From 917bab919f6613ce44ab424bad7a39bfc6a6ec32 Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Fri, 9 Aug 2024 15:40:46 -0400
Subject: [PATCH] Add Freesurfer back in (#3)

---
 .circleci/config.yml  | 13 +++++++++++++
 Dockerfile            | 24 ++++++++++++++++++++++++
 Dockerfile_Freesurfer | 35 +++++++++++++++++++++++++++++++++++
 setup_build.sh        |  3 +++
 4 files changed, 75 insertions(+)
 create mode 100644 Dockerfile_Freesurfer

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 58af617..4aed311 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -52,6 +52,13 @@ build: &build
 
 jobs:
 
+  build_FreeSurfer:
+    environment:
+      VERSION_TAG: "TAG_FREESURFER"
+      IMG_NAME: "qsirecon-freesurfer"
+      BUILD_FILE: "Dockerfile_FreeSurfer"
+    <<: *build
+
   build_3Tissue:
     environment:
       VERSION_TAG: "TAG_3TISSUE"
@@ -148,6 +155,11 @@ workflows:
   version: 2
   build_test_deploy:
     jobs:
+      - build_FreeSurfer:
+          filters:
+            tags:
+              only: /.*/
+
       - build_3Tissue:
           filters:
             tags:
@@ -194,6 +206,7 @@ workflows:
 
       - deployable:
           requires:
+            - build_FreeSurfer
             - build_3Tissue
             - build_MRtrix3
             - build_DSIStudio
diff --git a/Dockerfile b/Dockerfile
index 68cad0f..ee15b1f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,3 +1,4 @@
+ARG TAG_FREESURFER
 ARG TAG_ANTS
 ARG TAG_MRTRIX3
 ARG TAG_3TISSUE
@@ -8,6 +9,7 @@ ARG TAG_TORTOISE
 ARG TAG_TORTOISECUDA
 
 # COPY can't handle variables, so here we go
+FROM pennlinc/qsirecon-freesurfer:${TAG_FREESURFER} as build_freesurfer
 FROM pennlinc/qsirecon-ants:${TAG_ANTS} as build_ants
 FROM pennlinc/qsirecon-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3
 FROM pennlinc/qsirecon-3tissue:${TAG_3TISSUE} as build_3tissue
@@ -43,6 +45,28 @@ COPY --from=build_3tissue /opt/3Tissue /opt/3Tissue
 ENV PATH="$PATH:/opt/mrtrix3-latest/bin:/opt/3Tissue/bin" \
     MRTRIX3_DEPS="bzip2 ca-certificates curl libpng16-16 libblas3 liblapack3"
 
+## Freesurfer
+COPY --from=build_freesurfer /opt/freesurfer /opt/freesurfer
+# Simulate SetUpFreeSurfer.sh
+ENV FSL_DIR="/opt/conda/envs/fslqsirecon" \
+    OS="Linux" \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA="" \
+    FSF_OUTPUT_FORMAT="nii.gz" \
+    FREESURFER_HOME="/opt/freesurfer"
+ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
+    FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
+    MNI_DIR="$FREESURFER_HOME/mni" \
+    LOCAL_DIR="$FREESURFER_HOME/local" \
+    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
+    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
+    MNI_DATAPATH="$FREESURFER_HOME/mni/data"
+ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
+    MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
+    PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH" \
+    FREESURFER_DEPS="bc ca-certificates curl libgomp1 libxmu6 libxt6 tcsh perl"
+RUN chmod a+rx /opt/freesurfer/bin/mri_synthseg /opt/freesurfer/bin/mri_synthstrip
+
 ## AFNI
 COPY --from=build_afni /opt/afni-latest /opt/afni-latest
 ENV PATH="$PATH:/opt/afni-latest" \
diff --git a/Dockerfile_Freesurfer b/Dockerfile_Freesurfer
new file mode 100644
index 0000000..b1f919b
--- /dev/null
+++ b/Dockerfile_Freesurfer
@@ -0,0 +1,35 @@
+FROM freesurfer/freesurfer:7.3.1 as freesurfer
+FROM ubuntu:18.04
+ARG TAG_ANTS
+
+COPY --from=freesurfer \
+  /usr/local/freesurfer/bin/mri_rigid_register \
+  /opt/freesurfer/bin/mri_rigid_register
+
+COPY --from=freesurfer \
+  /usr/local/freesurfer/bin/mri_robust_register  \
+  /opt/freesurfer/bin/mri_robust_register
+
+COPY --from=freesurfer \
+  /usr/local/freesurfer/bin/mri_robust_template \
+  /opt/freesurfer/bin/mri_robust_template
+
+COPY --from=freesurfer \
+  /usr/local/freesurfer/bin/lta_convert  \
+  /opt/freesurfer/bin/lta_convert
+
+COPY --from=freesurfer \
+  /usr/local/freesurfer/bin/lta_diff  \
+  /opt/freesurfer/bin/lta_diff
+
+COPY --from=freesurfer \
+  /usr/local/freesurfer/python/scripts/mri_synthseg  \
+  /opt/freesurfer/bin/mri_synthseg
+
+COPY --from=freesurfer \
+  /usr/local/freesurfer/models  \
+  /opt/freesurfer/models
+
+COPY --from=freesurfer \
+  /usr/local/freesurfer/python/scripts/mri_synthstrip  \
+  /opt/freesurfer/bin/mri_synthstrip
diff --git a/setup_build.sh b/setup_build.sh
index d67e8c1..1401208 100644
--- a/setup_build.sh
+++ b/setup_build.sh
@@ -8,6 +8,7 @@ fi
 export BUILD_TAG
 
 # Versions of the components
+export TAG_FREESURFER=23.3.0
 export TAG_ANTS=24.4.24
 export TAG_MRTRIX3=24.4.24
 export TAG_3TISSUE=24.4.24
@@ -21,6 +22,7 @@ echo "Settings:"
 echo "----------"
 echo ""
 echo "BUILD_TAG=${BUILD_TAG}"
+echo "TAG_FREESURFER=${TAG_FREESURFER}"
 echo "TAG_ANTS=${TAG_ANTS}"
 echo "TAG_MRTRIX3=${TAG_MRTRIX3}"
 echo "TAG_3TISSUE=${TAG_3TISSUE}"
@@ -39,6 +41,7 @@ do_build() {
     BUILDKIT_PROGRESS=plain \
     docker build -t \
         pennlinc/qsirecon_build:${THIS_TAG} \
+        --build-arg TAG_FREESURFER=${TAG_FREESURFER} \
         --build-arg TAG_ANTS=${TAG_ANTS} \
         --build-arg TAG_MRTRIX3=${TAG_MRTRIX3} \
         --build-arg TAG_3TISSUE=${TAG_3TISSUE} \