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Merged
merged 4 commits into from
Mar 4, 2017
Merged

ENH: Add -hires and -expert flags to ReconAll #1857

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71c9538
Add -hires and -expert flags to ReconAll
effigies Mar 1, 2017
260a275
Add ExpertOptions interface to freesurfer.utils
effigies Mar 2, 2017
af036f7
Accept expert options as a dictionary
effigies Mar 3, 2017
2aa325e
Explicitly add extra options to ReconAllInputSpec
effigies Mar 3, 2017
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65 changes: 65 additions & 0 deletions nipype/interfaces/freesurfer/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -632,10 +632,42 @@ class ReconAllInputSpec(CommandLineInputSpec):
desc="Number of processors to use in parallel")
parallel = traits.Bool(argstr="-parallel",
desc="Enable parallel execution")
hires = traits.Bool(argstr="-hires", min_ver='6.0.0',
desc="Conform to minimum voxel size (for voxels < 1mm)")
expert = File(exists=True, argstr='-expert %s',
desc="Set parameters using expert file")
subjects_dir = Directory(exists=True, argstr='-sd %s', hash_files=False,
desc='path to subjects directory', genfile=True)
flags = traits.Str(argstr='%s', desc='additional parameters')

# Expert options
talairach = traits.Str(desc="Flags to pass to talairach commands", xor=['expert'])
mri_normalize = traits.Str(desc="Flags to pass to mri_normalize commands", xor=['expert'])
mri_watershed = traits.Str(desc="Flags to pass to mri_watershed commands", xor=['expert'])
mri_em_register = traits.Str(desc="Flags to pass to mri_em_register commands", xor=['expert'])
mri_ca_normalize = traits.Str(desc="Flags to pass to mri_ca_normalize commands", xor=['expert'])
mri_ca_register = traits.Str(desc="Flags to pass to mri_ca_register commands", xor=['expert'])
mri_remove_neck = traits.Str(desc="Flags to pass to mri_remove_neck commands", xor=['expert'])
mri_ca_label = traits.Str(desc="Flags to pass to mri_ca_label commands", xor=['expert'])
mri_segstats = traits.Str(desc="Flags to pass to mri_segstats commands", xor=['expert'])
mri_mask = traits.Str(desc="Flags to pass to mri_mask commands", xor=['expert'])
mri_segment = traits.Str(desc="Flags to pass to mri_segment commands", xor=['expert'])
mri_edit_wm_with_aseg = traits.Str(desc="Flags to pass to mri_edit_wm_with_aseg commands", xor=['expert'])
mri_pretess = traits.Str(desc="Flags to pass to mri_pretess commands", xor=['expert'])
mri_fill = traits.Str(desc="Flags to pass to mri_fill commands", xor=['expert'])
mri_tessellate = traits.Str(desc="Flags to pass to mri_tessellate commands", xor=['expert'])
mris_smooth = traits.Str(desc="Flags to pass to mri_smooth commands", xor=['expert'])
mris_inflate = traits.Str(desc="Flags to pass to mri_inflate commands", xor=['expert'])
mris_sphere = traits.Str(desc="Flags to pass to mris_sphere commands", xor=['expert'])
mris_fix_topology = traits.Str(desc="Flags to pass to mris_fix_topology commands", xor=['expert'])
mris_make_surfaces = traits.Str(desc="Flags to pass to mris_make_surfaces commands", xor=['expert'])
mris_surf2vol = traits.Str(desc="Flags to pass to mris_surf2vol commands", xor=['expert'])
mris_register = traits.Str(desc="Flags to pass to mris_register commands", xor=['expert'])
mrisp_paint = traits.Str(desc="Flags to pass to mrisp_paint commands", xor=['expert'])
mris_ca_label = traits.Str(desc="Flags to pass to mris_ca_label commands", xor=['expert'])
mris_anatomical_stats = traits.Str(desc="Flags to pass to mris_anatomical_stats commands", xor=['expert'])
mri_aparc2aseg = traits.Str(desc="Flags to pass to mri_aparc2aseg commands", xor=['expert'])


class ReconAllOutputSpec(FreeSurferSource.output_spec):
subjects_dir = Directory(exists=True, desc='Freesurfer subjects directory.')
Expand Down Expand Up @@ -851,6 +883,16 @@ class ReconAll(CommandLine):

