Merge pull request #1991 from effigies/enh/reconall_directives

ENH: Update multi-stage recon-all directives

Author: satra

nipype/interfaces/freesurfer/preprocess.py

@@ -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")
@@ -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'
@@ -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'], []),
@@ -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 = [
+            ('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'], []),
@@ -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',
@@ -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',
@@ -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
         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
+        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
@@ -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: