def __init__(self, env_subject):
"""Initialize the environment path for 'average' subject fsaverage_sym.
Parameters
----------
env_subject : string
Path to directory containing subject fsaverage_sym.
"""
add_subject_path(env_subject)
def setUp(self):
"""Clean-up eventual existing client cache directory. Create fresh SCO
client instance."""
# Set file names for subject and image group files for upload
self.SUBJECT_FILE = os.path.join(DATA_DIR, 'subjects/ernie.tar.gz')
self.IMAGES_ARCHIVE = os.path.join(DATA_DIR, 'images/small-sample.tar')
# Add Freesurfer subject path
add_subject_path(ENV_DIR)
# Delete data store directory if exists
if os.path.isdir(CLIENT_DIR):
shutil.rmtree(CLIENT_DIR)
# Create fresh instance of SCO data store
self.sco = SCOClient(api_url=API_URL, data_dir=CLIENT_DIR)
def setUp(self):
"""Clean-up eventual existing test data store. Create fresh data store
instance."""
# Set file names for subject and image group files for upload
self.SUBJECT_FILE = os.path.join(DATA_DIR, 'subjects/ernie.tar.gz')
self.IMAGES_ARCHIVE = os.path.join(DATA_DIR, 'images/small-sample.tar')
# Add Freesurfer subject path
add_subject_path(ENV_DIR)
# Delete data store directory if exists
if os.path.isdir(API_DIR):
shutil.rmtree(API_DIR)
# Drop test database
MongoClient().drop_database('test_sco')
mongo = MongoDBFactory(db_name='test_sco')
# Create fresh instance of SCO data store
self.db = SCODataStore(mongo, API_DIR)
self.engine = SCOEngine(mongo)
def setUp(self):
"""Clean-up eventual existing test data store. Create fresh data store
instance."""
# Set file names for subject and image group files for upload
self.SUBJECT_FILE = os.path.join(DATA_DIR, 'subjects/kay2008_subj1.tar.gz')
self.IMAGES_ARCHIVE = os.path.join(DATA_DIR, 'images/sample_images.tar.gz')
self.FUNC_DATA = os.path.join(DATA_DIR, 'func/sample.nii')
# Add Freesurfer subject path
add_subject_path(ENV_DIR)
# Delete data store directory if exists
if os.path.isdir(API_DIR):
shutil.rmtree(API_DIR)
# Drop test database
MongoClient().drop_database('test_sco')
mongo = MongoDBFactory(db_name='test_sco')
# Load models
init_registry_from_json(mongo, MODELS_FILE)
# Create fresh instance of SCO data store
self.db = SCODataStore(mongo, API_DIR)
self.engine = SCOEngine(mongo)
def compare_with_Kay2013(
image_base_path,
stimuli_idx,
voxel_idx=None,
subject='test-sub',
subject_dir='/home/billbrod/Documents/SCO-test-data/Freesurfer_subjects',
stimulus_pixels_per_degree=53,
normalized_pixels_per_degree=12,
stimulus_aperture_edge_width=0,
max_eccentricity=7.5,
**kwargs):
"""Run python SCO and Matlab SOC on the same batch of images
Arguments
---------
image_base_path: string. This is assumed to either be a directory, in which case the model will
be run on every image in the directory, or a .mat file containing the image stimuli, in which
case they will be loaded in and used.
stimuli_idx: array. Which stimuli from image_base_path we should use. These are assumed
to be integers that we use as indexes into the stimulus_images (if image_base_path is a .mat
file) or stimulus_image_filenames (if it's a directory), and we only pass those specified
images/filenames to the model.
voxel_idx: array or None, optional. Which voxels to run the model for and create
predictions. If None or unset, will run the model for all voxels. Else will use the optional
calculator sco.anatomy.core.calc_voxel_selector to subset the voxels and run only those indices
correspond to those included in this array.
subject_dir: string or None. If not None, will add this to neuropythy.freesurfer's subject
paths
subject: string. The specific subject to run on.
