the measured 3D+time signal.
contrasts (dict): keys are contrast labels and values are arithmetic
expressions involving regressor names. Valid names are:
* names of experimental conditions as defined in fmri_data
* constant
hrf_model: "Canonical", "Canonical with Derivative", "FIR"
residuals_model: "spherical", "ar1"
fit_method: "ols", "kalman" (If residuals_model is "ar1" then method
is set to "kalman" and this argument is ignored)
fir_delays: list of integers indicating the delay of each FIR coefficient
(in terms of scans). Eg if TR = 2s. and we want a FIR
duration of 20s.: fir_delays=range(10)
Returns:
(glm instance, design matrix, dict of contrasts of objects)
Examples:
>>> from pyhrf.core import FmriData
>>> from pyhrf.glm import glm_nipy
>>> g,dmtx,con = glm_nipy(FmriData.from_vol_ui())
>>> g,dmtx,con = glm_nipy(FmriData.from_vol_ui(), \
contrasts={'A-V':'audio-video'})
"""
paradigm = fmri_data.paradigm.to_nipy_paradigm()
# BOLD data
Y = fmri_data.bold.T
n_scans = Y.shape[1]
# pyhrf.verbose(1, 'Input BOLD: nvox=%d, nscans=%d' %Y.shape)
# Design matrix
frametimes = np.linspace(0, (n_scans-1)*fmri_data.tr, n_scans)
design_matrix = dm.make_dmtx(frametimes, paradigm,
hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut,
fir_delays=fir_delays)
ns, nr = design_matrix.matrix.shape
pyhrf.verbose(2, 'Design matrix built with %d regressors:' %nr)
for rn in design_matrix.names:
pyhrf.verbose(2, ' - %s' %rn)
# ax = design_matrix.show()
# ax.set_position([.05, .25, .9, .65])
# ax.set_title('Design matrix')
# plt.savefig(op.join(output_dir, 'design_matrix.png'))
# GLM fit
my_glm = glm.glm()
pyhrf.verbose(2, 'Fit GLM - method: %s, residual model: %s' \
%(fit_method,residuals_model))
my_glm.fit(Y.T, design_matrix.matrix, method=fit_method,
model=residuals_model)
from pyhrf.tools import map_dict
from pyhrf.paradigm import contrasts_to_spm_vec
if rescale_results:
# Rescale by the norm of the HRF:
# from nipy.modalities.fmri.hemodynamic_models import _hrf_kernel, \
# sample_condition
# oversampling = 16
# hrfs = _hrf_kernel(hrf_model, fmri_data.tr, oversampling,
# fir_delays=fir_delays)
# hframetimes = np.linspace(0, 32., int(32./fmri_data.tr))
# hr_regressor, hr_frametimes = sample_condition(
# (np.array([0]),np.array([0]),np.array([1])),
# hframetimes, oversampling)
# from scipy.interpolate import interp1d
# for i in xrange(len(hrfs)):
# f = interp1d(hr_frametimes, hrfs[i])
# hrfs[i] = f(hframetimes).T
# n_conds = len(fmri_data.paradigm.stimOnsets)
# for i in xrange(n_conds * len(hrfs)):
# h = hrfs[i%len(hrfs)]
# my_glm.beta[i] = my_glm.beta[i] * (h**2).sum()**.5
#my_glm.variance = np.zeros_like(my_glm.beta)
if 1:
if rescale_results and rescale_factor is None:
#Rescale by the norm of each regressor in the design matrix
dm_reg_norms = (design_matrix.matrix**2).sum(0)**.5
pyhrf.verbose(2,'GLM results (beta and con effects) are '\
'rescaled by reg norm. Weights: %s ' \
%str(dm_reg_norms))
for ib in xrange(my_glm.beta.shape[0]):
my_glm.beta[ib] = my_glm.beta[ib] * dm_reg_norms[ib]
#my_glm.nvbeta[ib,:] = my_glm.nvbeta[ib,:] * dm_reg_norms[ib]**2
else:
pyhrf.verbose(2,'GLM results (beta and con effects) are '\
'rescaled by input scale factor.')
