Merge pull request #195 from effigies/enh/mri_coreg

[RTM] ENH: Add MRICoregRPT interface

Author: oesteban

.circle/pytests.sh

@@ -11,17 +11,17 @@ set -x         # Print command traces before executing command.
 code=0
 
 if [ "${CIRCLE_NODE_TOTAL:-1}" == "1" ]; then
-    docker run -ti -v /etc/localtime:/etc/localtime:ro --env SAVE_CIRCLE_ARTIFACTS="/scratch" -v ${SCRATCH}/py3:/scratch -w /scratch --entrypoint=/usr/local/miniconda/bin/py.test niworkflows:py3 /root/niworkflows -n ${CIRCLE_NPROCS:-4} -v --junit-xml=/scratch/pytest.xml && \
-    docker run -ti -v /etc/localtime:/etc/localtime:ro --env SAVE_CIRCLE_ARTIFACTS="/scratch" -v ${SCRATCH}/py2:/scratch -w /scratch --entrypoint=/usr/local/miniconda/bin/py.test niworkflows:py2 /root/niworkflows -n ${CIRCLE_NPROCS:-4} -v --junit-xml=/scratch/pytest.xml
+    docker run -ti --env SAVE_CIRCLE_ARTIFACTS="/scratch" -v ${SCRATCH}/py3:/scratch -w /scratch --entrypoint=/usr/local/miniconda/bin/py.test niworkflows:py3 /root/niworkflows -n ${CIRCLE_NPROCS:-4} -v --junit-xml=/scratch/pytest.xml && \
+    docker run -ti --env SAVE_CIRCLE_ARTIFACTS="/scratch" -v ${SCRATCH}/py2:/scratch -w /scratch --entrypoint=/usr/local/miniconda/bin/py.test niworkflows:py2 /root/niworkflows -n ${CIRCLE_NPROCS:-4} -v --junit-xml=/scratch/pytest.xml
     code=$(( $code + $? ))
 else
     case ${CIRCLE_NODE_INDEX} in
     0)
-        docker run -ti -v /etc/localtime:/etc/localtime:ro --env SAVE_CIRCLE_ARTIFACTS="/scratch" -v ${SCRATCH}/py3:/scratch -w /scratch --entrypoint=/usr/local/miniconda/bin/py.test niworkflows:py3 /root/niworkflows -n ${CIRCLE_NPROCS:-4} -v --junit-xml=/scratch/pytest.xml
+        docker run -ti --env SAVE_CIRCLE_ARTIFACTS="/scratch" -v ${SCRATCH}/py3:/scratch -w /scratch --entrypoint=/usr/local/miniconda/bin/py.test niworkflows:py3 /root/niworkflows -n ${CIRCLE_NPROCS:-4} -v --junit-xml=/scratch/pytest.xml
         code=$(( $code + $? ))
         ;;
     1)
-        docker run -ti -v /etc/localtime:/etc/localtime:ro --env SAVE_CIRCLE_ARTIFACTS="/scratch" -v ${SCRATCH}/py2:/scratch -w /scratch --entrypoint=/usr/local/miniconda/bin/py.test niworkflows:py2 /root/niworkflows -n ${CIRCLE_NPROCS:-4} -v --junit-xml=/scratch/pytest.xml
+        docker run -ti --env SAVE_CIRCLE_ARTIFACTS="/scratch" -v ${SCRATCH}/py2:/scratch -w /scratch --entrypoint=/usr/local/miniconda/bin/py.test niworkflows:py2 /root/niworkflows -n ${CIRCLE_NPROCS:-4} -v --junit-xml=/scratch/pytest.xml
         code=$(( $code + $? ))
         ;;
     esac
@@ -31,4 +31,4 @@ fi
 cp $SCRATCH/py3/*.xml ${CIRCLE_TEST_REPORTS}/py3/  || true
 cp $SCRATCH/py2/*.xml ${CIRCLE_TEST_REPORTS}/py2/  || true
 
-exit $code
+exit $code

Dockerfile

@@ -1,43 +1,93 @@
-# Copyright (c) 2016, The developers of the Stanford CRN
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright notice, this
-#   list of conditions and the following disclaimer.
-#
-# * Redistributions in binary form must reproduce the above copyright notice,
-#   this list of conditions and the following disclaimer in the documentation
-#   and/or other materials provided with the distribution.
-#
-# * Neither the name of crn_base nor the names of its
-#   contributors may be used to endorse or promote products derived from
-#   this software without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# This Dockerfile is to be built for testing purposes inside CircleCI,
-# not for distribution within Docker hub.
-# For that purpose, the Dockerfile is found in build/Dockerfile.
+# Use Ubuntu 16.04 LTS
+FROM ubuntu:xenial-20161213
 