"""
if subject_dir is not None and subject_dir not in nfs.subject_paths():
nfs.add_subject_path(subject_dir)
# if there's just one value and not a list
if not hasattr(stimuli_idx, '__iter__'):
stimuli_idx = [stimuli_idx]
stimuli_idx = np.asarray(stimuli_idx)
voxel_idx = np.asarray(voxel_idx)
if voxel_idx is not None:
if not hasattr(voxel_idx, '__iter__'):
voxel_idx = [voxel_idx]
anat_chain = (
('import', anatomy_core.import_benson14_volumes_from_freesurfer),
('calc_pRF_centers',
anatomy_core.calc_pRFs_from_freesurfer_retinotopy_volumes),
('calc_voxel_selector', anatomy_core.calc_voxel_selector),
('calc_anatomy_defualt_parameters',
anatomy_core.calc_anatomy_default_parameters),
('calc_pRF_sizes', anatomy_core.calc_Kay2013_pRF_sizes))
anat_chain = calc_chain(anat_chain)
if 'voxel_idx' not in kwargs:
kwargs['voxel_idx'] = voxel_idx
else:
anat_chain = calc_anatomy
if os.path.isdir(image_base_path):
# Interestingly enough, this works regardless of whether image_base_path ends in os.sep or
# not.
stimulus_image_filenames = glob.glob(image_base_path + os.sep + "*")
# imghdr.what(img) returns something if img is an image file (it returns a stirng
# specifying whta type of image it is). If it's not an image file, it returns None.
stimulus_image_filenames = np.asarray(
[img for img in stimulus_image_filenames if imghdr.what(img)])
stimulus_image_filenames = stimulus_image_filenames[stimuli_idx]
if 'stimulus_image_filenames' not in kwargs:
kwargs['stimulus_image_filenames'] = stimulus_image_filenames
# here, stimuli_names can simply be the filenames we're using
stimuli_names = [
os.path.split(fn)[-1] for fn in stimulus_image_filenames
]
# and we use the default sco_chain (with the possible exception of anat_chain, see above)
sco_chain = (('calc_anatomy', anat_chain), ('calc_stimulus',
calc_stimulus),
('calc_contrast', calc_contrast), ('calc_pRF', calc_pRF),
('calc_normalization', calc_normalization))
# if it's a .mat file
elif os.path.splitext(image_base_path)[1] == ".mat":
# in this case, we assume it's stimuli.mat from
# http://kendrickkay.net/socmodel/index.html#contentsofstimuli. We want to grab only the
# 'images' key from this and only images 226 through 260/end (stimulus set 3; note that we
# have to convert from MATLAB's 1-indexing to python's 0-indexing), since each entry is a
# single frame and thus easy to handle.
stimulus_images = sio.loadmat(image_base_path)
if stimulus_images['images'].ndim == 2 and stimulus_images[
'images'].shape[0] == 1:
# then we need to unfold the stimulus_images; each stimulus is 3 dimensional (several
# two dimensional images), so if it's only two dimensional and the first dimension is
# 1, this is collapsed across that dimension (happens when not all stimuli are the same
# size).
stimulus_images = stimulus_images['images'][0, stimuli_idx]
else:
# else we can just grab the corresponding images
stimulus_images = stimulus_images['images'][stimuli_idx]
# some of the stimuli have multiple frames associated with them; we want to predict all of
# them separately, but remember that they were grouped together for later visualization. I
# can't figure out how to get this loop into a list comprehension, so we'll have to deal
# with the slight slowdown. stimuli_names is an array we create to keep track of these
# images. We will return it to the calling code and eventually pass it to create_model_df.
tmp = []
stimuli_names = []
for idx, im in zip(stimuli_idx, stimulus_images):
if len(im.shape) == 3:
for i in range(im.shape[2]):
tmp.append(im[:, :, i])
stimuli_names.append("%04d_sub%02d" % (idx, i))
else:
tmp.append(im)
stimuli_names.append("%04d" % idx)
stimuli_names = np.asarray(stimuli_names)
stimulus_images = np.asarray(tmp)
if 'stimulus_images' not in kwargs:
kwargs.update({'stimulus_images': stimulus_images})
kwargs.update({'stimulus_image_filenames': None})
sco_chain = (('calc_anatomy', anat_chain), ('calc_stimulus',
calc_stimulus),
('calc_contrast', calc_contrast), ('calc_pRF', calc_pRF),
('calc_normalization', calc_normalization))
else:
raise Exception(
"Don't know how to handle image_base_path %s, must be directory or .mat "
"file" % image_base_path)
# This prepares the sco_chain, making it a callable object
sco_chain = calc_chain(sco_chain)
