Merge pull request #4 from flywheel-apps/fslupgrade

FSL upgrade

Dockerfile

@@ -101,17 +101,23 @@ RUN apt-get update && \
     curl -sSL http://neuro.debian.net/lists/trusty.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
     apt-key add /tmp/neurodebian_pgpkey.txt && \
     apt-get update && \
-    apt-get install -y fsl-core && \
+    apt-get install -y dc && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+## Install FSL 5.0.10
+WORKDIR /opt/
+RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py && \
+        chmod +x fslinstaller.py && \
+        ./fslinstaller.py -q -d /usr/local/fsl -V 5.0.10
+
 # Configure FSL environment
-ENV FSLDIR=/usr/share/fsl/5.0
+ENV FSLDIR=/usr/local/fsl
 ENV FSL_DIR="${FSLDIR}"
 ENV FSLOUTPUTTYPE=NIFTI_GZ
-ENV PATH=/usr/lib/fsl/5.0:$PATH
+ENV PATH=/usr/local/fsl/bin:$PATH
 ENV FSLMULTIFILEQUIT=TRUE
-ENV POSSUMDIR=/usr/share/fsl/5.0
-ENV LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
+ENV POSSUMDIR=/usr/local/fsl/
+ENV LD_LIBRARY_PATH=/usr/local/fsl/lib:$LD_LIBRARY_PATH
 ENV FSLTCLSH=/usr/bin/tclsh
 ENV FSLWISH=/usr/bin/wish
 ENV FSLOUTPUTTYPE=NIFTI_GZ
@@ -131,14 +137,14 @@ ENV CARET7DIR=/usr/bin
 RUN apt-get -y update && \
     apt-get install -y wget && \
     apt-get install -y --no-install-recommends python-numpy && \
-    wget -nv https://github.com/Washington-University/Pipelines/archive/90b0766636ba83f06c9198206cc7fa90117b0b11.tar.gz -O pipelines.tar.gz && \
-    cd /opt/ && \
-    tar zxvf /pipelines.tar.gz && \
-    mv /opt/*ipelines* /opt/HCP-Pipelines && \
-    rm /pipelines.tar.gz && \
-    cd / && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+WORKDIR /opt/
+RUN wget -nv https://github.com/Washington-University/Pipelines/archive/90b0766636ba83f06c9198206cc7fa90117b0b11.tar.gz -O pipelines.tar.gz && \
+    tar zxvf pipelines.tar.gz && \
+    rm pipelines.tar.gz && \
+    mv /opt/*ipelines* /opt/HCP-Pipelines
+
 ENV HCPPIPEDIR=/opt/HCP-Pipelines
 
 # Manual patche for hcp_fix, re-compiled PostFix and RSS, etc.

manifest.json

@@ -8,9 +8,9 @@
   "url": "https://github.com/Washington-University/Pipelines",
   "source": "https://github.com/flywheel-apps/hcp-icafix",
   "cite": "(1) G. Salimi-Khorshidi, G. Douaud, C.F. Beckmann, M.F. Glasser, L. Griffanti S.M. Smith. Automatic denoising of functional MRI data: Combining independent component analysis and hierarchical fusion of classifiers. NeuroImage, 90:449-68, 2014 (2) L. Griffanti, G. Salimi-Khorshidi, C.F. Beckmann, E.J. Auerbach, G. Douaud, C.E. Sexton, E. Zsoldos, K. Ebmeier, N. Filippini, C.E. Mackay, S. Moeller, J.G. Xu, E. Yacoub, G. Baselli, K. Ugurbil, K.L. Miller, and S.M. Smith. ICA-based artefact removal and accelerated fMRI acquisition for improved resting state network imaging. NeuroImage, 95:232-47, 2014",
-  "version": "0.1.7",
+  "version": "0.2.0",
   "custom": {
-    "docker-image": "flywheel/hcp-icafix:0.1.7",
+    "docker-image": "flywheel/hcp-icafix:0.2.0",
     "flywheel": {
       "suite": "Human Connectome Project"
     }