Merge pull request #1857 from effigies/reconall_newparams

ENH: Add -hires and -expert flags to ReconAll

Author: satra

nipype/interfaces/freesurfer/preprocess.py

@@ -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.')
@@ -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()
 
@@ -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
@@ -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',

nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py

@@ -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',
@@ -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',