[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-builder as freesurfer
+
+ARG FREESURFER_VERSION
+
+# shell settings
+WORKDIR /root
+
+# install utils
+RUN apt-get -y update
+RUN apt-get -y install bc \
+    libgomp \
+    perl \
+    tar \
+    tcsh \
+    wget \
+    vim-common \
+    mesa-libGL \
+    libXext \
+    libSM \
+    libXrender \
+    libXmu
+
+# install fs
+RUN wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${FREESURFER_VERSION}/freesurfer_ubuntu22${FREESURFER_VERSION}_amd64.deb && \
+    dpkg -i freesurfer_${FREESURFER_VERSION}_amd64.deb
+    rm freesurfer_${FREESURFER_VERSION}_amd64.deb
+
+# setup fs env
+ENV OS Linux
+ENV PATH /usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ENV FREESURFER_HOME /usr/local/freesurfer
+ENV FREESURFER /usr/local/freesurfer
+ENV SUBJECTS_DIR /usr/local/freesurfer/subjects
+ENV LOCAL_DIR /usr/local/freesurfer/local
+ENV FSFAST_HOME /usr/local/freesurfer/fsfast
+ENV FMRI_ANALYSIS_DIR /usr/local/freesurfer/fsfast
+ENV FUNCTIONALS_DIR /usr/local/freesurfer/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/mni/bin
+ENV MINC_LIB_DIR /usr/local/freesurfer/mni/lib
+ENV MNI_DIR /usr/local/freesurfer/mni
+ENV MNI_DATAPATH /usr/local/freesurfer/mni/data
+ENV MNI_PERL5LIB /usr/local/freesurfer/mni/share/perl5
+ENV PERL5LIB /usr/local/freesurfer/mni/share/perl5
+
+ENV FS_LICENSE='/license.txt'

docker-bake.hcl

@@ -116,6 +116,10 @@ variable "SCILUS_TAG" {
 variable "FLOWS_TAG" {
 }
 
+variable "FS_VERSION" {
+    default = "7.4.1"
+}
+
 # ==============================================================================
 # UTILITY FUNCTIONS
 # ==============================================================================
@@ -149,6 +153,10 @@ group "dmriqcpy" {
     targets = ["dmriqcpy", "dmriqcpy-test"]
 }
 
+group "freesurfer" {
+    targets = ["freesurfer"]
+}
+
 # ==============================================================================
 # TEST TARGETS
 # ==============================================================================
@@ -308,6 +316,19 @@ target "scilus-fsl" {
     output = ["type=docker"]
 }
 
+target "scilus-freesurfer" {
+    inherits = ["freesurfer"]
+    contexts = {
+        freesurfer-base = "target:scilus-base"
+    }
+    cache-from = [
+        "type=registry,ref=${dockerhub-user-pull}/build-cache:scilus-deps",
+        "type=registry,ref=scilus/build-cache:scilus-deps"
+    ]
+    tags = notequal("", DEPS_TAG) ? stamp_tag("scilus/scilus-deps:${DEPS_TAG}", timestamp()) : []
+    output = ["type=docker"]
+}
+
 target "scilus-mrtrix" {
     inherits = ["mrtrix"]
     contexts = {
@@ -413,6 +434,24 @@ target "fsl" {
     output = ["type=cacheonly"]
 }
 
+target "freesurfer" {
+    dockerfile = "freesurfer.Dockerfile"
+    context = "./containers/freesurfer.context"
+    target = "freesurfer-install"
+    contexts = {
+        freesurfer-base = "docker-image://${base-install-image}"
+        freesurfer-builder = "docker-image://${base-build-image}"
+    }
+    args = {
+        FREESURFER_VERSION = "${fs-version}"
+    }
+    cache-from = [
+        "type=registry,ref=${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

@@ -9,6 +9,7 @@ scilpy-version="1.6.0"
 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"