ENH: Add initial FastSurfer interface (WIP)

.zenodo.json

@@ -46,6 +46,12 @@
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729",
       "type": "Researcher"
+    },
+    {
+      "affiliation": "Beckman Institute for Advanced Science & Technology, University of Illinois at Urbana-Champaign, IL, USA",
+      "name": "Camacho, Paul B.",
+      "orcid": "0000-0001-9048-7307",
+      "type": "Researcher"
     }
   ],
   "keywords": [

Dockerfile

@@ -22,10 +22,17 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-# Use Ubuntu 20.04 LTS
-FROM ubuntu:focal-20210416
+## Start with ubuntu base as in FastSurfer Docker image
+## https://github.com/Deep-MI/FastSurfer/blob/0749f38e656ed0da977c408b4383db88e1a8b563/Docker/Dockerfile
 
+FROM ubuntu:focal-20210416
 # Prepare environment
+ENV DEBIAN_FRONTEND="noninteractive"
+ENV LANG=C.UTF-8
+ARG PYTHON_VERSION=3.8
+ARG CONDA_FILE=Miniconda3-py38_4.11.0-Linux-x86_64.sh
+ENV DEBIAN_FRONTEND=noninteractive
+
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     apt-utils \
@@ -34,6 +41,9 @@ RUN apt-get update && \
                     bzip2 \
                     ca-certificates \
                     curl \
+                    wget \
+                    upx \
+                    file \
                     git \
                     libtool \
                     lsb-release \
@@ -43,14 +53,44 @@ RUN apt-get update && \
                     xvfb && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-ENV DEBIAN_FRONTEND="noninteractive" \
-    LANG="en_US.UTF-8" \
-    LC_ALL="en_US.UTF-8"
+# git clone dev branch of FastSurfer
+RUN cd /opt && mkdir /fastsurfer \
+    && git clone -b v.1.1.2 https://github.com/Deep-MI/FastSurfer.git \
+    && cp /opt/FastSurfer/fastsurfer_env_gpu.yml /fastsurfer/fastsurfer_env_gpu.yml 
+
+# Install conda
+RUN wget --no-check-certificate -qO ~/miniconda.sh https://repo.continuum.io/miniconda/$CONDA_FILE  && \
+     chmod +x ~/miniconda.sh && \
+     ~/miniconda.sh -b -p /opt/conda && \
+     rm ~/miniconda.sh 
 
 # Installing freesurfer
 COPY docker/files/freesurfer7.2-exclude.txt /usr/local/etc/freesurfer7.2-exclude.txt
 RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz \
-    | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.2-exclude.txt
+     | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.2-exclude.txt
+
+# Install required packages for freesurfer to run
+RUN apt-get update && apt-get install -y --no-install-recommends \
+      tcsh \
+      time \
+      bc \
+      gawk \
+      libgomp1 && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* 
+
+# Add FreeSurfer Environment variables
+ENV OS=Linux \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA= \
+    SUBJECTS_DIR=/opt/freesurfer/subjects \
+    FSF_OUTPUT_FORMAT=nii.gz \
+    FREESURFER_HOME=/opt/freesurfer \
+    PYTHONUNBUFFERED=0 \
+    PATH=/opt/freesurfer/bin:$PATH
+
+# Copy fastsurfer from git folder
+RUN cp -R /opt/FastSurfer/* /fastsurfer/
 
 # Simulate SetUpFreeSurfer.sh
 ENV FSL_DIR="/opt/fsl-6.0.5.1" \
@@ -90,6 +130,7 @@ RUN apt-get update -qq \
            libxrender1 \
            libxt6 \
            sudo \
+           curl \
            wget \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* \
@@ -226,8 +267,8 @@ WORKDIR $ANTSPATH
 RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
     | tar -xzC $ANTSPATH --strip-components 1
 
-# nipreps/miniconda:py39_0525.0
-COPY --from=nipreps/miniconda@sha256:40fffd37963502dcd8549773559fc21182f52460e59e0ad6398a84faf6055641 /opt/conda /opt/conda
+# nipreps/miniconda:py38_1.4.1
+COPY --from=nipreps/miniconda@sha256:ebbff214e6c9dc50ccc6fdbe679df1ffcbceaa45b47a75d6e34e8a064ef178da /opt/conda /opt/conda
 
 RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
     echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
@@ -253,7 +294,8 @@ ENV HOME="/home/smriprep" \
     LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
 
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> $HOME/.bashrc && \
-    echo "conda activate base" >> $HOME/.bashrc
+    echo "conda activate base" >> $HOME/.bashrc && \
+    echo "$FREESURFER_HOME/SetUpFreeSurfer.sh" >> $HOME/.bashrc
 
 # Precaching atlases
 COPY scripts/fetch_templates.py fetch_templates.py
@@ -268,8 +310,11 @@ COPY . /src/smriprep
 ARG VERSION
 # Force static versioning within container
 RUN echo "${VERSION}" > /src/smriprep/smriprep/VERSION && \
-    echo "include smriprep/VERSION" >> /src/smriprep/MANIFEST.in && \
-    /opt/conda/bin/python -m pip install --no-cache-dir "/src/smriprep[all]"
+    echo "include smriprep/${VERSION}" >> /src/smriprep/MANIFEST.in && \
+    /opt/conda/bin/python -m pip install --no-cache-dir "/src/smriprep[all]" && \
+    /opt/conda/bin/python -m pip install --no-cache-dir nibabel==4.0.2
+
+RUN conda env update -n base --file /fastsurfer/fastsurfer_env_gpu.yml
 
 RUN find $HOME -type d -exec chmod go=u {} + && \
     find $HOME -type f -exec chmod go=u {} + && \
@@ -280,6 +325,8 @@ RUN find $HOME -type d -exec chmod go=u {} + && \
 ENV FREESURFER="/opt/freesurfer"
 
 ENV IS_DOCKER_8395080871=1
+ENV FASTSURFER_HOME=/fastsurfer
+ENV PATH="/fastsurfer:/$PATH"
 
 RUN ldconfig
 WORKDIR /tmp