From 6e4ec600a05ef36edbadb9a69b983062f01bb03d Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Tue, 18 Jul 2023 10:47:20 -0400
Subject: [PATCH] Add AtlasPack atlases to Docker image (#22)

* Add AtlasPack atlases.

* Update path.

* Update Dockerfile

* Update Dockerfile
---
 Dockerfile | 46 +++++++++++++++++++++++++++-------------------
 1 file changed, 27 insertions(+), 19 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 8eaa70e..24974dc 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,8 +1,16 @@
 FROM pennlinc/xcp_d:0.1.3 as build_fsl
+FROM pennlinc/atlaspack:0.0.4 as atlaspack
 FROM ubuntu:bionic-20220531
 
 COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
 
+# Download atlases from AtlasPack
+RUN mkdir /AtlasPack
+COPY --from=atlaspack /AtlasPack/tpl-fsLR_*.dlabel.nii /AtlasPack/
+COPY --from=atlaspack /AtlasPack/tpl-MNI152NLin6Asym_*.nii.gz /AtlasPack/
+COPY --from=atlaspack /AtlasPack/atlas-4S*.tsv /AtlasPack/
+COPY --from=atlaspack /AtlasPack/*.json /AtlasPack/
+
 # Install basic libraries
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
@@ -120,24 +128,24 @@ ENV FSLDIR="/opt/fsl" \
 
 # Install FreeSurfer
 RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
-    --exclude='freesurfer/diffusion' \
-    --exclude='freesurfer/docs' \
-    --exclude='freesurfer/fsfast' \
-    --exclude='freesurfer/lib/cuda' \
-    --exclude='freesurfer/lib/qt' \
-    --exclude='freesurfer/matlab' \
-    --exclude='freesurfer/mni/share/man' \
-    --exclude='freesurfer/subjects/fsaverage_sym' \
-    --exclude='freesurfer/subjects/fsaverage3' \
-    --exclude='freesurfer/subjects/fsaverage4' \
-    --exclude='freesurfer/subjects/cvs_avg35' \
-    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
-    --exclude='freesurfer/subjects/bert' \
-    --exclude='freesurfer/subjects/lh.EC_average' \
-    --exclude='freesurfer/subjects/rh.EC_average' \
-    --exclude='freesurfer/subjects/sample-*.mgz' \
-    --exclude='freesurfer/subjects/V1_average' \
-    --exclude='freesurfer/trctrain'
+    --exclude="freesurfer/diffusion" \
+    --exclude="freesurfer/docs" \
+    --exclude="freesurfer/fsfast" \
+    --exclude="freesurfer/lib/cuda" \
+    --exclude="freesurfer/lib/qt" \
+    --exclude="freesurfer/matlab" \
+    --exclude="freesurfer/mni/share/man" \
+    --exclude="freesurfer/subjects/fsaverage_sym" \
+    --exclude="freesurfer/subjects/fsaverage3" \
+    --exclude="freesurfer/subjects/fsaverage4" \
+    --exclude="freesurfer/subjects/cvs_avg35" \
+    --exclude="freesurfer/subjects/cvs_avg35_inMNI152" \
+    --exclude="freesurfer/subjects/bert" \
+    --exclude="freesurfer/subjects/lh.EC_average" \
+    --exclude="freesurfer/subjects/rh.EC_average" \
+    --exclude="freesurfer/subjects/sample-*.mgz" \
+    --exclude="freesurfer/subjects/V1_average" \
+    --exclude="freesurfer/trctrain"
 
 ENV FREESURFER_HOME="/opt/freesurfer" \
     FSF_OUTPUT_FORMAT="nii.gz"
@@ -188,7 +196,7 @@ ENV HOME="/home/xcp_d"
 # Update pip, which AFNI installs (probably)
 RUN pip install --no-cache-dir --upgrade pip
 
-# Precaching fonts, set 'Agg' as default backend for matplotlib
+# Precaching fonts, set "Agg" as default backend for matplotlib
 RUN python -c "from matplotlib import font_manager" && \
     sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )