Merge pull request #510 from oesteban/enh/489

[ENH] Intensity harmonization in the anatomical workflow
nipreps · May 22, 2017 · a761c37 · a761c37
2 parents 0298bac + 56ef5c3
commit a761c37
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diff --git a/mriqc/data/testdata/T1w.csv b/mriqc/data/testdata/T1w.csv
@@ -1,5 +1,5 @@
 subject_id,cjv,cnr,efc,fber,fwhm_avg,fwhm_x,fwhm_y,fwhm_z,icvs_csf,icvs_gm,icvs_wm,inu_med,inu_range,qi_1,qi_2,rpve_csf,rpve_gm,rpve_wm,size_x,size_y,size_z,snr_csf,snr_gm,snr_total,snr_wm,snrd_csf,snrd_gm,snrd_total,snrd_wm,spacing_x,spacing_y,spacing_z,summary_bg_k,summary_bg_mean,summary_bg_p05,summary_bg_p95,summary_bg_stdv,summary_csf_k,summary_csf_mean,summary_csf_p05,summary_csf_p95,summary_csf_stdv,summary_gm_k,summary_gm_mean,summary_gm_p05,summary_gm_p95,summary_gm_stdv,summary_wm_k,summary_wm_mean,summary_wm_p05,summary_wm_p95,summary_wm_stdv,tpm_overlap_csf,tpm_overlap_gm,tpm_overlap_wm,wm2max
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diff --git a/mriqc/interfaces/__init__.py b/mriqc/interfaces/__init__.py
@@ -8,7 +8,7 @@
 from __future__ import absolute_import
 from __future__ import unicode_literals
 
-from mriqc.interfaces.anatomical import StructuralQC, ArtifactMask, ComputeQI2
+from mriqc.interfaces.anatomical import StructuralQC, ArtifactMask, ComputeQI2, Harmonize
 from mriqc.interfaces.functional import FunctionalQC, Spikes
 from mriqc.interfaces.bids import ReadSidecarJSON, IQMFileSink
 from mriqc.interfaces.viz import PlotMosaic, PlotContours, PlotSpikes

diff --git a/mriqc/interfaces/anatomical.py b/mriqc/interfaces/anatomical.py
@@ -7,7 +7,7 @@
 # @Date:   2016-01-05 11:29:40
 # @Email:  code@oscaresteban.es
 # @Last modified by:   oesteban
-# @Last Modified time: 2017-05-17 16:54:26
+# @Last Modified time: 2017-05-19 16:36:34
 """ Nipype interfaces to support anatomical workflow """
 from __future__ import print_function, division, absolute_import, unicode_literals
 import os.path as op
@@ -17,6 +17,7 @@
 from builtins import zip
 
 from nipype import logging
+from nipype.utils.filemanip import fname_presuffix
 from nipype.interfaces.base import (traits, TraitedSpec, File,
                                     InputMultiPath, BaseInterfaceInputSpec)
 
@@ -122,7 +123,7 @@ def _run_interface(self, runtime):  # pylint: disable=R0914
         self._results['efc'] = efc(inudata)
 
         # M2WM
-        self._results['wm2max'] = wm2max(imdata, segdata)
+        self._results['wm2max'] = wm2max(inudata, segdata)
 
         # Artifacts
         self._results['qi_1'] = art_qi1(airdata, artdata)
@@ -147,18 +148,18 @@ def _run_interface(self, runtime):  # pylint: disable=R0914
         self._results['rpve'] = rpve(pvmdata, segdata)
 
         # Summary stats
-        self._results['summary'] = summary_stats(imdata, pvmdata, airdata)
+        self._results['summary'] = summary_stats(inudata, pvmdata, airdata)
 
         # Image specs
-        self._results['size'] = {'x': int(imdata.shape[0]),
-                                 'y': int(imdata.shape[1]),
-                                 'z': int(imdata.shape[2])}
+        self._results['size'] = {'x': int(inudata.shape[0]),
+                                 'y': int(inudata.shape[1]),
+                                 'z': int(inudata.shape[2])}
         self._results['spacing'] = {
             i: float(v) for i, v in zip(
                 ['x', 'y', 'z'], imnii.get_header().get_zooms()[:3])}
 
         try:
-            self._results['size']['t'] = int(imdata.shape[3])
+            self._results['size']['t'] = int(inudata.shape[3])
         except IndexError:
             pass
 
