diff --git a/Dockerfile b/Dockerfile index 297c148..ee2ee0f 100644 --- a/Dockerfile +++ b/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. diff --git a/manifest.json b/manifest.json index 06533a0..43243cc 100644 --- a/manifest.json +++ b/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" }