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merged 4 commits into from
May 10, 2017
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ENH: Update multi-stage recon-all directives #1991

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c8bae35
ENH: Update multi-stage recon-all directives
effigies May 2, 2017
a3d2b06
DOC: Add doctests for fiddly ReconAll invocations
effigies May 2, 2017
7493a1c
FIX: Update argument handling, doctests
effigies May 3, 2017
8fcc097
RF: Refine step checking for partial directives
effigies May 4, 2017
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259 changes: 161 additions & 98 deletions nipype/interfaces/freesurfer/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -611,10 +611,18 @@ def _gen_filename(self, name):
class ReconAllInputSpec(CommandLineInputSpec):
subject_id = traits.Str("recon_all", argstr='-subjid %s',
desc='subject name', usedefault=True)
directive = traits.Enum('all', 'autorecon1', 'autorecon2', 'autorecon2-cp',
'autorecon2-wm', 'autorecon2-inflate1',
'autorecon2-perhemi', 'autorecon3', 'localGI',
'qcache', argstr='-%s', desc='process directive',
directive = traits.Enum('all', 'autorecon1',
# autorecon2 variants
'autorecon2', 'autorecon2-volonly',
'autorecon2-perhemi', 'autorecon2-inflate1',
'autorecon2-cp', 'autorecon2-wm',
# autorecon3 variants
'autorecon3', 'autorecon3-T2pial',
# Mix of autorecon2 and autorecon3 steps
'autorecon-pial', 'autorecon-hemi',
# Not "multi-stage flags"
'localGI', 'qcache',
argstr='-%s', desc='process directive',
usedefault=True, position=0)
hemi = traits.Enum('lh', 'rh', desc='hemisphere to process',
argstr="-hemi %s")
Expand Down Expand Up @@ -709,6 +717,38 @@ class ReconAll(CommandLine):
>>> reconall.inputs.flags = ["-cw256", "-qcache"]
>>> reconall.cmdline # doctest: +ALLOW_UNICODE
'recon-all -all -i structural.nii -cw256 -qcache -subjid foo -sd .'

Hemisphere may be specified regardless of directive:

>>> reconall.inputs.flags = []
>>> reconall.inputs.hemi = 'lh'
>>> reconall.cmdline # doctest: +ALLOW_UNICODE
'recon-all -all -i structural.nii -hemi lh -subjid foo -sd .'

``-autorecon-hemi`` uses the ``-hemi`` input to specify the hemisphere
to operate upon:

>>> reconall.inputs.directive = 'autorecon-hemi'
>>> reconall.cmdline # doctest: +ALLOW_UNICODE
'recon-all -autorecon-hemi lh -i structural.nii -subjid foo -sd .'

Hippocampal subfields can accept T1 and T2 images:

>>> reconall_subfields = ReconAll()
>>> reconall_subfields.inputs.subject_id = 'foo'
>>> reconall_subfields.inputs.directive = 'all'
>>> reconall_subfields.inputs.subjects_dir = '.'
>>> reconall_subfields.inputs.T1_files = 'structural.nii'
>>> reconall_subfields.inputs.hippocampal_subfields_T1 = True
>>> reconall_subfields.cmdline # doctest: +ALLOW_UNICODE
'recon-all -all -i structural.nii -hippocampal-subfields-T1 -subjid foo -sd .'
>>> reconall_subfields.inputs.hippocampal_subfields_T2 = (
... 'structural.nii', 'test')
>>> reconall_subfields.cmdline # doctest: +ALLOW_UNICODE
'recon-all -all -i structural.nii -hippocampal-subfields-T1T2 structural.nii test -subjid foo -sd .'
>>> reconall_subfields.inputs.hippocampal_subfields_T1 = False
>>> reconall_subfields.cmdline # doctest: +ALLOW_UNICODE
'recon-all -all -i structural.nii -hippocampal-subfields-T2 structural.nii test -subjid foo -sd .'
"""