# in order to handle the fact that the Kay2013 matlab code only deals with spatial orientation
# of 3 cpd, we have to define a new pRF_frequency_preference_function to replace the default.
def freq_pref(e, s, l):
# This takes in the eccentricity, size, and area, but we don't use any of them, since we
# just want to use 3 cpd and ignore everything else. And this must be floats.
return {3.0: 1.0}
if 'pRF_frequency_preference_function' not in kwargs:
kwargs['pRF_frequency_preference_function'] = freq_pref
# And this runs it. To make sure it has the same size as the the images used in Kendrick's
# code, we set the normalized_stimulus_aperture, normalized_aperture_edge_width, and
# normalized_pixels_per_degree values.
results = sco_chain(
subject=subject,
max_eccentricity=max_eccentricity,
normalized_stimulus_aperture=max_eccentricity *
normalized_pixels_per_degree,
stimulus_pixels_per_degree=stimulus_pixels_per_degree,
normalized_pixels_per_degree=normalized_pixels_per_degree,
stimulus_aperture_edge_width=stimulus_aperture_edge_width,
**kwargs)
return results, stimuli_names
def surface_to_ribbon_command(args):
'''
surface_to_rubbon_command(args) can be given a list of arguments, such as sys.argv[1:]; these
arguments may include any options and must include exactly one subject id and one output
filename. Additionally one or two surface input filenames must be given. The surface files are
projected into the ribbon and written to the output filename. For more information see the
string stored in surface_to_ribbon_help.
'''
# Parse the arguments
(args, opts) = _surface_to_ribbon_parser(args)
# First, help?
if opts['help']:
print surface_to_ribbon_help
return 1
# and if we are verbose, lets setup a note function
verbose = opts['verbose']
def note(s):
if verbose: print s
return verbose
# Add the subjects directory, if there is one
if 'subjects_dir' in opts and opts['subjects_dir'] is not None:
add_subject_path(opts['subjects_dir'])
# figure out our arguments:
(lhfl, rhfl) = (opts['lh_file'], opts['rh_file'])
if len(args) == 0:
raise ValueError('Not enough arguments provided!')
elif len(args) == 1:
# must be that the subject is in the env?
sub = find_subject_path(os.getenv('SUBJECT'))
outfl = args[0]
elif len(args) == 2:
sbpth = find_subject_path(args[0])
if sbpth is not None:
sub = sbpth
else:
sub = find_subject_path(os.getenv('SUBJECT'))
if lhfl is not None: rhfl = args[0]
elif rhfl is not None: lhfl = args[0]
else: raise ValueError('Given arg is not a subject: %s' % args[0])
outfl = args[1]
elif len(args) == 3:
sbpth0 = find_subject_path(args[0])
sbpth1 = find_subject_path(args[1])
if sbpth0 is not None:
sub = sbpth0
if lhfl is not None: rhfl = args[1]
elif rhfl is not None: lhfl = args[1]
else: raise ValueError('Too many arguments given: %s' % args[1])
elif sbpth1 is not None:
sub = sbpth1
if lhfl is not None: rhfl = args[0]
elif rhfl is not None: lhfl = args[0]
else: raise ValueError('Too many arguments given: %s' % args[0])
else:
sub = find_subject_path(os.getenv('SUBJECT'))
if lhfl is not None or rhfl is not None:
raise ValueError('Too many arguments and no subject given')
(lhfl, rhfl) = args
outfl = args[2]
elif len(args) == 4:
if lhfl is not None or rhfl is not None:
raise ValueError('Too many arguments and no subject given')
subidx = next((i for (i,a) in enumerate(args) if find_subject_path(a) is not None), None)
if subidx is None: raise ValueError('No subject given')
sub = find_subject_path(args[subidx])
del args[subidx]
(lhfl, rhfl, outfl) = args
else:
raise ValueError('Too many arguments provided!')