-FROM poldracklab/neuroimaging-core:freesurfer-0.0.2
+# Pre-cache neurodebian key
+COPY docker/files/neurodebian.gpg /root/.neurodebian.gpg
 
-# Install cwebp
+# Prepare environment
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    curl \
+                    bzip2 \
+                    ca-certificates \
+                    xvfb \
+                    cython3 \
+                    build-essential \
+                    autoconf \
+                    libtool \
+                    pkg-config && \
+    curl -sSL http://neuro.debian.net/lists/xenial.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key add /root/.neurodebian.gpg && \
+    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true) && \
+    apt-get update
+
+# Installing freesurfer
+RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
+    --exclude='freesurfer/trctrain' \
+    --exclude='freesurfer/subjects/fsaverage_sym' \
+    --exclude='freesurfer/subjects/fsaverage3' \
+    --exclude='freesurfer/subjects/fsaverage4' \
+    --exclude='freesurfer/subjects/cvs_avg35' \
+    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
+    --exclude='freesurfer/subjects/bert' \
+    --exclude='freesurfer/subjects/V1_average' \
+    --exclude='freesurfer/average/mult-comp-cor' \
+    --exclude='freesurfer/lib/cuda' \
+    --exclude='freesurfer/lib/qt'
+
+ENV FSL_DIR=/usr/share/fsl/5.0 \
+    OS=Linux \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA= \
+    FSF_OUTPUT_FORMAT=nii.gz \
+    FREESURFER_HOME=/opt/freesurfer
+ENV SUBJECTS_DIR=$FREESURFER_HOME/subjects \
+    FUNCTIONALS_DIR=$FREESURFER_HOME/sessions \
+    MNI_DIR=$FREESURFER_HOME/mni \
+    LOCAL_DIR=$FREESURFER_HOME/local \
+    FSFAST_HOME=$FREESURFER_HOME/fsfast \
+    MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
+    MINC_LIB_DIR=$FREESURFER_HOME/mni/lib \
+    MNI_DATAPATH=$FREESURFER_HOME/mni/data \
+    FMRI_ANALYSIS_DIR=$FREESURFER_HOME/fsfast
+ENV PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
+    MNI_PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
+    PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH
+RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
+
+# Installing Neurodebian packages (FSL, AFNI, git)
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    fsl-core=5.0.9-4~nd16.04+1 \
+                    fsl-mni152-templates=5.0.7-2 \
+                    afni=16.2.07~dfsg.1-5~nd16.04+1
+
+ENV FSLDIR=/usr/share/fsl/5.0 \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    FSLMULTIFILEQUIT=TRUE \
+    POSSUMDIR=/usr/share/fsl/5.0 \
+    LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
+    FSLTCLSH=/usr/bin/tclsh \
+    FSLWISH=/usr/bin/wish \
+    AFNI_MODELPATH=/usr/lib/afni/models \
+    AFNI_IMSAVE_WARNINGS=NO \
+    AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
+    AFNI_PLUGINPATH=/usr/lib/afni/plugins
+ENV PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
+
+# Installing ANTs 2.2.0 (NeuroDocker build)
+ENV ANTSPATH=/usr/lib/ants
+RUN mkdir -p $ANTSPATH && \
+    curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
+    | tar -xzC $ANTSPATH --strip-components 1
+ENV PATH=$ANTSPATH:$PATH
+
+# Installing WEBP tools
 RUN curl -sSLO "http://downloads.webmproject.org/releases/webp/libwebp-0.5.2-linux-x86-64.tar.gz" && \
   tar -xf libwebp-0.5.2-linux-x86-64.tar.gz && cd libwebp-0.5.2-linux-x86-64/bin && \
   mv cwebp /usr/local/bin/ && rm -rf libwebp-0.5.2-linux-x86-64
 
-# Install nodejs -> svgo
+# Installing SVGO
 RUN curl -sL https://deb.nodesource.com/setup_7.x | bash -
 RUN apt-get install -y nodejs
 RUN npm install -g svgo
@@ -73,4 +123,4 @@ RUN cd niworkflows && \
     python -c 'from niworkflows.data.getters import get_mni_template_ras; get_mni_template_ras()' && \
     python -c 'from niworkflows.data.getters import get_ds003_downsampled; get_ds003_downsampled()' && \
     python -c 'from niworkflows.data.getters import get_ants_oasis_template_ras; get_ants_oasis_template_ras()' && \
-    python -c 'from niworkflows.data.getters import get_mni_icbm152_nlin_asym_09c; get_mni_icbm152_nlin_asym_09c()'
+    python -c 'from niworkflows.data.getters import get_mni_icbm152_nlin_asym_09c; get_mni_icbm152_nlin_asym_09c()'