_cmd = 'recon-all'
Expand Down Expand Up @@ -744,7 +784,7 @@ class ReconAll(CommandLine):
'mri/brainmask.mgz'], []),
]
if Info.looseversion() < LooseVersion("6.0.0"):
_autorecon2_steps = [
_autorecon2_volonly_steps = [
('gcareg', ['mri/transforms/talairach.lta'], []),
('canorm', ['mri/norm.mgz'], []),
('careg', ['mri/transforms/talairach.m3z'], []),
Expand All @@ -765,65 +805,51 @@ class ReconAll(CommandLine):
('fill', ['mri/filled.mgz',
# 'scripts/ponscc.cut.log',
], []),
('tessellate', ['surf/lh.orig.nofix', 'surf/rh.orig.nofix'], []),
('smooth1', ['surf/lh.smoothwm.nofix', 'surf/rh.smoothwm.nofix'],
[]),
('inflate1', ['surf/lh.inflated.nofix', 'surf/rh.inflated.nofix'],
[]),
('qsphere', ['surf/lh.qsphere.nofix', 'surf/rh.qsphere.nofix'],
[]),
('fix', ['surf/lh.orig', 'surf/rh.orig'], []),
('white', ['surf/lh.white', 'surf/rh.white',
'surf/lh.curv', 'surf/rh.curv',
'surf/lh.area', 'surf/rh.area',
'label/lh.cortex.label', 'label/rh.cortex.label'], []),
('smooth2', ['surf/lh.smoothwm', 'surf/rh.smoothwm'], []),
('inflate2', ['surf/lh.inflated', 'surf/rh.inflated',
'surf/lh.sulc', 'surf/rh.sulc',
'surf/lh.inflated.H', 'surf/rh.inflated.H',
'surf/lh.inflated.K', 'surf/rh.inflated.K'], []),
]
_autorecon2_lh_steps = [
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only a nitpick - is there a reason this is called _lh_ as opposed to say _hemi_

otherwise looks reasonable to me.

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Because I specify lh in the filenames. I then make a rh copy below, just swapping the filenames out.