if sub is None: raise ValueError('No subject specified or found in $SUBJECT')
if lhfl is None and rhfl is None: raise ValueError('No surfaces provided')
# check the method
method = opts['method'].lower()
if method != 'weighted' and method != 'max':
raise ValueError('Unsupported method: %s' % method)
# and the datatype
if opts['dtype'] is None: dtyp = None
elif opts['dtype'].lower() == 'float': dtyp = np.float32
elif opts['dtype'].lower() == 'int': dtyp = np.int32
else: raise ValueError('Type argument must be float or int')
# Now, load the data:
note('Reading surfaces...')
(lhdat, rhdat) = (None, None)
if lhfl is not None:
note(' - Reading LH file: %s' % lhfl)
lhdat = read_surf_file(lhfl)
if rhfl is not None:
note(' - Reading RH file: %s' % rhfl)
rhdat = read_surf_file(rhfl)
(dat, hemi) = (rhdat, 'rh') if lhdat is None else \
(lhdat, 'lh') if rhdat is None else \
((lhdat, rhdat), None)
note('Generating vertex-to-voxel mapping...')
sub = freesurfer_subject(sub)
s2r = cortex_to_ribbon_map(sub, hemi=hemi)
# okay, make the volume...
note('Generating volume...')
vol = cortex_to_ribbon(sub, dat,
map=s2r, hemi=hemi, method=method, fill=opts['fill'], dtype=dtyp)
# and write out the file
note('Exporting volume file: %s' % outfl)
vol.to_filename(outfl)
note('surface_to_ribbon complete!')
return 0
def calc_arguments(args):
'''
calc_arguments is a calculator that parses the command-line arguments for the registration
command and produces the subject, the model, the log function, and the additional options.
'''
(args, opts) = _retinotopy_parser(args)
# We do some of the options right here...
if opts['help']:
print(info, file=sys.stdout)
sys.exit(1)
# and if we are verbose, lets setup a note function
verbose = opts['verbose']
def note(s):
if verbose:
print(s, file=sys.stdout)
sys.stdout.flush()
return verbose
def error(s):
print(s, file=sys.stderr)
sys.stderr.flush()
sys.exit(1)
if len(args) < 1: error('subject argument is required')
try: # we try FreeSurfer first:
import neuropythy.freesurfer as fs
# Add the subjects directory, if there is one
if 'subjects_dir' in opts and opts['subjects_dir'] is not None:
fs.add_subject_path(opts['subjects_dir'])
# Get the subject now
sub = fs.subject(args[0])
except Exception: sub = None
if sub is None:
try: # As an alternative, try HCP
import neuropythy.hcp as hcp
# Add the subjects directory, if there is one
if 'subjects_dir' in opts and opts['subjects_dir'] is not None:
hcp.add_subject_path(opts['subjects_dir'])
sub = hcp.subject(args[0])
except Exception: sub = None
if sub is None: error('Failed to load subject %s' % args[0])
# and the model
if len(args) > 1: mdl_name = args[1]
elif opts['model_sym']: mdl_name = 'schira'
else: mdl_name = 'benson17'
try:
if opts['model_sym']:
model = {h:retinotopy_model(mdl_name).persist() for h in ['lh', 'rh']}
else:
model = {h:retinotopy_model(mdl_name, hemi=h).persist() for h in ['lh', 'rh']}
except Exception: error('Could not load retinotopy model %s' % mdl_name)
# Now, we want to run a few filters on the options
# Parse the simple numbers
for o in ['weight_min', 'scale', 'max_step_size', 'max_out_eccen',
'max_in_eccen', 'min_in_eccen', 'field_sign_weight', 'radius_weight']:
opts[o] = float(opts[o])
opts['max_steps'] = int(opts['max_steps'])
# Make a note:
note('Processing subject: %s' % sub.name)
del opts['help']
del opts['verbose']
del opts['subjects_dir']
# That's all we need!
return pimms.merge(opts,
{'subject': sub.persist(),
'model': pyr.pmap(model),
'options': pyr.pmap(opts),
'note': note,
'error': error})
def register_retinotopy_command(args):
'''
register_retinotopy_command(args) can be given a list of arguments, such as sys.argv[1:]; these
arguments may include any options and must include at least one subject id. All subjects whose
ids are given are registered to a retinotopy model, and the resulting registration, as well as
the predictions made by the model in the registration, are exported.