circle.yml

@@ -1,4 +1,8 @@
 machine:
+  # Update docker to 1.9
+  pre:
+    - sudo curl -L -o /usr/bin/docker 'https://s3-external-1.amazonaws.com/circle-downloads/docker-1.9.1-circleci'
+    - sudo chmod 0755 /usr/bin/docker
   environment:
     SCRATCH: "$HOME/scratch"
     CIRCLE_NPROCS: 2
@@ -8,7 +12,6 @@ machine:
 
 dependencies:
   cache_directories:
-    - "~/docker"
     - "~/data"
 
   pre:
@@ -18,12 +21,9 @@ dependencies:
     - git submodule init && (git submodule update || true)
     - git submodule sync && git -C nipype fetch origin && git submodule update
   override:
-    - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi :
-        timeout: 6000
+    - docker pull poldracklab/fmriprep:latest || true
     - docker build --rm=false -t niworkflows:py3 .
     - docker build --rm=false -t niworkflows:py2 --build-arg PYTHON_MAJOR=2 .
-    - docker save poldracklab/neuroimaging-core:freesurfer-0.0.2 niworkflows:py3 niworkflows:py2 > ~/docker/image.tar :
-        timeout: 6000
 test:
   override:
     - bash .circle/pytests.sh :

docker/files/neurodebian.gpg

@@ -0,0 +1,71 @@
+-----BEGIN PGP PUBLIC KEY BLOCK-----
+Version: GnuPG v1
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+-----END PGP PUBLIC KEY BLOCK-----

nipype

@@ -195,6 +195,44 @@ def _post_run_hook(self, runtime):
             self._fixed_image, self._moving_image)
 
 
+class MRICoregInputSpecRPT(nrc.RegistrationRCInputSpec,
+                           fs.registration.MRICoregInputSpec):
+    pass
+
+
+class MRICoregOutputSpecRPT(nrc.ReportCapableOutputSpec,
+                            fs.registration.MRICoregOutputSpec):
+    pass
+
+
+class MRICoregRPT(nrc.RegistrationRC, fs.MRICoreg):
+    input_spec = MRICoregInputSpecRPT
+    output_spec = MRICoregOutputSpecRPT
+
+    def _post_run_hook(self, runtime):
+        outputs = self.aggregate_outputs(runtime=runtime)
+
+        if isdefined(self.inputs.reference_file):
+            target_file = self.inputs.reference_file
+        else:
+            target_file = os.path.join(self.inputs.subjects_dir,
+                                       self.inputs.subject_id, 'mri',
+                                       'brainmask.mgz')
+
+        # Apply transform for simplicity
+        mri_vol2vol = fs.ApplyVolTransform(
+            source_file=self.inputs.source_file,
+            target_file=target_file,
+            lta_file=outputs.out_lta_file)
+        res = mri_vol2vol.run()
+
+        self._fixed_image = target_file
+        self._moving_image = res.outputs.transformed_file
+        NIWORKFLOWS_LOG.info(
+            'Report - setting fixed (%s) and moving (%s) images',
+            self._fixed_image, self._moving_image)
+
+
 class SimpleBeforeAfterInputSpecRPT(nrc.RegistrationRCInputSpec):
     before = File(exists=True, mandatory=True, desc='file before')
     after = File(exists=True, mandatory=True, desc='file after')

niworkflows/interfaces/registration.py

@@ -18,7 +18,7 @@
 
 from niworkflows.interfaces.registration import (
     FLIRTRPT, RobustMNINormalizationRPT, ANTSRegistrationRPT, BBRegisterRPT,
-    ApplyXFMRPT, SimpleBeforeAfterRPT)
+    MRICoregRPT, ApplyXFMRPT, SimpleBeforeAfterRPT)
 from niworkflows.interfaces.segmentation import FASTRPT, ReconAllRPT
 from niworkflows.interfaces.masks import BETRPT, BrainExtractionRPT, \
     SimpleShowMaskRPT
@@ -59,6 +59,14 @@ def test_FLIRTRPT(self):
         _smoke_test_report(flirt_rpt, 'testFLIRT.svg')
 
 
+    def test_MRICoregRPT(self):
+        """ the FLIRT report capable test """
+        mri_coreg_rpt = MRICoregRPT(generate_report=True,
+                                    source_file=self.moving,
+                                    reference_file=self.reference)
+        _smoke_test_report(mri_coreg_rpt, 'testMRICoreg.svg')
+
+
     def test_ApplyXFMRPT(self):
         """ the ApplyXFM report capable test """
         flirt_rpt = FLIRTRPT(generate_report=False, in_file=self.moving,