[WIP] Add Freesurfer container

containers/freesurfer.context/freesurfer.Dockerfile

@@ -0,0 +1,54 @@
+# docker build for distributing a base fs 7.2.0 container
+
+FROM freesurfer-base as freesurfer
+
+ARG FREESURFER_VERSION
+ENV FREESURFER_VERSION=${FREESURFER_VERSION:-${FREESURFER_VERSION}}
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# shell settings
+WORKDIR /
+
+# install utils
+RUN apt-get -y update
+RUN apt-get -y install bc perl tar tcsh wget vim-common 
+
+RUN apt-get -y install language-pack-en libx11-dev gettext xterm x11-apps csh xorg-dev libncurses5 libgl1 libegl1 xorg xserver-xorg-video-intel libglu1-mesa libjpeg62 libopengl0 libwayland-cursor0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-render-util0 libxcb-render0 libxcb-util1 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxkbcommon-x11-0 libxkbcommon0
+
+RUN echo ${FREESURFER_VERSION}
+
+# install fs
+ADD freesurfer_ubuntu22-${FREESURFER_VERSION}_amd64.deb /
+## RUN wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${FREESURFER_VERSION}/freesurfer_ubuntu22-${FREESURFER_VERSION}_amd64.deb && \
+RUN dpkg -i freesurfer_ubuntu22-${FREESURFER_VERSION}_amd64.deb && \
+    rm freesurfer_ubuntu22-${FREESURFER_VERSION}_amd64.deb
+
+# setup fs env
+ENV OS Linux
+ENV PATH /usr/local/freesurfer/${FREESURFER_VERSION}/bin:/usr/local/freesurfer/${FREESURFER_VERSION}/fsfast/bin:/usr/local/freesurfer/${FREESURFER_VERSION}/tktools:/usr/local/freesurfer/${FREESURFER_VERSION}/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
+ENV FREESURFER_HOME /usr/local/freesurfer/${FREESURFER_VERSION}
+ENV FREESURFER /usr/local/freesurfer/${FREESURFER_VERSION}
+ENV SUBJECTS_DIR /usr/local/freesurfer/${FREESURFER_VERSION}/subjects
+ENV LOCAL_DIR /usr/local/freesurfer/${FREESURFER_VERSION}/local
+ENV FSFAST_HOME /usr/local/freesurfer/${FREESURFER_VERSION}/fsfast
+ENV FMRI_ANALYSIS_DIR /usr/local/freesurfer/${FREESURFER_VERSION}/fsfast
+ENV FUNCTIONALS_DIR /usr/local/freesurfer/${FREESURFER_VERSION}/sessions
+
+# set default fs options
+ENV FS_OVERRIDE 0
+ENV FIX_VERTEX_AREA ""
+ENV FSF_OUTPUT_FORMAT nii.gz
+
+# mni env requirements
+ENV MINC_BIN_DIR /usr/local/freesurfer/${FREESURFER_VERSION}/mni/bin
+ENV MINC_LIB_DIR /usr/local/freesurfer/${FREESURFER_VERSION}/mni/lib
+ENV MNI_DIR /usr/local/freesurfer/${FREESURFER_VERSION}/mni
+ENV MNI_DATAPATH /usr/local/freesurfer/${FREESURFER_VERSION}/mni/data
+ENV MNI_PERL5LIB /usr/local/freesurfer/${FREESURFER_VERSION}/mni/share/perl5
+ENV PERL5LIB /usr/local/freesurfer/${FREESURFER_VERSION}/mni/share/perl5
+
+ENV FS_LICENSE='/license.txt'
+
+RUN ( [ -f "VERSION" ] || touch VERSION ) && \
+    echo "freesurfer => ${FREESURFER_VERSION}\n" >> VERSION

docker-bake.hcl

@@ -116,6 +116,13 @@ variable "SCILUS_TAG" {
 variable "FLOWS_TAG" {
 }
 
+variable "FREESURFER_TAG" {
+}
+
+variable "FREESURFER_VERSION" {
+    default = "7.4.1"
+}
+
 # ==============================================================================
 # UTILITY FUNCTIONS
 # ==============================================================================
@@ -149,6 +156,10 @@ group "dmriqcpy" {
     targets = ["dmriqcpy", "dmriqcpy-test"]
 }
 
+group "freesurfer" {
+    targets = ["scilus-freesurfer"]
+}
+
 # ==============================================================================
 # TEST TARGETS
 # ==============================================================================
@@ -308,6 +319,19 @@ target "scilus-fsl" {
     output = ["type=docker"]
 }
 
+target "scilus-freesurfer" {
+    inherits = ["freesurfer"]
+    contexts = {
+        freesurfer-base = "target:scilus"
+    }
+    cache-from = [
+        "type=registry,ref=${dockerhub-user-pull}/build-cache:scilus",
+        "type=registry,ref=scilus/build-cache:scilus"
+    ]
+    tags = notequal("", SCILUS_TAG) ? stamp_tag("scilus/scilus-freesurfer:${SCILUS_TAG}", timestamp()) : ["scilus-freesurfer:local"]
+    output = ["type=docker"]
+}
+
 target "scilus-mrtrix" {
     inherits = ["mrtrix"]
     contexts = {
@@ -413,6 +437,23 @@ target "fsl" {
     output = ["type=cacheonly"]
 }
 
+target "freesurfer" {
+    dockerfile = "freesurfer.Dockerfile"
+    context = "./containers/freesurfer.context"
+    target = "freesurfer"
+    contexts = {
+        freesurfer-base = "docker-image://${base-install-image}"
+    }
+    args = {
+        FREESURFER_VERSION = "${freesurfer-version}"
+    }
+    cache-from = [
+        "type=registry,ref=${dockerhub-user-pull}/build-cache:freesurfer",
+        "type=registry,ref=scilus/build-cache:freesurfer"
+    ]
+    output = ["type=cacheonly"]
+}
+
 target "mrtrix" {
     dockerfile = "mrtrix.Dockerfile"
     context = "./containers"

versioning.hcl

@@ -4,11 +4,12 @@ base-install-image="nvidia/cuda:11.7.1-runtime-ubuntu22.04"
 base-build-image="ubuntu:jammy-20230301"
 
 dmriqcpy-version="0.1.7"
-scilpy-version="1.6.0"
+scilpy-version="2.0.2"
 
 ants-version="2.4.3"
 cmake-version="3.16.3"
 fsl-version="6.0.6"
+freesurfer-version="7.4.1"
 mrtrix-version="3.0.4"
 mesa-version="22.0.5"
 vtk-version="9.2.6"