'''
# Parse the arguments
(args, opts) = _retinotopy_parser(args)
# First, help?
if opts['help']:
print register_retinotopy_help
return 1
# and if we are verbose, lets setup a note function
verbose = opts['verbose']
def note(s):
if verbose: print s
return verbose
# Add the subjects directory, if there is one
if 'subjects_dir' in opts and opts['subjects_dir'] is not None:
add_subject_path(opts['subjects_dir'])
# Parse the simple numbers
for o in ['weight_cutoff', 'edge_strength', 'angle_strength', 'func_strength',
'max_step_size', 'max_out_eccen']:
opts[o] = float(opts[o])
opts['max_steps'] = int(opts['max_steps'])
# These are for now not supported: #TODO
if opts['angle_math'] or opts['angle_radians'] or opts['eccen_radians']:
print 'Mathematical angles and angles not in degrees are not yet supported.'
return 1
# The remainder of the args can wait for now; walk through the subjects:
tag_key = {'eccen': 'eccentricity', 'angle': 'polar_angle', 'label': 'V123_label'}
for subnm in args:
sub = freesurfer_subject(subnm)
note('Processing subject: %s' % sub.id)
# we need to register this subject...
res = {}
ow = not opts['no_overwrite']
for h in ['LH','RH']:
note(' Processing hemisphere: %s' % h)
hemi = sub.__getattr__(h)
# See if we are loading custom values...
(ang,ecc,wgt) = (None,None,None)
suffix = '_' + h.lower() + '_file'
if opts['angle' + suffix] is not None: ang = _guess_surf_file(opts['angle' + suffix])
if opts['eccen' + suffix] is not None: ecc = _guess_surf_file(opts['eccen' + suffix])
if opts['weight' + suffix] is not None: wgt = _guess_surf_file(opts['weight' + suffix])
# Do the registration
note(' - Running Registration...')
res[h] = register_retinotopy(hemi, V123_model(),
polar_angle=ang, eccentricity=ecc, weight=wgt,
weight_cutoff=opts['weight_cutoff'],
partial_voluming_correction=opts['part_vol_correct'],
edge_scale=opts['edge_strength'],
angle_scale=opts['angle_strength'],
functional_scale=opts['func_strength'],
prior=opts['prior'],
max_predicted_eccen=opts['max_out_eccen'],
max_steps=opts['max_steps'],
max_step_size=opts['max_step_size'])
# Perform the hemi-specific outputs now:
if not opts['no_reg_export']:
regnm = '.'.join([h.lower(), opts['registration_name'], 'sphere', 'reg'])
flnm = (os.path.join(sub.directory, 'surf', regnm) if h == 'LH' else
os.path.join(sub.directory, 'xhemi', 'surf', regnm))
if ow or not os.path.exist(flnm):
note(' - Exporting registration file: %s' % flnm)
fsio.write_geometry(flnm, res[h].coordinates.T, res[h].faces.T,
'Created by neuropythy (github.com/noahbenson/neuropythy)')
else:
note(' - Skipping registration file: %s (file exists)' % flnm)
if not opts['no_surf_export']:
for dim in ['angle', 'eccen', 'label']:
flnm = os.path.join(sub.directory, 'surf',
'.'.join([h.lower(), opts[dim + '_tag'], 'mgz']))
if ow or not os.path.exist(flnm):
note(' - Exporting prediction file: %s' % flnm)
img = fsmgh.MGHImage(
np.asarray([[res[h].prop(tag_key[dim])]],
dtype=(np.int32 if dim == 'label' else np.float32)),
np.eye(4))
img.to_filename(flnm)
else:
note(' - Skipping prediction file: %s (file exists)' % flnm)
# Do the volume exports here
if not opts['no_vol_export']:
note(' Processing volume data...')
