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[WIP] Add Freesurfer container #23

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[WIP] Add Freesurfer container #23

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867b055
first test for freesurfer container
arnaudbore Apr 23, 2024
449eb0d
answer AVC comments
arnaudbore Apr 25, 2024
d358d0c
fix dockerfile
arnaudbore May 8, 2024
30ac80b
fix versions
arnaudbore May 17, 2024
ee47466
add freesurfer version in PATH
arnaudbore Jun 2, 2024
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54 changes: 54 additions & 0 deletions containers/freesurfer.context/freesurfer.Dockerfile
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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-base as freesurfer

ARG FREESURFER_VERSION
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ENV FREESURFER_VERSION=${FREESURFER_VERSION:-${FREESURFER_VERSION}}
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Revert this. The latter part sets the default if (1) ARG is not defined or (2) then variable is not defined in env.


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
41 changes: 41 additions & 0 deletions docker-bake.hcl
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Expand Up @@ -116,6 +116,13 @@ variable "SCILUS_TAG" {
variable "FLOWS_TAG" {
}

variable "FREESURFER_TAG" {
}

variable "FREESURFER_VERSION" {
default = "7.4.1"
}

# ==============================================================================
# UTILITY FUNCTIONS
# ==============================================================================
Expand Down Expand Up @@ -149,6 +156,10 @@ group "dmriqcpy" {
targets = ["dmriqcpy", "dmriqcpy-test"]
}

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

# ==============================================================================
# TEST TARGETS
# ==============================================================================
Expand Down Expand Up @@ -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 = {
Expand Down Expand Up @@ -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"
Expand Down
3 changes: 2 additions & 1 deletion versioning.hcl
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Expand Up @@ -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"
Expand Down