Merge pull request #669 from chrisfilo/enh/afni_update

AFNI update

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
 =====
 

Dockerfile

@@ -10,7 +10,6 @@ RUN apt-get update && \
                     curl \
                     bzip2 \
                     ca-certificates \
-                    xvfb  \
                     cython3 \
                     build-essential \
                     autoconf \
@@ -20,12 +19,11 @@ RUN apt-get update && \
     apt-key add /root/.neurodebian.gpg && \
     (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
 
-# Installing Neurodebian packages (FSL, AFNI, git)
+# Installing Neurodebian packages (FSL, git)
 RUN apt-get update  && \
     apt-get install -y --no-install-recommends \
                     fsl-core \
-                    fsl-mni152-templates \
-                    afni
+                    fsl-mni152-templates
 
 ENV FSLDIR=/usr/share/fsl/5.0 \
     FSLOUTPUTTYPE=NIFTI_GZ \
@@ -34,12 +32,33 @@ ENV FSLDIR=/usr/share/fsl/5.0 \
     LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
     FSLTCLSH=/usr/bin/tclsh \
     FSLWISH=/usr/bin/wish \
-    AFNI_MODELPATH=/usr/lib/afni/models \
-    AFNI_IMSAVE_WARNINGS=NO \
-    AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
-    AFNI_PLUGINPATH=/usr/lib/afni/plugins \
     PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
 
+# Installing AFNI (version 17_3_03 archived on OSF)
+RUN apt-get update -qq && apt-get install -yq --no-install-recommends ed gsl-bin libglu1-mesa-dev libglib2.0-0 libglw1-mesa \
+    libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb && \
+    libs_path=/usr/lib/x86_64-linux-gnu && \
+    if [ -f $libs_path/libgsl.so.19 ]; then \
+           ln $libs_path/libgsl.so.19 $libs_path/libgsl.so.0; \
+    fi && \
+    echo "Install libxp (not in all ubuntu/debian repositories)" && \
+    apt-get install -yq --no-install-recommends libxp6 \
+    || /bin/bash -c " \
+       curl --retry 5 -o /tmp/libxp6.deb -sSL http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
+       && dpkg -i /tmp/libxp6.deb && rm -f /tmp/libxp6.deb" && \
+    echo "Install libpng12 (not in all ubuntu/debian repositories" && \
+    apt-get install -yq --no-install-recommends libpng12-0 \
+    || /bin/bash -c " \
+       curl -o /tmp/libpng12.deb -sSL http://mirrors.kernel.org/debian/pool/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
+       && dpkg -i /tmp/libpng12.deb && rm -f /tmp/libpng12.deb" && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    mkdir -p /opt/afni && \
+    curl -o afni.tar.gz -sSLO "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5a0dd9a7b83f69027512a12b" && \
+    tar zxv -C /opt/afni --strip-components=1 -f afni.tar.gz && \
+    rm -rf afni.tar.gz
+ENV PATH=/opt/afni:$PATH
+
 # Installing and setting up ANTs
 RUN mkdir -p /opt/ants && \
     curl -sSL "https://github.com/stnava/ANTs/releases/download/v2.1.0/Linux_Ubuntu14.04.tar.bz2" \

mriqc/workflows/anatomical.py

@@ -54,6 +54,7 @@
 from ..interfaces import (StructuralQC, ArtifactMask, ReadSidecarJSON,
                           ConformImage, ComputeQI2, IQMFileSink, RotationMask)
 from ..utils.misc import check_folder
+from .utils import get_fwhmx
 WFLOGGER = logging.getLogger('mriqc.workflow')
 
 
@@ -241,8 +242,9 @@ def compute_iqms(settings, modality='T1w', name='ComputeIQMs'):
     }
 
     # AFNI check smoothing
-    fwhm = pe.Node(afni.FWHMx(combine=True, detrend=True), name='smoothness')
-    # fwhm.inputs.acf = True  # add when AFNI >= 16
+    fwhm_interface = get_fwhmx()
+
+    fwhm = pe.Node(fwhm_interface, name='smoothness')
 
     # Harmonize
     homog = pe.Node(Harmonize(), name='harmonize')
@@ -308,6 +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
@@ -222,7 +223,8 @@ def compute_iqms(settings, name='ComputeIQMs'):
                      mem_gb=biggest_file_gb * 3)
 
     # AFNI quality measures
-    fwhm = pe.Node(afni.FWHMx(combine=True, detrend=True), name='smoothness')
+    fwhm_interface = get_fwhmx()
+    fwhm = pe.Node(fwhm_interface, name='smoothness')
     # fwhm.inputs.acf = True  # add when AFNI >= 16
     outliers = pe.Node(afni.OutlierCount(fraction=True, out_file='outliers.out'),
                        name='outliers', mem_gb=biggest_file_gb * 2.5)

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 +162,13 @@ 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 = StrictVersion('%s.%s.%s' % afni.Info.version())
+    if afni_version >= StrictVersion("2017.2.3"):
+        fwhm_args['args'] = '-ShowMeClassicFWHM'
+        fwhm_args['acf'] = True
+    fwhm_interface = afni.FWHMx(**fwhm_args)
+    return fwhm_interface