# Use input rescale factors:
for ib in xrange(rescale_factor.shape[0]):
my_glm.beta[ib] = my_glm.beta[ib] * rescale_factor[ib]
#TOCHECK: nvbeta seems to be a covar matrix between reg
# -> we dont get position-specific variances ...
#my_glm.nvbeta[ib,:] = my_glm.nvbeta[ib,:] * rescale_factor[ib]**2
if contrasts is not None:
con_vectors = contrasts_to_spm_vec(design_matrix.names, contrasts)
# if rescale_results:
# for con_vec in con_vectors.itervalues():
# con_vec *= dm_reg_norms
contrast_result = map_dict(my_glm.contrast, con_vectors)
else:
contrast_result = None
return my_glm, design_matrix, contrast_result
#actually: not possible to compute PPM from glm results
#Should relaunch estimation with propoer model under SPM
#def PPMcalculus_glmWN(beta, var_beta, dm, threshold_value):
'''
fmri_series = [
os.path.join(
fmri_dir,
'%s_series_%s_rh_smooth5.gii' % (subject, session))
for session in sessions
]
# compute the mask
if side == False:
mean_img = glob.glob(os.path.join(fmri_dir, 'mean*.nii'))[0]
mask_array = compute_mask_files(mean_img, epi_mask, True,
inf_threshold, sup_threshold)[0]
# get the contrasts
n_reg = make_dmtx(frametimes,
add_regs=reg_matrix,
drift_model=drift_model,
hfcut=hfcut).matrix.shape[1]
contrasts, all_reg = make_contrasts(sessions, n_reg)
contrast_obj = {}
for (sess, (session,
fmri_data)) in enumerate(zip(sessions, fmri_series)):
# create design matrices
reg = all_reg[2 * sess:2 * sess + 2] # fixme
design_matrix = make_dmtx(frametimes,
add_regs=reg_matrix,
add_reg_names=reg,
drift_model=drift_model,
hfcut=hfcut)
# design matrix
TR = 7
N_SCANS = 84
conditions = ['listen'] * 7
duration = TR * 6 * np.ones(7)
onset = np.arange(6, N_SCANS, 12) * TR
paradigm = BlockParadigm(con_id=conditions,
onset=onset,
duration=duration)
frametimes = np.linspace(0, (N_SCANS - 1) * TR, N_SCANS)
design_mat = design_matrix.make_dmtx(frametimes, paradigm,
hrf_model='Canonical',
drift_model='Cosine',
hfcut=168)
design_mat.show()
# general linear model
glm = FMRILinearModel(input_image, design_mat.matrix, mask='compute')
glm.fit()
# contrasts
c = np.hstack([1, np.zeros(len(design_mat.names)-1)])
z_map, t_map, eff_map, var_map = glm.contrast(c,
contrast_type='t',
def _make_design_matrix(run_frame, hrf_model='canonical', drift_model='cosine', orthogonalize=None):
# print ' %s' % ' '.join(run_frame[['study', 'subject', 'model', 'task', 'run']].values[0])
bold_file = run_frame.preproc_bold.unique()[0]
n_scans = nb.load(bold_file).shape[-1]
tr = float(run_frame.TR.unique()[0])
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
movement_regressors = run_frame.movement.unique()[0]
movement_regressors = np.recfromtxt(movement_regressors) \
if isinstance(movement_regressors, basestring) else None
names = []
times = []
durations = []
amplitudes = []
for condition_id, condition_name, condition_file in run_frame[['condition', 'condition_name', 'condition_file']].values:
conditions = _csv_to_dict(condition_file)
if condition_id == 'empty_evs':
conditions = sorted(conditions.keys())
for c in conditions:
names.append(['cond%03i' % int(c)])
times.append([0])
durations.append([0])
amplitudes.append([0])
else:
keys = sorted(conditions.keys())
times.append(np.array(keys).astype('float'))
names.append(['%s_%s' % (condition_id, condition_name)] * len(keys))
durations.append([float(conditions[k][0]) for k in keys])
amplitudes.append([float(conditions[k][1]) for k in keys])
times = np.concatenate(times).ravel()
order = np.argsort(times)
times = times[order]
names = np.concatenate(names)[order]
durations = np.concatenate(durations)[order]
amplitudes = np.concatenate(amplitudes)[order]
if durations.sum() == 0:
paradigm = EventRelatedParadigm(names, times, amplitudes)
else:
paradigm = BlockParadigm(names, times, durations, amplitudes)