_steps = _autorecon1_steps + _autorecon2_steps + _autorecon3_steps

_binaries = ['talairach', 'mri_normalize', 'mri_watershed',
'mri_em_register', 'mri_ca_normalize', 'mri_ca_register',
'mri_remove_neck', 'mri_ca_label', 'mri_segstats',
'mri_mask', 'mri_segment', 'mri_edit_wm_with_aseg',
'mri_pretess', 'mri_fill', 'mri_tessellate', 'mris_smooth',
'mris_inflate', 'mris_sphere', 'mris_fix_topology',
'mris_make_surfaces', 'mris_surf2vol', 'mris_register',
'mrisp_paint', 'mris_ca_label', 'mris_anatomical_stats',
'mri_aparc2aseg']

def _gen_subjects_dir(self):
return os.getcwd()

Expand Down Expand Up @@ -900,6 +942,11 @@ def _format_arg(self, name, trait_spec, value):
@property
def cmdline(self):
cmd = super(ReconAll, self).cmdline

# Adds '-expert' flag if expert flags are passed
# Mutually exclusive with 'expert' input parameter
cmd += self._prep_expert_file()

if not self._is_resuming():
return cmd
subjects_dir = self.inputs.subjects_dir
Expand Down Expand Up @@ -933,6 +980,24 @@ def cmdline(self):
iflogger.info('resume recon-all : %s' % cmd)
return cmd

def _prep_expert_file(self):
if isdefined(self.inputs.expert):
return ''

lines = []
for binary in self._binaries:
args = getattr(self.inputs, binary)
if isdefined(args):
lines.append('{} {}\n'.format(binary, args))

if lines == []:
return ''

expert_fname = os.path.abspath('expert.opts')
with open(expert_fname, 'w') as fobj:
fobj.write(''.join(lines))
return ' -expert {}'.format(expert_fname)


class BBRegisterInputSpec(FSTraitedSpec):
subject_id = traits.Str(argstr='--s %s',
Expand Down
57 changes: 57 additions & 0 deletions nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,68 @@ def test_ReconAll_inputs():
environ=dict(nohash=True,
usedefault=True,
),
expert=dict(argstr='-expert %s',
),
flags=dict(argstr='%s',
),
hemi=dict(argstr='-hemi %s',
),
hires=dict(argstr='-hires',
min_ver='6.0.0',
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
mri_aparc2aseg=dict(xor=['expert'],
),
mri_ca_label=dict(xor=['expert'],
),
mri_ca_normalize=dict(xor=['expert'],
),
mri_ca_register=dict(xor=['expert'],
),
mri_edit_wm_with_aseg=dict(xor=['expert'],
),
mri_em_register=dict(xor=['expert'],
),
mri_fill=dict(xor=['expert'],
),
mri_mask=dict(xor=['expert'],
),
mri_normalize=dict(xor=['expert'],
),
mri_pretess=dict(xor=['expert'],
),
mri_remove_neck=dict(xor=['expert'],
),
mri_segment=dict(xor=['expert'],
),
mri_segstats=dict(xor=['expert'],
),
mri_tessellate=dict(xor=['expert'],
),
mri_watershed=dict(xor=['expert'],
),
mris_anatomical_stats=dict(xor=['expert'],
),
mris_ca_label=dict(xor=['expert'],
),
mris_fix_topology=dict(xor=['expert'],
),
mris_inflate=dict(xor=['expert'],
),
mris_make_surfaces=dict(xor=['expert'],
),
mris_register=dict(xor=['expert'],
),
mris_smooth=dict(xor=['expert'],
),
mris_sphere=dict(xor=['expert'],
),
mris_surf2vol=dict(xor=['expert'],
),
mrisp_paint=dict(xor=['expert'],
),
openmp=dict(argstr='-openmp %d',
),
parallel=dict(argstr='-parallel',
Expand All @@ -36,6 +91,8 @@ def test_ReconAll_inputs():
genfile=True,
hash_files=False,
),
talairach=dict(xor=['expert'],
),
terminal_output=dict(nohash=True,
),
use_T2=dict(argstr='-T2pial',
Expand Down