('tessellate', ['surf/lh.orig.nofix'], []),
('smooth1', ['surf/lh.smoothwm.nofix'], []),
('inflate1', ['surf/lh.inflated.nofix'], []),
('qsphere', ['surf/lh.qsphere.nofix'], []),
('fix', ['surf/lh.orig'], []),
('white', ['surf/lh.white', 'surf/lh.curv', 'surf/lh.area',
'label/lh.cortex.label'], []),
('smooth2', ['surf/lh.smoothwm'], []),
('inflate2', ['surf/lh.inflated', 'surf/lh.sulc',
'surf/lh.inflated.H', 'surf/lh.inflated.K'], []),
# Undocumented in ReconAllTableStableV5.3
('curvstats', ['stats/lh.curv.stats', 'stats/rh.curv.stats'], []),
('curvstats', ['stats/lh.curv.stats'], []),
]
_autorecon3_steps = [
('sphere', ['surf/lh.sphere', 'surf/rh.sphere'], []),
('surfreg', ['surf/lh.sphere.reg', 'surf/rh.sphere.reg'], []),
('jacobian_white', ['surf/lh.jacobian_white',
'surf/rh.jacobian_white'], []),
('avgcurv', ['surf/lh.avg_curv', 'surf/rh.avg_curv'], []),
('cortparc', ['label/lh.aparc.annot', 'label/rh.aparc.annot'], []),
('pial', ['surf/lh.pial', 'surf/rh.pial',
'surf/lh.curv.pial', 'surf/rh.curv.pial',
'surf/lh.area.pial', 'surf/rh.area.pial',
'surf/lh.thickness', 'surf/rh.thickness'], []),
_autorecon3_lh_steps = [
('sphere', ['surf/lh.sphere'], []),
('surfreg', ['surf/lh.sphere.reg'], []),
('jacobian_white', ['surf/lh.jacobian_white'], []),
('avgcurv', ['surf/lh.avg_curv'], []),
('cortparc', ['label/lh.aparc.annot'], []),
('pial', ['surf/lh.pial', 'surf/lh.curv.pial', 'surf/lh.area.pial',
'surf/lh.thickness'], []),
# Misnamed outputs in ReconAllTableStableV5.3: ?h.w-c.pct.mgz
('pctsurfcon', ['surf/lh.w-g.pct.mgh', 'surf/rh.w-g.pct.mgh'], []),
('parcstats', ['stats/lh.aparc.stats', 'stats/rh.aparc.stats',
'label/aparc.annot.a2009s.ctab'], []),
('cortparc2', ['label/lh.aparc.a2009s.annot',
'label/rh.aparc.a2009s.annot'], []),
('parcstats2', ['stats/lh.aparc.a2009s.stats',
'stats/rh.aparc.a2009s.stats',
'label/aparc.annot.a2009s.ctab'], []),
('pctsurfcon', ['surf/lh.w-g.pct.mgh'], []),
('parcstats', ['stats/lh.aparc.stats'], []),
('cortparc2', ['label/lh.aparc.a2009s.annot'], []),
('parcstats2', ['stats/lh.aparc.a2009s.stats'], []),
# Undocumented in ReconAllTableStableV5.3
('cortparc3', ['label/lh.aparc.DKTatlas40.annot',
'label/rh.aparc.DKTatlas40.annot'], []),
('cortparc3', ['label/lh.aparc.DKTatlas40.annot'], []),
# Undocumented in ReconAllTableStableV5.3
('parcstats3', ['stats/lh.aparc.a2009s.stats',
'stats/rh.aparc.a2009s.stats',
'label/aparc.annot.a2009s.ctab'], []),
('parcstats3', ['stats/lh.aparc.a2009s.stats'], []),
('label-exvivo-ec', ['label/lh.entorhinal_exvivo.label'], []),
]
_autorecon3_added_steps = [
('cortribbon', ['mri/lh.ribbon.mgz', 'mri/rh.ribbon.mgz',
'mri/ribbon.mgz'], []),
('segstats', ['stats/aseg.stats'], []),
('aparc2aseg', ['mri/aparc+aseg.mgz',
'mri/aparc.a2009s+aseg.mgz'], []),
('wmparc', ['mri/wmparc.mgz', 'stats/wmparc.stats'], []),
('balabels', ['label/BA.ctab', 'label/BA.thresh.ctab'], []),
('label-exvivo-ec', ['label/lh.entorhinal_exvivo.label',
'label/rh.entorhinal_exvivo.label'], []),
]
else:
_autorecon2_steps = [
_autorecon2_volonly_steps = [
('gcareg', ['mri/transforms/talairach.lta'], []),
('canorm', ['mri/norm.mgz'], []),
('careg', ['mri/transforms/talairach.m3z'], []),
Expand All @@ -838,53 +864,39 @@ class ReconAll(CommandLine):
('fill', ['mri/filled.mgz',
# 'scripts/ponscc.cut.log',
], []),
('tessellate', ['surf/lh.orig.nofix', 'surf/rh.orig.nofix'], []),
('smooth1', ['surf/lh.smoothwm.nofix', 'surf/rh.smoothwm.nofix'],