if movement_regressors is None:
design_matrix = make_dmtx(
frametimes, paradigm, hrf_model=hrf_model,
drift_model=drift_model)
else:
mov_reg_names = ['movement_%i' % r
for r in range(movement_regressors.shape[1])]
design_matrix = make_dmtx(
frametimes, paradigm, hrf_model=hrf_model,
drift_model=drift_model,
add_regs=movement_regressors, add_reg_names=mov_reg_names)
# orthogonalize regressors
if orthogonalize is not None and not 'derivative' in hrf_model:
task_id = run_frame.task.unique()[0]
for x, y in orthogonalize[orthogonalize.index == task_id].values:
x_ = design_matrix.matrix[:, x]
y_ = design_matrix.matrix[:, y]
z = _orthogonalize_vectors(x_, y_)
design_matrix.matrix[:, x] = z
return bold_file, pd.DataFrame(dict(zip(design_matrix.names, design_matrix.matrix.T)))
struct_as_record=False)
faces_onsets = timing['onsets'][0].ravel()
scrambled_onsets = timing['onsets'][1].ravel()
onsets = np.hstack((faces_onsets, scrambled_onsets))
onsets *= tr # because onsets were reporting in 'scans' units
conditions = ['faces'] * len(faces_onsets) + ['scrambled'
] * len(scrambled_onsets)
paradigm = EventRelatedParadigm(conditions, onsets)
# build design matrix
frametimes = np.linspace(0, (n_scans - 1) * tr, n_scans)
design_matrix = make_dmtx(
frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
hfcut=hfcut,
add_reg_names=['tx', 'ty', 'tz', 'rx', 'ry', 'rz'],
add_regs=np.loadtxt(subject_data.realignment_parameters[x]))
design_matrices.append(design_matrix)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
# more interesting contrasts
contrasts['faces-scrambled'] = contrasts['faces'] - contrasts['scrambled']
contrasts['scrambled-faces'] = -contrasts['faces-scrambled']
tr = 1.0
nscans = 128
frametimes = np.linspace(0, (nscans - 1) * tr, nscans)
# experimental paradigm
conditions = ['c0', 'c0', 'c0', 'c1', 'c1', 'c1', 'c3', 'c3', 'c3']
onsets = [30, 70, 100, 10, 30, 90, 30, 40, 60]
hrf_model = 'canonical'
motion = np.cumsum(np.random.randn(128, 6), 0)
add_reg_names = ['tx', 'ty', 'tz', 'rx', 'ry', 'rz']
#event-related design matrix
paradigm = EventRelatedParadigm(conditions, onsets)
X1 = make_dmtx(
frametimes, paradigm, drift_model='polynomial', drift_order=3,
add_regs=motion, add_reg_names=add_reg_names)
# block design matrix
duration = 7 * np.ones(9)
paradigm = BlockParadigm(con_id=conditions, onset=onsets,
duration=duration)
X2 = make_dmtx(frametimes, paradigm, drift_model='polynomial',
drift_order=3)
# FIR model
paradigm = EventRelatedParadigm(conditions, onsets)
hrf_model = 'FIR'
X3 = make_dmtx(frametimes, paradigm, hrf_model='fir',
drift_model='polynomial', drift_order=3,
def do_glm_for_subject(subject_id, bold_base_folder, trial_base_folder,
output_base_folder):
subject_dir = path(bold_base_folder) / ("sub%03d" % subject_id)
output_dir = (path(output_base_folder) / ("sub%03d" % subject_id) /
"model001")
print output_dir
if not output_dir.exists():
output_dir.makedirs()
anat_file = subject_dir / "highres001.nii"
anat = nb.load(anat_file)
run_ids = range(1, 10)
task_bold_files = [subject_dir.glob("task001_run%03d/rbold*.nii"
% rid)[0]
for rid in run_ids]
task_mvt_files = [subject_dir.glob("task001_run%03d/rp_bold*.txt" %
rid)[0]
for rid in run_ids]
trial_files = [(path(trial_base_folder) / ("Sub%02d" % subject_id) /
"BOLD" / "Trials" / ("run_%02d_spmdef.txt" % rid))
for rid in range(1, 10)]
stats_start_time = pretty_time()
paradigms = []
design_matrices = []
n_scans = []
all_frametimes = []
list_of_contrast_dicts = [] # one dict per run
for bold_file, mvt_file, trial_file in zip(task_bold_files,
task_mvt_files,
trial_files):
_n_scans = nb.load(bold_file).shape[-1]
n_scans.append(_n_scans)
paradigm = make_paradigm(trial_file)
paradigms.append(paradigm)
movements = np.loadtxt(mvt_file)
tr = 2.
