def estimate_structure():
"""
CLI for estimating PVs from a single surface
"""
parser = CommonParser(
'ref',
'struct2ref',
'flirt',
'struct',
'super',
'out',
'surf',
'coords',
description="Estimate PVs for a structure defined by a single surface."
)
kwargs = vars(parser.parse_args())
ext = '.nii.gz'
if not kwargs.get('out'):
namebase = op.splitext(utils._splitExts(kwargs['ref'])[0])[0]
sname = op.splitext(utils._splitExts(kwargs['surf'])[0])[0]
outdir = op.dirname(kwargs['ref'])
kwargs['out'] = op.join(outdir, '%s_%s_pvs%s' % (namebase, sname, ext))
else:
if not kwargs['out'].endswith(ext):
kwargs['out'] += ext
# Estimate
PVs = pvestimation.structure(**kwargs)
# Output
print('Saving output at', kwargs['out'])
refSpace = ImageSpace(kwargs['ref'])
refSpace.save_image(PVs, kwargs['out'])
def estimate_cortex():
"""
CLI for estimating PVs from cortex (either L,R, or both)
"""
parser = CommonParser(
'ref',
'struct2ref',
'fsdir',
'LPS',
'RPS',
'RWS',
'LWS',
'flirt',
'struct',
'cores',
'out',
'ones',
'super',
description="Estimate PVs for L/R cortical hemispheres")
kwargs = vars(parser.parse_args())
# Estimation
PVs = pvestimation.cortex(**kwargs)
# Output
ext = '.nii.gz'
if not kwargs.get('out'):
namebase = op.splitext(utils._splitExts(kwargs['ref'])[0])[0]
outdir = op.join(op.dirname(kwargs['ref']), namebase + '_cortexpvs')
else:
outdir = kwargs['out']
utils._weak_mkdir(outdir)
refSpace = ImageSpace(kwargs['ref'])
print('Saving output at', outdir)
p = op.join(outdir, 'stacked' + ext)
refSpace.save_image(PVs, p)
for i, t in enumerate(['GM', 'WM', 'nonbrain']):
p = op.join(outdir, t + ext)
refSpace.save_image(PVs[:, :, :, i], p)
def estimate_complete():
"""
CLI for estimating PVs for L/R cortex and subcortex
"""
parser = CommonParser(
'ref',
'struct2ref',
'fslanat',
'fsdir',
'firstdir',
'fastdir',
'LPS',
'LWS',
'RPS',
'RWS',
'ones',
'super',
'cores',
'out',
'flirt',
'struct',
description=(
"Estimate PVs for cortex and all structures identified "
"by FIRST within a reference image space. Use FAST to fill in "
"non-surface PVs"))
kwargs = vars(parser.parse_args())
# Unless we have been given prepared fslanat dir, we will provide the path
# to the next function to create one
if type(kwargs.get('fslanat')) is str:
if not op.isdir(kwargs.get('fslanat')):
raise RuntimeError("fslanat dir %s does not exist" %
kwargs['fslanat'])
else:
if not all([(('fastdir' in kwargs) and ('firstdir' in kwargs)),
(('LPS' in kwargs) and ('RPS' in kwargs))]):
raise RuntimeError(
"Either separate -firstdir and -fastdir" +
" must be provided, or an -fslanat dir must be provided")
output = pvestimation.complete(**kwargs)
# Output paths. If given -out then use that as output, otherwise
# save alongside reference image
ext = '.nii.gz'
if not kwargs.get('out'):
namebase = op.splitext(utils._splitExts(kwargs['ref'])[0])[0]
outdir = op.join(op.dirname(kwargs['ref']), namebase + '_surfpvs')
else:
outdir = kwargs['out']
# Make output dirs if they do not exist.
intermediatedir = op.join(outdir, 'intermediate_pvs')
utils._weak_mkdir(outdir)
utils._weak_mkdir(intermediatedir)
# Load the reference image space and save the various outputs.
# 'stacked' goes in the outdir, all others go in outdir/intermediate
refSpace = ImageSpace(kwargs['ref'])
print('Saving output at', outdir)
for k, o in output.items():
if k in ['stacked', 'GM', 'WM', 'nonbrain']:
path = op.join(outdir, k + ext)
else:
path = op.join(intermediatedir, k + ext)
refSpace.save_image(o, path)