note(' - Calculating cortex-to-ribbon mapping...')
surf2rib = cortex_to_ribbon_map(sub, hemi=None)
for dim in ['angle', 'eccen', 'label']:
flnm = os.path.join(sub.directory, 'mri', opts[dim + '_tag'] + '.mgz')
if ow or not os.path.exist(flnm):
note(' - Generating volume file: %s' % flnm)
vol = cortex_to_ribbon(sub,
(res['LH'].prop(tag_key[dim]),
res['RH'].prop(tag_key[dim])),
map=surf2rib,
dtype=(np.int32 if dim == 'label' else np.float32))
note(' - Exporting volume file: %s' % flnm)
vol.to_filename(flnm)
else:
note(' - Skipping volume file: %s (file exists)' % flnm)
# That is it for this subject!
note(' Subject %s finished!' % sub.id)
# And if we made it here, all was successful.
return 0
opts = {
'stimulus': image_files,
'subject': subject_dir,
'stimulus_edge_value': 0.5,
'gabor_orientations' : 8,
'pixels_per_degree': d2p,
'normalized_pixels_per_degree' : d2p,
'max_eccentricity': max_eccen,
'aperture_edge_width': 0,
'aperture_radius': max_eccen,
'output_directory': output_dir,
'measurements_filename': func_filename
}
add_subject_path(env_dir)
model = sco.build_model('benson17')
data = model(opts)
print data['exported_files']
if generate_cortical_images:
cortex_idcs = data['cortex_indices']
measurement_idcs = data['measurement_indices']
# Get the filename of the predicted results out of the exported_files list:
pred_filename = os.path.join(output_dir, 'prediction.nii.gz')
# use nibabel (import nibabel as nib) to load this file
pred_nii = nib.load(pred_filename)
def benson14_retinotopy_command(*args):
'''
benson14_retinotopy_command(args...) runs the benson14_retinotopy command; see
benson14_retinotopy_help for mor information.
'''
# Parse the arguments...
(args, opts) = _benson14_parser(args)
# help?
if opts['help']:
print benson14_retinotopy_help
return 1
# verbose?
verbose = opts['verbose']
def note(s):
if verbose: print s
return verbose
# Add the subjects directory, if there is one
if 'subjects_dir' in opts and opts['subjects_dir'] is not None:
add_subject_path(opts['subjects_dir'])
ow = not opts['no_overwrite']
nse = opts['no_surf_export']
nve = opts['no_vol_export']
tr = {'polar_angle': opts['angle_tag'],
'eccentricity': opts['eccen_tag'],
'v123roi': opts['label_tag']}
# okay, now go through the subjects...
for subnm in args:
note('Processing subject %s:' % subnm)
sub = freesurfer_subject(subnm)
note(' - Interpolating template...')
(lhdat, rhdat) = benson14_retinotopy(sub)
# Export surfaces
if nse:
note(' - Skipping surface export.')
else:
note(' - Exporting surfaces:')
for (t,dat) in lhdat.iteritems():
flnm = os.path.join(sub.directory, 'surf', 'lh.' + tr[t] + '.mgz')
if ow or not os.path.exist(flnm):
note(' - Exporting LH prediction file: %s' % flnm)
img = fsmgh.MGHImage(
np.asarray([[dat]], dtype=(np.int32 if t == 'v123roi' else np.float32)),
np.eye(4))
img.to_filename(flnm)
else:
note(' - Not overwriting existing file: %s' % flnm)
# Export volumes
if nve:
note(' - Skipping volume export.')
else:
surf2rib = cortex_to_ribbon_map(sub, hemi=None)
note(' - Exporting Volumes:')
for t in lhdat.keys():
flnm = os.path.join(sub.directory, 'mri', tr[t] + '.mgz')
if ow or not os.path.exist(flnm):
note(' - Preparing volume file: %s' % flnm)
vol = cortex_to_ribbon(sub,
(lhdat[t], rhdat[t]),
map=surf2rib,
dtype=(np.int32 if t == 'v123roi' else np.float32))
note(' - Exporting volume file: %s' % flnm)
vol.to_filename(flnm)
else:
note(' - Not overwriting existing file: %s' % flnm)
note(' Subject %s finished!' % sub.id)
return 0
def benson14_retinotopy_command(*args):
'''
benson14_retinotopy_command(args...) runs the benson14_retinotopy command; see
benson14_retinotopy_help for mor information.