drift_model = "Cosine"
hrf_model = "Canonical With Derivative"
hfcut = 128.
frametimes = np.linspace(0, (_n_scans - 1) * tr, _n_scans)
design_matrix = make_dmtx(
frametimes,
paradigm,
hrf_model=hrf_model,
drift_model=drift_model,
hfcut=hfcut,
add_regs=movements,
add_reg_names=[
"Tx", "Ty", "Tz", "R1", "R2", "R3"])
design_matrices.append(design_matrix)
all_frametimes.append(frametimes)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(
n_columns)[2 * i]
# more interesting contrasts"""
contrasts['Famous-Unfamiliar'] = contrasts[
'Famous'] - contrasts['Unfamiliar']
contrasts['Unfamiliar-Famous'] = -contrasts['Famous-Unfamiliar']
contrasts['Famous-Scrambled'] = contrasts[
'Famous'] - contrasts['Scrambled']
contrasts['Scrambled-Famous'] = -contrasts['Famous-Scrambled']
contrasts['Unfamiliar-Scrambled'] = contrasts[
'Unfamiliar'] - contrasts['Scrambled']
contrasts['Scrambled-Unfamiliar'] = -contrasts['Unfamiliar-Scrambled']
list_of_contrast_dicts.append(contrasts)
# importat maps
z_maps = {}
effects_maps = {}
fmri_glm = FMRILinearModel(task_bold_files,
[dm.matrix for dm in design_matrices],
mask="compute")
fmri_glm.fit(do_scaling=True, model="ar1")
# replicate contrasts across runs
contrasts = dict((cid, [contrasts[cid]
for contrasts in list_of_contrast_dicts])
for cid, cval in contrasts.iteritems())
# compute effects
for contrast_id, contrast_val in contrasts.iteritems():
print "\tcontrast id: %s" % contrast_id
z_map, eff_map, var_map = fmri_glm.contrast(
contrast_val,
con_id=contrast_id,
output_z=True,
output_stat=False,
output_effects=True,
output_variance=True
)
for map_type, out_map in zip(['z', 'effects', 'variance'],
[z_map, eff_map, var_map]):
map_dir = output_dir / ('%s_maps' % map_type)
if not map_dir.exists():
map_dir.makedirs()
map_path = map_dir / ('%s.nii.gz' % contrast_id)
print "\t\tWriting %s ..." % map_path
nb.save(out_map, map_path)
# collect zmaps for contrasts we're interested in
if map_type == 'z':
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
if map_type == "variance":
effects_maps[contrast_id] = map_path
stats_report_dir = output_dir / "report"
if not stats_report_dir.exists():
stats_report_dir.makedirs()
stats_report_filename = stats_report_dir / "report_stats.html"
# remove repeated contrasts
contrasts = dict((cid, cval[0]) for cid, cval in contrasts.iteritems())
slicer = 'z'
cut_coords = [-20, -10, 0, 10, 20, 30, 40, 50]
threshold = 3.
