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[WIP] Add Freesurfer container #23

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54 changes: 54 additions & 0 deletions containers/freesurfer.context/freesurfer.Dockerfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@
# docker build for distributing a base fs 7.2.0 container

FROM freesurfer-builder as freesurfer

ARG FREESURFER_VERSION
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# shell settings
WORKDIR /root
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# 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'
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39 changes: 39 additions & 0 deletions docker-bake.hcl
Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,10 @@ variable "SCILUS_TAG" {
variable "FLOWS_TAG" {
}

variable "FS_VERSION" {
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default = "7.4.1"
}

# ==============================================================================
# UTILITY FUNCTIONS
# ==============================================================================
Expand Down Expand Up @@ -149,6 +153,10 @@ group "dmriqcpy" {
targets = ["dmriqcpy", "dmriqcpy-test"]
}

group "freesurfer" {
targets = ["freesurfer"]
}

# ==============================================================================
# TEST TARGETS
# ==============================================================================
Expand Down Expand Up @@ -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()) : []
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output = ["type=docker"]
}

target "scilus-mrtrix" {
inherits = ["mrtrix"]
contexts = {
Expand Down Expand Up @@ -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}"
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}
args = {
FREESURFER_VERSION = "${fs-version}"
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}
cache-from = [
"type=registry,ref=${dockerhub-user-pull}/build-cache:freesurfer",
"type=registry,ref=scilus/build-cache:freesurfer"
]
output = ["type=cacheonly"]
}

target "mrtrix" {
dockerfile = "mrtrix.Dockerfile"
context = "./containers"
Expand Down
1 change: 1 addition & 0 deletions versioning.hcl
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down