@@ -278,6 +279,51 @@ def _run_interface(self, runtime):
         return runtime
 
 
+class HarmonizeInputSpec(BaseInterfaceInputSpec):
+    in_file = File(exists=True, mandatory=True, desc='input data (after bias correction)')
+    wm_mask = File(exists=True, mandatory=True, desc='white-matter mask')
+    erodemsk = traits.Bool(True, usedefault=True, desc='erode mask')
+
+
+class HarmonizeOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='input data (after intensity harmonization)')
+
+
+class Harmonize(SimpleInterface):
+    """
+    Computes the artifact mask using the method described in [Mortamet2009]_.
+    """
+    input_spec = HarmonizeInputSpec
+    output_spec = HarmonizeOutputSpec
+
+    def _run_interface(self, runtime):
+
+        in_file = nb.load(self.inputs.in_file)
+        wm_mask = nb.load(self.inputs.wm_mask).get_data()
+        wm_mask[wm_mask < 0.9] = 0
+        wm_mask[wm_mask > 0] = 1
+        wm_mask = wm_mask.astype(np.uint8)
+
+        if self.inputs.erodemsk:
+            # Create a structural element to be used in an opening operation.
+            struc = nd.generate_binary_structure(3, 2)
+            # Perform an opening operation on the background data.
+            wm_mask = nd.binary_opening(wm_mask, structure=struc).astype(np.uint8)
+
+        data = in_file.get_data()
+        data *= 1000.0 / np.median(data[wm_mask > 0])
+
+        out_file = fname_presuffix(self.inputs.in_file,
+                                   suffix='_harmonized', newpath='.')
+        in_file.__class__(data, in_file.affine, in_file.header).to_filename(
+            out_file)
+
+        self._results['out_file'] = out_file
+
+        return runtime
+
+
+
 def artifact_mask(imdata, airdata, distance, zscore=10.):
     """Computes a mask of artifacts found in the air region"""
     from statsmodels.robust.scale import mad

diff --git a/mriqc/workflows/anatomical.py b/mriqc/workflows/anatomical.py
@@ -95,7 +95,7 @@ def anat_qc_workflow(dataset, settings, mod='T1w', name='anatMRIQC'):
     # 1. Reorient anatomical image
     to_ras = pe.Node(ConformImage(), name='conform')
     # 2. Skull-stripping (afni)
-    asw = skullstrip_wf(n4_nthreads=settings.get('ants_nthreads', 1))
+    asw = skullstrip_wf(n4_nthreads=settings.get('ants_nthreads', 1), unifize=False)
     # 3. Head mask
     hmsk = headmsk_wf()
     # 4. Spatial Normalization, using ANTs
@@ -237,6 +237,7 @@ def compute_iqms(settings, modality='T1w', name='ComputeIQMs'):
 
     """
     from mriqc.workflows.utils import _tofloat
+    from mriqc.interfaces.anatomical import Harmonize
 
     workflow = pe.Workflow(name=name)
     inputnode = pe.Node(niu.IdentityInterface(fields=[
@@ -253,6 +254,9 @@ def compute_iqms(settings, modality='T1w', name='ComputeIQMs'):
     fwhm = pe.Node(afni.FWHMx(combine=True, detrend=True), name='smoothness')
     # fwhm.inputs.acf = True  # add when AFNI >= 16
 
+    # Harmonize
+    homog = pe.Node(Harmonize(), name='harmonize')
+
     # Mortamet's QI2
     getqi2 = pe.Node(ComputeQI2(erodemsk=settings.get('testing', False)),
                      name='ComputeQI2')
@@ -272,6 +276,9 @@ def compute_iqms(settings, modality='T1w', name='ComputeIQMs'):
                        name='datasink')
     datasink.inputs.modality = modality
 
