Merge pull request #1326 from BRAINSia/FreeSurferBreakout

ENH: FreeSurfer Wrappings for Recon-All Workflow

Author: satra

CHANGES

@@ -25,6 +25,7 @@ Next release
 * ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
 * FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
 * FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
+* ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
 
 Release 0.11.0 (September 15, 2015)
 ============

CHANGES.orig

@@ -0,0 +1,90 @@
+#!/usr/bin/env python
+"""
+================
+sMRI: FSReconAll
+================
+
+This script, smri_fsreconall.py, demonstrates the ability to use the
+reconall nipype workflow with a set of subjects and then make an average
+subject::
+
+    python smri_fsreconall.py
+
+Import necessary modules from nipype.
+"""
+
+import os
+
+import nipype.pipeline.engine as pe
+import nipype.interfaces.io as nio
+from nipype.workflows.smri.freesurfer import create_reconall_workflow
+from nipype.interfaces.freesurfer.utils import MakeAverageSubject
+from nipype.interfaces.utility import IdentityInterface
+
+"""
+Assign the tutorial directory
+"""
+
+tutorial_dir = os.path.abspath('smri_fsreconall_tutorial')
+if not os.path.isdir(tutorial_dir):
+    os.mkdir(tutorial_dir)
+
+"""
+Define the workflow directories
+"""
+
+subject_list = ['s1', 's3']
+data_dir = os.path.abspath('data')
+subjects_dir = os.path.join(tutorial_dir, 'subjects_dir')
+if not os.path.exists(subjects_dir):
+    os.mkdir(subjects_dir)
+
+wf = pe.Workflow(name="l1workflow")
+wf.base_dir = os.path.join(tutorial_dir, 'workdir')
+
+"""
+Create inputspec
+"""
+
+inputspec = pe.Node(interface=IdentityInterface(['subject_id']),
+                    name="inputspec")
+inputspec.iterables = ("subject_id", subject_list)
+
+"""
+Grab data
+"""
+
+datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
+                                               outfields=['struct']),
+                        name='datasource')
+datasource.inputs.base_directory = data_dir
+datasource.inputs.template = '%s/%s.nii'
+datasource.inputs.template_args = dict(struct=[['subject_id', 'struct']])
+datasource.inputs.subject_id = subject_list
+datasource.inputs.sort_filelist = True
+
+wf.connect(inputspec, 'subject_id', datasource, 'subject_id')
+
+"""
+Run recon-all
+"""
+
+recon_all = create_reconall_workflow()
+recon_all.inputs.inputspec.subjects_dir = subjects_dir
+
+wf.connect(datasource, 'struct', recon_all, 'inputspec.T1_files')
+wf.connect(inputspec, 'subject_id', recon_all, 'inputspec.subject_id')
+
+"""
+Make average subject
+"""
+
+average = pe.JoinNode(interface=MakeAverageSubject(),
+                      joinsource="inputspec",
+                      joinfield="subjects_ids",
+                      name="average")
+average.inputs.subjects_dir = subjects_dir
+
+wf.connect(recon_all, 'postdatasink_outputspec.subject_id', average, 'subjects_ids')
+
+wf.run("MultiProc", plugin_args={'n_procs': 4})