[]),
('inflate1', ['surf/lh.inflated.nofix', 'surf/rh.inflated.nofix'],
[]),
('qsphere', ['surf/lh.qsphere.nofix', 'surf/rh.qsphere.nofix'],
[]),
('fix', ['surf/lh.orig', 'surf/rh.orig'], []),
('white', ['surf/lh.white.preaparc', 'surf/rh.white.preaparc',
'surf/lh.curv', 'surf/rh.curv',
'surf/lh.area', 'surf/rh.area',
'label/lh.cortex.label', 'label/rh.cortex.label'], []),
('smooth2', ['surf/lh.smoothwm', 'surf/rh.smoothwm'], []),
('inflate2', ['surf/lh.inflated', 'surf/rh.inflated',
'surf/lh.sulc', 'surf/rh.sulc'], []),
('curvHK', ['surf/lh.white.H', 'surf/rh.white.H',
'surf/lh.white.K', 'surf/rh.white.K',
'surf/lh.inflated.H', 'surf/rh.inflated.H',
'surf/lh.inflated.K', 'surf/rh.inflated.K'], []),
('curvstats', ['stats/lh.curv.stats', 'stats/rh.curv.stats'], []),
]
_autorecon3_steps = [
('sphere', ['surf/lh.sphere', 'surf/rh.sphere'], []),
('surfreg', ['surf/lh.sphere.reg', 'surf/rh.sphere.reg'], []),
('jacobian_white', ['surf/lh.jacobian_white',
'surf/rh.jacobian_white'], []),
('avgcurv', ['surf/lh.avg_curv', 'surf/rh.avg_curv'], []),
('cortparc', ['label/lh.aparc.annot', 'label/rh.aparc.annot'], []),
('pial', ['surf/lh.pial', 'surf/rh.pial',
'surf/lh.curv.pial', 'surf/rh.curv.pial',
'surf/lh.area.pial', 'surf/rh.area.pial',
'surf/lh.thickness', 'surf/rh.thickness'], []),
_autorecon2_lh_steps = [
('tessellate', ['surf/lh.orig.nofix'], []),
('smooth1', ['surf/lh.smoothwm.nofix'], []),
('inflate1', ['surf/lh.inflated.nofix'], []),
('qsphere', ['surf/lh.qsphere.nofix'], []),
('fix', ['surf/lh.orig'], []),
('white', ['surf/lh.white.preaparc', 'surf/lh.curv',
'surf/lh.area', 'label/lh.cortex.label'], []),
('smooth2', ['surf/lh.smoothwm'], []),
('inflate2', ['surf/lh.inflated', 'surf/lh.sulc'], []),
('curvHK', ['surf/lh.white.H', 'surf/lh.white.K',
'surf/lh.inflated.H', 'surf/lh.inflated.K'], []),
('curvstats', ['stats/lh.curv.stats'], []),
]
_autorecon3_lh_steps = [
('sphere', ['surf/lh.sphere'], []),
('surfreg', ['surf/lh.sphere.reg'], []),
('jacobian_white', ['surf/lh.jacobian_white'], []),
('avgcurv', ['surf/lh.avg_curv'], []),
('cortparc', ['label/lh.aparc.annot'], []),
('pial', ['surf/lh.pial', 'surf/lh.curv.pial',
'surf/lh.area.pial', 'surf/lh.thickness'], []),
('parcstats', ['stats/lh.aparc.stats'], []),
('cortparc2', ['label/lh.aparc.a2009s.annot'], []),
('parcstats2', ['stats/lh.aparc.a2009s.stats'], []),
('cortparc3', ['label/lh.aparc.DKTatlas.annot'], []),
('parcstats3', ['stats/lh.aparc.DKTatlas.stats'], []),
('pctsurfcon', ['surf/lh.w-g.pct.mgh'], []),
]
_autorecon3_added_steps = [
('cortribbon', ['mri/lh.ribbon.mgz', 'mri/rh.ribbon.mgz',
'mri/ribbon.mgz'], []),
('parcstats', ['stats/lh.aparc.stats', 'stats/rh.aparc.stats',
'label/aparc.annot.ctab'], []),
('cortparc2', ['label/lh.aparc.a2009s.annot',
'label/rh.aparc.a2009s.annot'], []),
('parcstats2', ['stats/lh.aparc.a2009s.stats',
'stats/rh.aparc.a2009s.stats',
'label/aparc.annot.a2009s.ctab'], []),
('cortparc3', ['label/lh.aparc.DKTatlas.annot',
'label/rh.aparc.DKTatlas.annot'], []),
('parcstats3', ['stats/lh.aparc.DKTatlas.stats',
'stats/rh.aparc.DKTatlas.stats',
'label/aparc.annot.DKTatlas.ctab'], []),
('pctsurfcon', ['surf/lh.w-g.pct.mgh', 'surf/rh.w-g.pct.mgh'], []),
('hyporelabel', ['mri/aseg.presurf.hypos.mgz'], []),
('aparc2aseg', ['mri/aparc+aseg.mgz',
'mri/aparc.a2009s+aseg.mgz',
Expand All @@ -900,6 +912,30 @@ class ReconAll(CommandLine):
'label/rh.entorhinal_exvivo.label'], []),
]