+    def _getwm(inlist):
+        return inlist[-1]
+
     workflow.connect([
         (inputnode, datasink, [('subject_id', 'subject_id'),
                                ('session_id', 'session_id'),
@@ -281,8 +288,9 @@ def compute_iqms(settings, modality='T1w', name='ComputeIQMs'):
                                ('metadata', 'metadata')]),
         (inputnode, getqi2, [('orig', 'in_file'),
                              ('airmask', 'air_msk')]),
-        (inputnode, measures, [('inu_corrected', 'in_noinu'),
-                               ('in_inu', 'in_bias'),
+        (inputnode, homog, [('inu_corrected', 'in_file'),
+                            (('pvms', _getwm), 'wm_mask')]),
+        (inputnode, measures, [('in_inu', 'in_bias'),
                                ('orig', 'in_file'),
                                ('airmask', 'air_msk'),
                                ('headmask', 'head_msk'),
@@ -293,12 +301,13 @@ def compute_iqms(settings, modality='T1w', name='ComputeIQMs'):
                            ('brainmask', 'mask')]),
         (inputnode, invt, [('orig', 'reference_image'),
                            ('inverse_composite_transform', 'transforms')]),
+        (homog, measures, [('out_file', 'in_noinu')]),
         (invt, measures, [('output_image', 'mni_tpms')]),
         (fwhm, measures, [(('fwhm', _tofloat), 'in_fwhm')]),
         (measures, datasink, [('out_qc', 'root')]),
         (getqi2, datasink, [('qi2', 'qi_2')]),
         (getqi2, outputnode, [('out_file', 'out_noisefit')]),
-        (datasink, outputnode, [('out_file', 'out_file')])
+        (datasink, outputnode, [('out_file', 'out_file')]),
     ])
     return workflow
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,3 +1,3 @@
 numpy>=1.12.0
 git+https://github.com/nipy/nipype.git@f92a333b0d191773aa9cefd87fba869b87ab1414#egg=nipype
-git+https://github.com/poldracklab/niworkflows.git@8b0838a6717904c9c171486d5fddb6568202ef5a#egg=niworkflows
+git+https://github.com/poldracklab/niworkflows.git@57f9609790628bed0285823943403472e95ac70f#egg=niworkflows
diff --git a/tests/nii_T1w.txt b/tests/nii_T1w.txt
@@ -34,15 +34,19 @@ aaafd84713bf0e7b43e45845c3c93228de07e735 /scratch/work/workflow_enumerator/anatM
 5feb2b8a1ff88237d5631f5e66a80304f21778d3 /scratch/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..circle-tests..sub-51187..anat..sub-51187_T1w.nii.gz/ArtifactMask/sub-51187_T1w_conformed_noart-air.nii.gz
 c75931ec5f1e1f5104bd25b90507be24e484aba0 /scratch/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..circle-tests..sub-51187..anat..sub-51187_T1w.nii.gz/Binarize/1mm_headmask_trans_bin.nii.gz
 083245f8226f08929d764e5d599665e84ee43d1f /scratch/work/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..data..circle-tests..sub-51187..anat..sub-51187_T1w.nii.gz/invert_xfm/1mm_headmask_trans.nii.gz
+0089f13ee49aa6a1e6d23e902d5478bc0e455709 /scratch/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..circle-tests..sub-50137..anat..sub-50137_T1w.nii.gz/harmonize/sub-50137_T1w_conformed_corrected_harmonized.nii.gz
 29cb0e176238cfdc8a8d0762cfc17792299d1d4e /scratch/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..circle-tests..sub-50137..anat..sub-50137_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t10/1mm_tpm_csf_trans.nii.gz
 52923c01b6af7557869ba5080c9f3915fca971a6 /scratch/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..circle-tests..sub-50137..anat..sub-50137_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t11/1mm_tpm_gm_trans.nii.gz
 13b33085ef4661932f79575c704fad84dc3feb27 /scratch/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..circle-tests..sub-50137..anat..sub-50137_T1w.nii.gz/MNItpms2t1/mapflow/_MNItpms2t12/1mm_tpm_wm_trans.nii.gz
+694f1916b589e295304f01b21f20d4a207c35a32 /scratch/work/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..data..circle-tests..sub-50152..anat..sub-50152_T1w.nii.gz/harmonize/sub-50152_T1w_conformed_corrected_harmonized.nii.gz
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