cluster_th = 15
generate_subject_stats_report(
stats_report_filename,
contrasts,
z_maps,
fmri_glm.mask,
anat_affine=anat.get_affine(),
anat=anat.get_data(),
threshold=threshold,
cluster_th=cluster_th,
slicer=slicer,
cut_coords=cut_coords,
design_matrices=design_matrices,
subject_id="sub%03d" % subject_id,
start_time=stats_start_time,
title="GLM for subject %s" % ("sub%03d" % subject_id),
# additional ``kwargs`` for more informative report
TR=tr,
n_scans=n_scans,
hfcut=hfcut,
drift_model=drift_model,
hrf_model=hrf_model,
paradigm=dict(("Run_%02i" % (run_id), paradigms[run_id - 1])
for run_id in run_ids),
frametimes=dict(("Run_%02i" % (run_id), all_frametimes[run_id - 1])
for run_id in run_ids),
# fwhm=fwhm
)
return fmri_glm
if side == False:
# in the volume, compute a mask o fthe brain
mask_array = compute_mask_files(fmri_series[0], epi_mask, True,
inf_threshold, sup_threshold)[0]
# Specify the contrasts
contrasts = make_contrasts(sessions, odd=subject in
['sujet10', 'sujet12'])
contrast_obj = {}
for (sess, (session, fmri_data)) in enumerate(zip(
sessions, fmri_series)):
# create design matrices
reg = all_reg[4 * sess: 4 * sess + 4] # fixme
design_matrix = make_dmtx(
frametimes, add_regs=reg_matrix, add_reg_names=reg,
drift_model=drift_model, hfcut=hf_cut)
# plot the design matrix
ax = design_matrix.show()
ax.set_position([.05, .25, .9, .65])
ax.set_title('Design matrix')
pylab.savefig(os.path.join(write_dir, 'design_matrix_%s.png') %\
session)
# get the data
if side == False:
Y, _ = data_scaling(np.array([load(f).get_data()[mask_array]
for f in fmri_data]))
affine = load(fmri_data[0]).get_affine()
else:
Y, _ = data_scaling(np.array(
_duration = 6
epoch_duration = _duration * tr
conditions = ['rest', 'active'] * 8
duration = epoch_duration * np.ones(len(conditions))
onset = np.linspace(0, (len(conditions) - 1) * epoch_duration,
len(conditions))
paradigm = BlockParadigm(con_id=conditions, onset=onset, duration=duration)
hfcut = 2 * 2 * epoch_duration
# construct design matrix
nscans = len(subject_data.func[0])
frametimes = np.linspace(0, (nscans - 1) * tr, nscans)
drift_model = 'Cosine'
hrf_model = 'Canonical With Derivative'
design_matrix = make_dmtx(frametimes,
paradigm, hrf_model=hrf_model,
drift_model=drift_model, hfcut=hfcut)
# plot and save design matrix
ax = design_matrix.show()
ax.set_position([.05, .25, .9, .65])
ax.set_title('Design matrix')
dmat_outfile = os.path.join(subject_data.output_dir, 'design_matrix.png')
pl.savefig(dmat_outfile, bbox_inches="tight", dpi=200)
# specify contrasts
contrasts = {}
n_columns = len(design_matrix.names)
for i in xrange(paradigm.n_conditions):
contrasts['%s' % design_matrix.names[2 * i]] = np.eye(n_columns)[2 * i]
def runsub(sub,
thisContrast,
thisContrastStr,
filterLen,
filterOrd,
paramEst,
chunklen,
alphas=np.logspace(0, 3, 20),
debug=False,
write=False,
roi='grayMatter'):
thisSub = {sub: subList[sub]}
mc_params = lmvpa.loadmotionparams(paths, thisSub)
beta_events = lmvpa.loadevents(paths, thisSub)
dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi, c='trial_type')
thisDS = dsdict[sub]
# savitsky golay filtering
sg.sg_filter(thisDS, filterLen, filterOrd)
# gallant group zscores before regression.
# zscore w.r.t. rest trials
# zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
# zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
zscore(thisDS, chunks_attr='chunks')
