From 2c698382c57627c923775a91f93708b7000632bd Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Thu, 21 Jul 2016 18:31:56 -0700
Subject: [PATCH] [ENH] Move skull-stripping and reorient to NIworkflows

And close #140
---
 mriqc/workflows/anatomical.py | 48 +++--------------------------------
 requirements.txt              |  1 +
 2 files changed, 4 insertions(+), 45 deletions(-)

diff --git a/mriqc/workflows/anatomical.py b/mriqc/workflows/anatomical.py
index 04a08e23e..93cc60bca 100644
--- a/mriqc/workflows/anatomical.py
+++ b/mriqc/workflows/anatomical.py
@@ -18,6 +18,9 @@
 from nipype.interfaces import ants
 from nipype.interfaces.afni import preprocess as afp
 
+from niworkflows.anat.skullstrip import afni_wf as skullstrip_wf
+from niworkflows.common import reorient as mri_reorient_wf
+
 from mriqc.workflows.utils import fwhm_dict
 from mriqc.interfaces.qc import StructuralQC
 from mriqc.interfaces.anatomical import ArtifactMask
@@ -178,26 +181,6 @@ def anat_qc_workflow(name='MRIQC_Anat', settings=None):
     return workflow
 
 
-def mri_reorient_wf(name='ReorientWorkflow'):
-    """A workflow to reorient images to 'RPI' orientation"""
-    workflow = pe.Workflow(name=name)
-
-    inputnode = pe.Node(niu.IdentityInterface(fields=['in_file']),
-                        name='inputnode')
-    outputnode = pe.Node(niu.IdentityInterface(
-        fields=['out_file']), name='outputnode')
-
-    deoblique = pe.Node(afp.Refit(deoblique=True), name='deoblique')
-    reorient = pe.Node(afp.Resample(
-        orientation='RPI', outputtype='NIFTI_GZ'), name='reorient')
-    workflow.connect([
-        (inputnode, deoblique, [('in_file', 'in_file')]),
-        (deoblique, reorient, [('out_file', 'in_file')]),
-        (reorient, outputnode, [('out_file', 'out_file')])
-    ])
-    return workflow
-
-
 def headmsk_wf(name='HeadMaskWorkflow'):
     """Computes a head mask as in [Mortamet2009]_."""
 
@@ -322,31 +305,6 @@ def _invt_flags(transforms):
     ])
     return workflow
 
-
-def skullstrip_wf(name='SkullStripWorkflow'):
-    """ Skull-stripping workflow """
-
-    workflow = pe.Workflow(name=name)
-    inputnode = pe.Node(niu.IdentityInterface(fields=['in_file']),
-                        name='inputnode')
-    outputnode = pe.Node(niu.IdentityInterface(fields=['out_file', 'out_mask', 'head_mask']),
-                         name='outputnode')
-
-    sstrip = pe.Node(afp.SkullStrip(outputtype='NIFTI_GZ'), name='skullstrip')
-    sstrip_orig_vol = pe.Node(afp.Calc(
-        expr='a*step(b)', outputtype='NIFTI_GZ'), name='sstrip_orig_vol')
-    binarize = pe.Node(fsl.Threshold(args='-bin', thresh=1.e-3), name='binarize')
-
-    workflow.connect([
-        (inputnode, sstrip, [('in_file', 'in_file')]),
-        (inputnode, sstrip_orig_vol, [('in_file', 'in_file_a')]),
-        (sstrip, sstrip_orig_vol, [('out_file', 'in_file_b')]),
-        (sstrip_orig_vol, binarize, [('out_file', 'in_file')]),
-        (sstrip_orig_vol, outputnode, [('out_file', 'out_file')]),
-        (binarize, outputnode, [('out_file', 'out_mask')])
-    ])
-    return workflow
-
 def _get_wm(in_file, wm_val=3, out_file=None):
     import os.path as op
     import numpy as np
diff --git a/requirements.txt b/requirements.txt
index d337bd53c..ef321ee84 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,6 +6,7 @@ nitime
 nilearn
 dipy
 -e git+https://github.com/nipy/nipype#egg=nipype
+niworkflows
 lockfile
 jinja2
 seaborn