changelog + func skullstrip

CHANGES.txt

@@ -1,9 +1,13 @@
+0.9.10
+======
+
+  * [FIX] Updated AFNI to 17.3.03. Resolves errors regarding opening display by 3dSkullStrip (#669)
+
 0.9.9
 =====
 
   * [ENH] Update nipype to fix $DISPLAY problem of AFNI's 3dSkullStrip
 
-
 0.9.8
 =====
 

mriqc/workflows/anatomical.py

@@ -54,7 +54,7 @@
 from ..interfaces import (StructuralQC, ArtifactMask, ReadSidecarJSON,
                           ConformImage, ComputeQI2, IQMFileSink, RotationMask)
 from ..utils.misc import check_folder
-from distutils.version import StrictVersion
+from .utils import get_fwhmx
 WFLOGGER = logging.getLogger('mriqc.workflow')
 
 
@@ -242,16 +242,7 @@ def compute_iqms(settings, modality='T1w', name='ComputeIQMs'):
     }
 
     # AFNI check smoothing
-    fwhm_args = {"combine": True,
-                 "detrend": True}
-    afni_version_tpl = afni.Info.version()
-    afni_version = StrictVersion(".".join([str(afni_version_tpl[0]),
-                                           str(afni_version_tpl[1]),
-                                           str(afni_version_tpl[2])]))
-    if afni_version >= StrictVersion("2017.2.3"):
-        fwhm_args['args'] = '-ShowMeClassicFWHM'
-        fwhm_args['acf'] = True
-    fwhm_interface = afni.FWHMx(**fwhm_args)
+    fwhm_interface = get_fwhmx()
 
     fwhm = pe.Node(fwhm_interface, name='smoothness')
 
@@ -319,6 +310,7 @@ def _getwm(inlist):
     ])
     return workflow
 
+
 def individual_reports(settings, name='ReportsWorkflow'):
     """
     Encapsulates nodes writing plots

mriqc/workflows/functional.py

@@ -39,6 +39,7 @@
 from niworkflows.nipype.interfaces import utility as niu
 from niworkflows.nipype.interfaces import afni, ants, fsl
 
+from .utils import get_fwhmx
 from .. import DEFAULTS, logging
 from ..interfaces import ReadSidecarJSON, FunctionalQC, Spikes, IQMFileSink
 from ..utils.misc import check_folder, reorient_and_discard_non_steady
@@ -222,6 +223,7 @@ def compute_iqms(settings, name='ComputeIQMs'):
                      mem_gb=biggest_file_gb * 3)
 
     # AFNI quality measures
+    fwhm_interface = get_fwhmx()
     fwhm = pe.Node(afni.FWHMx(combine=True, detrend=True), name='smoothness')
     # fwhm.inputs.acf = True  # add when AFNI >= 16
     outliers = pe.Node(afni.OutlierCount(fraction=True, out_file='outliers.out'),

mriqc/workflows/utils.py

@@ -9,6 +9,8 @@
 # @Last modified by:   oesteban
 """Helper functions for the workflows"""
 from __future__ import print_function, division, absolute_import, unicode_literals
+from distutils.version import StrictVersion
+from niworkflows.nipype.interfaces import afni
 from builtins import range
 
 def _tofloat(inlist):
@@ -160,3 +162,16 @@ def slice_wise_fft(in_file, ftmask=None, spike_thres=3., out_prefix=None):
     np.savetxt(out_spikes, spikes_list, fmt=b'%d', delimiter=b'\t', header='TR\tZ')
 
     return len(spikes_list), out_spikes, out_fft
+
+def get_fwhmx():
+    fwhm_args = {"combine": True,
+                 "detrend": True}
+    afni_version_tpl = afni.Info.version()
+    afni_version = StrictVersion(".".join([str(afni_version_tpl[0]),
+                                           str(afni_version_tpl[1]),
+                                           str(afni_version_tpl[2])]))
+    if afni_version >= StrictVersion("2017.2.3"):
+        fwhm_args['args'] = '-ShowMeClassicFWHM'
+        fwhm_args['acf'] = True
+    fwhm_interface = afni.FWHMx(**fwhm_args)
+    return fwhm_interface