[ENH] Add a activation count map interface

Author: oesteban

nipype/algorithms/stats.py

@@ -0,0 +1,65 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+Managing statistical maps
+"""
+from __future__ import (print_function, division, unicode_literals,
+                        absolute_import)
+import os
+import nibabel as nb
+import numpy as np
+
+from ..interfaces.base import (
+    BaseInterfaceInputSpec, TraitedSpec, SimpleInterface,
+    traits, InputMultiPath, File
+)
+
+
+class ACMInputSpec(BaseInterfaceInputSpec):
+    in_files = InputMultiPath(File(exists=True), mandatory=True,
+                              desc='input file, generally a list of z-stat maps')
+    threshold = traits.Float(1.65, usedefault=True,
+                             desc='binarization threshold. A z-value of 1.65 '
+                                  'corresponds to a two-sided test of p<.10')
+
+
+class ACMOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='output activation count map')
+    acm_pos = File(exists=True, desc='positive activation count map')
+    acm_neg = File(exists=True, desc='negative activation count map')
+
+
+class ACM(SimpleInterface):
+    """
+    Calculate a simple Activation Count Maps
+    """
+    input_spec = ACMInputSpec
+    output_spec = ACMOutputSpec
+
+    def _run_interface(self, runtime):
+        allmaps = nb.concat_images(
+            [nb.load(f) for f in self.inputs.in_files])
+        acm_pos = np.where(allmaps > self.inputs.threshold).astype(
+            float).mean(3)
+        acm_neg = np.where(allmaps < -1.0 * self.inputs.threshold).astype(
+            float).mean(3)
+
+        acm_diff = acm_pos - acm_neg
+
+        nii = nb.load(self.inputs.in_files[0])
+        self._results['out_file'] = os.path.join(
+            runtime.cwd, 'acm_diff.nii.gz')
+        self._results['acm_pos'] = os.path.join(
+            runtime.cwd, 'acm_pos.nii.gz')
+        self._results['acm_neg'] = os.path.join(
+            runtime.cwd, 'acm_neg.nii.gz')
+
+        nb.Nifti1Image(
+            acm_diff, nii.affine, nii.header).to_filename(self._results['out_file'])
+        nb.Nifti1Image(
+            acm_pos, nii.affine, nii.header).to_filename(self._results['acm_pos'])
+        nb.Nifti1Image(
+            acm_neg, nii.affine, nii.header).to_filename(self._results['acm_neg'])
+
+        return runtime