examples/smri_fsreconall.py

@@ -6,10 +6,21 @@
 from .preprocess import (ParseDICOMDir, UnpackSDICOMDir, MRIConvert, Resample,
                          ReconAll, BBRegister, ApplyVolTransform, Smooth,
                          DICOMConvert, RobustRegister, FitMSParams,
-                         SynthesizeFLASH)
-from .model import (MRISPreproc, GLMFit, OneSampleTTest, Binarize, Concatenate,
-                    SegStats, Label2Vol, MS_LDA)
+                         SynthesizeFLASH, MNIBiasCorrection, WatershedSkullStrip,
+                         Normalize, CANormalize, CARegister, CALabel, MRIsCALabel,
+                         SegmentCC, SegmentWM, EditWMwithAseg, ConcatenateLTA)
+from .model import (MRISPreproc, MRISPreprocReconAll, GLMFit, OneSampleTTest, Binarize,
+                    Concatenate, SegStats, SegStatsReconAll, Label2Vol, MS_LDA,
+                    Label2Label, Label2Annot, SphericalAverage)
 from .utils import (SampleToSurface, SurfaceSmooth, SurfaceTransform, Surface2VolTransform,
                     SurfaceSnapshots, ApplyMask, MRIsConvert, MRITessellate, MRIPretess,
                     MRIMarchingCubes, SmoothTessellation, MakeAverageSubject,
-                    ExtractMainComponent, Tkregister2)
+                    ExtractMainComponent, Tkregister2, AddXFormToHeader,
+                    CheckTalairachAlignment, TalairachAVI, TalairachQC, RemoveNeck,
+                    MRIFill, MRIsInflate, Sphere, FixTopology, EulerNumber,
+                    RemoveIntersection, MakeSurfaces, Curvature, CurvatureStats,
+                    Jacobian, MRIsCalc, VolumeMask, ParcellationStats, Contrast,
+                    RelabelHypointensities, Aparc2Aseg, Apas2Aseg)
+from .longitudinal import (RobustTemplate, FuseSegmentations)
+from .registration import (MPRtoMNI305, RegisterAVItoTalairach, EMRegister, Register,
+                           Paint)

nipype/algorithms/tests/test_auto_Overlap.py

@@ -20,7 +20,8 @@
 import os
 
 from ..base import (CommandLine, Directory,
-                    CommandLineInputSpec, isdefined)
+                    CommandLineInputSpec, isdefined,
+                    traits, TraitedSpec, File)
 from ...utils.filemanip import fname_presuffix
 
 
@@ -161,3 +162,61 @@ def version(self):
                 return ver.rstrip().split('-')[-1] + '.dev'
             else:
                 return ver.rstrip().split('-v')[-1]
+
+
+class FSScriptCommand(FSCommand):
+    """ Support for Freesurfer script commands with log inputs.terminal_output """
+    _terminal_output = 'file'
+    _always_run = False
+
+    def __init__(self, **inputs):
+        super(FSScriptCommand, self).__init__(**inputs)
+        self.set_default_terminal_output(self._terminal_output)
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['log_file'] = os.path.abspath('stdout.nipype')
+        return outputs
+
+
+class FSScriptOutputSpec(TraitedSpec):
+    log_file = File('stdout.nipype', usedefault=True,
+                    exists=True, desc="The output log")
+
+
+class FSTraitedSpecOpenMP(FSTraitedSpec):
+    num_threads = traits.Int(desc='allows for specifying more threads')
+
+
+class FSCommandOpenMP(FSCommand):
+    """Support for FS commands that utilize OpenMP
+
+    Sets the environment variable 'OMP_NUM_THREADS' to the number
+    of threads specified by the input num_threads.
+    """
+
+    input_spec = FSTraitedSpecOpenMP
+
+    _num_threads = None
+
+    def __init__(self, **inputs):
+        super(FSCommandOpenMP, self).__init__(**inputs)
+        self.inputs.on_trait_change(self._num_threads_update, 'num_threads')
+        if not self._num_threads:
+            self._num_threads = os.environ.get('OMP_NUM_THREADS', None)
+            if not self._num_threads:
+                self._num_threads = os.environ.get('NSLOTS', None)
+        if not isdefined(self.inputs.num_threads) and self._num_threads:
+            self.inputs.num_threads = int(self._num_threads)
+        self._num_threads_update()
+
+    def _num_threads_update(self):
+        if self.inputs.num_threads:
+            self.inputs.environ.update(
+                {'OMP_NUM_THREADS': str(self.inputs.num_threads)})
+
+    def run(self, **inputs):
+        if 'num_threads' in inputs:
+            self.inputs.num_threads = inputs['num_threads']
+        self._num_threads_update()
+        return super(FSCommandOpenMP, self).run(**inputs)