'''
# Parse the arguments...
(args, opts) = _benson14_parser(args)
# help?
if opts['help']:
print benson14_retinotopy_help
return 1
# verbose?
verbose = opts['verbose']
def note(s):
if verbose: print s
return verbose
# Add the subjects directory, if there is one
if 'subjects_dir' in opts and opts['subjects_dir'] is not None:
add_subject_path(opts['subjects_dir'])
ow = not opts['no_overwrite']
nse = opts['no_surf_export']
nve = opts['no_vol_export']
tr = {'polar_angle': opts['angle_tag'],
'eccentricity': opts['eccen_tag'],
'visual_area': opts['label_tag']}
# okay, now go through the subjects...
for subnm in args:
note('Processing subject %s:' % subnm)
sub = freesurfer_subject(subnm)
note(' - Interpolating template...')
(lhdat, rhdat) = predict_retinotopy(sub, template=opts['template'])
# Export surfaces
if nse:
note(' - Skipping surface export.')
else:
note(' - Exporting surfaces:')
for (t,dat) in lhdat.iteritems():
flnm = os.path.join(sub.directory, 'surf', 'lh.' + tr[t] + '.mgz')
if ow or not os.path.exist(flnm):
note(' - Exporting LH prediction file: %s' % flnm)
img = fsmgh.MGHImage(
np.asarray([[dat]], dtype=(np.int32 if t == 'visual_area' else np.float32)),
np.eye(4))
img.to_filename(flnm)
else:
note(' - Not overwriting existing file: %s' % flnm)
for (t,dat) in rhdat.iteritems():
flnm = os.path.join(sub.directory, 'surf', 'rh.' + tr[t] + '.mgz')
if ow or not os.path.exist(flnm):
note(' - Exporting RH prediction file: %s' % flnm)
img = fsmgh.MGHImage(
np.asarray([[dat]], dtype=(np.int32 if t == 'visual_area' else np.float32)),
np.eye(4))
img.to_filename(flnm)
else:
note(' - Not overwriting existing file: %s' % flnm)
# Export volumes
if nve:
note(' - Skipping volume export.')
else:
surf2rib = cortex_to_ribbon_map(sub, hemi=None)
note(' - Exporting Volumes:')
for t in lhdat.keys():
flnm = os.path.join(sub.directory, 'mri', tr[t] + '.mgz')
if ow or not os.path.exist(flnm):
note(' - Preparing volume file: %s' % flnm)
vol = cortex_to_ribbon(sub,
(lhdat[t], rhdat[t]),
map=surf2rib,
method=('max' if t == 'visual_area' else 'weighted'),
dtype=(np.int32 if t == 'visual_area' else np.float32))
note(' - Exporting volume file: %s' % flnm)
vol.to_filename(flnm)
else:
note(' - Not overwriting existing file: %s' % flnm)
note(' Subject %s finished!' % sub.id)
return 0
def register_retinotopy_command(args):
'''
register_retinotopy_command(args) can be given a list of arguments, such as sys.argv[1:]; these
arguments may include any options and must include at least one subject id. All subjects whose
ids are given are registered to a retinotopy model, and the resulting registration, as well as
the predictions made by the model in the registration, are exported.
'''
# Parse the arguments
(args, opts) = _retinotopy_parser(args)
# First, help?
if opts['help']:
print register_retinotopy_help
return 1
# and if we are verbose, lets setup a note function
verbose = opts['verbose']
def note(s):
if verbose: print s
return verbose
# Add the subjects directory, if there is one
if 'subjects_dir' in opts and opts['subjects_dir'] is not None:
add_subject_path(opts['subjects_dir'])
# Parse the simple numbers
for o in [
'weight_cutoff', 'edge_strength', 'angle_strength',
'func_strength', 'max_step_size', 'max_out_eccen'
]:
opts[o] = float(opts[o])
opts['max_steps'] = int(opts['max_steps'])
# These are for now not supported: #TODO
if opts['angle_math'] or opts['angle_radians'] or opts['eccen_radians']:
print 'Mathematical angles and angles not in degrees are not yet supported.'