# kay method: leave out a model run, use it to fit an HRF for each voxel
# huth method: essentially use FIR
# mumford method: deconvolution with canonical HRF
# refit events and regress...
# get timing data from timing files
# rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub])
rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub],
contrasts) # adding features
# we can model out motion and just not use those betas.
# Ridge
if isinstance(thisContrast, basestring):
thisContrast = [thisContrast]
# instead of binarizing each one, make them parametric
desX, rds = lmvpa.make_designmat(rds,
events,
time_attr='time_coords',
condition_attr=thisContrast,
design_kwargs={
'hrf_model': 'canonical',
'drift_model': 'blank'
},
regr_attrs=None)
# want to collapse ap and cr, but have anim separate
desX['motion'] = make_dmtx(rds.sa['time_coords'].value,
paradigm=None,
add_regs=mc_params[sub],
drift_model='blank')
des = lmvpa.make_parammat(desX, hrf='canonical', zscore=True)
# set chunklen and nchunks
# split by language and pictures
lidx = thisDS.chunks < thisDS.sa['chunks'].unique[len(
thisDS.sa['chunks'].unique) / 2]
pidx = thisDS.chunks >= thisDS.sa['chunks'].unique[len(
thisDS.sa['chunks'].unique) / 2]
ldes = cp.copy(des)
pdes = cp.copy(des)
ldes.matrix = ldes.matrix[lidx]
pdes.matrix = pdes.matrix[pidx]
nchunks = int(len(thisDS) * paramEst / chunklen)
nboots = 50
covarmat = None
mus = None
lwts, lalphas, lres, lceil = bsr.bootstrap_ridge(rds[lidx],
ldes,
chunklen=chunklen,
nchunks=nchunks,
cov0=covarmat,
mu0=mus,
part_attr='chunks',
mode='test',
alphas=alphas,
single_alpha=True,
normalpha=False,
nboots=nboots,
corrmin=.2,
singcutoff=1e-10,
joined=None,
plot=debug,
use_corr=True)
pwts, palphas, pres, pceil = bsr.bootstrap_ridge(rds[pidx],
pdes,
chunklen=chunklen,
nchunks=nchunks,
part_attr='chunks',
mode='test',
alphas=alphas,
single_alpha=True,
normalpha=False,
nboots=nboots,
corrmin=.2,
singcutoff=1e-10,
joined=None,
plot=debug,
use_corr=True)
print 'language ' + str(np.mean(lres))
# pictures within
print 'pictures: ' + str(np.mean(pres))
# need to change outstring
if write:
from mvpa2.base import dataset
map2nifti(thisDS, dataset.vstack([lres, pres])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_corrs.nii.gz'))
map2nifti(thisDS, dataset.vstack([lwts, pwts])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_weights.nii.gz'))
map2nifti(thisDS, dataset.vstack([lalphas, palphas])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_alphas.nii.gz'))
map2nifti(thisDS, dataset.vstack([lceil, pceil])) \
.to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
'_ridge_ceiling.nii.gz'))
del lres, pres, lwts, pwts, lalphas, palphas, lceil, pceil
crossSet = thisDS.copy()
crossSet.chunks[lidx] = 1
crossSet.chunks[pidx] = 2
cwts, calphas, cres, cceil = bsr.bootstrap_ridge(crossSet,
des,
chunklen=chunklen,
nchunks=nchunks,
part_attr='chunks',
mode='test',
alphas=alphas,
single_alpha=True,
normalpha=False,
nboots=nboots,
corrmin=.2,
singcutoff=1e-10,
joined=None,
use_corr=True)
print 'cross: ' + str(np.mean(cres))
if write:
map2nifti(thisDS, cres[0]).to_filename(
os.path.join(
paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
thisContrastStr + '_P2L_ridge_corr.nii.gz'))
map2nifti(thisDS, cres[1]).to_filename(
os.path.join(
paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
thisContrastStr + '_L2P_ridge_corr.nii.gz'))
map2nifti(thisDS, cwts[0]).to_filename(
os.path.join(
paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
thisContrastStr + '_P2L_ridge_weights.nii.gz'))
map2nifti(thisDS, cwts[1]).to_filename(
os.path.join(
paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
thisContrastStr + '_L2P_ridge_weights.nii.gz'))
map2nifti(thisDS, calphas[calphas.chunks == 1]).to_filename(
os.path.join(
paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
thisContrastStr + '_P2L_ridge_alphas.nii.gz'))
map2nifti(thisDS, calphas[calphas.chunks == 2]).to_filename(
os.path.join(
paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
thisContrastStr + '_L2P_ridge_alphas.nii.gz'))
map2nifti(thisDS, cceil[0]).to_filename(
os.path.join(
paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
thisContrastStr + '_P2L_ridge_ceiling.nii.gz'))
map2nifti(thisDS, cceil[1]).to_filename(
os.path.join(
paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
thisContrastStr + '_L2P_ridge_ceiling.nii.gz'))
del cres, cwts, calphas, cceil