# Fill out autorecon2 steps
_autorecon2_rh_steps = [
(step, [out.replace('lh', 'rh') for out in outs], ins)
for step, outs, ins in _autorecon2_lh_steps]
_autorecon2_perhemi_steps = [
(step, [of for out in outs
for of in (out, out.replace('lh', 'rh'))], ins)
for step, outs, ins in _autorecon2_lh_steps]
_autorecon2_steps = _autorecon2_volonly_steps + _autorecon2_perhemi_steps

# Fill out autorecon3 steps
_autorecon3_rh_steps = [
(step, [out.replace('lh', 'rh') for out in outs], ins)
for step, outs, ins in _autorecon3_lh_steps]
_autorecon3_perhemi_steps = [
(step, [of for out in outs
for of in (out, out.replace('lh', 'rh'))], ins)
for step, outs, ins in _autorecon3_lh_steps]
_autorecon3_steps = _autorecon3_perhemi_steps + _autorecon3_added_steps

# Fill out autorecon-hemi lh/rh steps
_autorecon_lh_steps = (_autorecon2_lh_steps + _autorecon3_lh_steps)
_autorecon_rh_steps = (_autorecon2_rh_steps + _autorecon3_rh_steps)

_steps = _autorecon1_steps + _autorecon2_steps + _autorecon3_steps

_binaries = ['talairach', 'mri_normalize', 'mri_watershed',
Expand Down Expand Up @@ -955,14 +991,24 @@ def _is_resuming(self):
def _format_arg(self, name, trait_spec, value):
if name == 'T1_files':
if self._is_resuming():
return ''
return None
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Switched to returning None just because that avoids the extra spaces in the cmdline string, making the doctests less painful to debug.

if name == 'hippocampal_subfields_T1' and \
isdefined(self.inputs.hippocampal_subfields_T2):
return ''
return None
if all((name == 'hippocampal_subfields_T2',
isdefined(self.inputs.hippocampal_subfields_T1) and
self.inputs.hippocampal_subfields_T1)):
trait_spec.argstr = trait_spec.argstr.replace('T2', 'T1T2')
argstr = trait_spec.argstr.replace('T2', 'T1T2')
return argstr % value
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This part here was a (minor) bug, in that trait_spec is non-ephemeral, so changing trait_spec.argstr changes it for all future calls. Unlikely to affect anything except the doctests, but still worth cleaning up.

if name == 'directive' and value == 'autorecon-hemi':
if not isdefined(self.inputs.hemi):
raise ValueError("Directive 'autorecon-hemi' requires hemi "
"input to be set")
value += ' ' + self.inputs.hemi
if all((name == 'hemi',
isdefined(self.inputs.directive) and
self.inputs.directive == 'autorecon-hemi')):
return None
return super(ReconAll, self)._format_arg(name, trait_spec, value)

@property
Expand All @@ -985,8 +1031,25 @@ def cmdline(self):
steps = []
elif directive == 'autorecon1':
steps = self._autorecon1_steps
elif directive == 'autorecon2-volonly':
steps = self._autorecon2_volonly_steps
elif directive == 'autorecon2-perhemi':
steps = self._autorecon2_perhemi_steps
elif directive.startswith('autorecon2'):
steps = self._autorecon2_steps
if isdefined(self.inputs.hemi):
if self.inputs.hemi == 'lh':
steps = (self._autorecon2_volonly_steps +
self._autorecon2_lh_steps)
else:
steps = (self._autorecon2_volonly_steps +
self._autorecon2_rh_steps)
else:
steps = self._autorecon2_steps
elif directive == 'autorecon-hemi':
if self.inputs.hemi == 'lh':
steps = self._autorecon_lh_steps
else:
steps = self._autorecon_rh_steps
elif directive == 'autorecon3':
steps = self._autorecon3_steps
else:
Expand Down