return 1
# The remainder of the args can wait for now; walk through the subjects:
tag_key = {
'eccen': 'eccentricity',
'angle': 'polar_angle',
'label': 'visual_area'
}
for subnm in args:
sub = freesurfer_subject(subnm)
note('Processing subject: %s' % sub.id)
# we need to register this subject...
res = {}
ow = not opts['no_overwrite']
for h in ['LH', 'RH']:
note(' Processing hemisphere: %s' % h)
hemi = sub.__getattr__(h)
# See if we are loading custom values...
(ang, ecc, wgt) = (None, None, None)
suffix = '_' + h.lower() + '_file'
if opts['angle' + suffix] is not None:
ang = _guess_surf_file(opts['angle' + suffix])
if opts['eccen' + suffix] is not None:
ecc = _guess_surf_file(opts['eccen' + suffix])
if opts['weight' + suffix] is not None:
wgt = _guess_surf_file(opts['weight' + suffix])
# Do the registration
note(' - Running Registration...')
res[h] = register_retinotopy(
hemi,
retinotopy_model(),
polar_angle=ang,
eccentricity=ecc,
weight=wgt,
weight_cutoff=opts['weight_cutoff'],
partial_voluming_correction=opts['part_vol_correct'],
edge_scale=opts['edge_strength'],
angle_scale=opts['angle_strength'],
functional_scale=opts['func_strength'],
prior=opts['prior'],
max_predicted_eccen=opts['max_out_eccen'],
max_steps=opts['max_steps'],
max_step_size=opts['max_step_size'])
# Perform the hemi-specific outputs now:
if not opts['no_reg_export']:
regnm = '.'.join(
[h.lower(), opts['registration_name'], 'sphere', 'reg'])
flnm = (os.path.join(sub.directory, 'surf', regnm)
if h == 'LH' else os.path.join(sub.directory, 'xhemi',
'surf', regnm))
if ow or not os.path.exist(flnm):
note(' - Exporting registration file: %s' % flnm)
fsio.write_geometry(
flnm, res[h].coordinates.T, res[h].faces.T,
'Created by neuropythy (github.com/noahbenson/neuropythy)'
)
else:
note(' - Skipping registration file: %s (file exists)' %
flnm)
if not opts['no_surf_export']:
for dim in ['angle', 'eccen', 'label']:
flnm = os.path.join(
sub.directory, 'surf',
'.'.join([h.lower(), opts[dim + '_tag'], 'mgz']))
if ow or not os.path.exist(flnm):
note(' - Exporting prediction file: %s' % flnm)
img = fsmgh.MGHImage(
np.asarray([[res[h].prop(tag_key[dim])]],
dtype=(np.int32 if dim == 'label' else
np.float32)), np.eye(4))
img.to_filename(flnm)
else:
note(' - Skipping prediction file: %s (file exists)'
% flnm)
# Do the volume exports here
if not opts['no_vol_export']:
note(' Processing volume data...')
note(' - Calculating cortex-to-ribbon mapping...')
surf2rib = cortex_to_ribbon_map(sub, hemi=None)
for dim in ['angle', 'eccen', 'label']:
flnm = os.path.join(sub.directory, 'mri',
opts[dim + '_tag'] + '.mgz')
if ow or not os.path.exist(flnm):
note(' - Generating volume file: %s' % flnm)
vol = cortex_to_ribbon(
sub, (res['LH'].prop(tag_key[dim]), res['RH'].prop(
tag_key[dim])),
map=surf2rib,
method=('max' if dim == 'label' else 'weighted'),
dtype=(np.int32 if dim == 'label' else np.float32))
note(' - Exporting volume file: %s' % flnm)
vol.to_filename(flnm)
else:
note(' - Skipping volume file: %s (file exists)' % flnm)
# That is it for this subject!
note(' Subject %s finished!' % sub.id)
# And if we made it here, all was successful.
return 0
