Add multi-frame PET motion correction

docker/Dockerfile.core

@@ -27,6 +27,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 
 RUN python3 -m pip install --no-cache-dir --default-timeout=120 --retries=10 \
       "conan>=2.0,<3" \
+      numpy \
       pandas \
       pytest
 

localizer/src/CMakeLists.txt

@@ -1,7 +1,7 @@
 # CMakeList.txt: DCCCcore Refactored Version
 cmake_minimum_required(VERSION 3.21)
 
-project(DCCCcore VERSION 4.2.6)
+project(DCCCcore VERSION 4.3.0)
 set(DCCCCORE_VERSION_SUFFIX "")
 set(DCCCCORE_SOFTWARE_VERSION "${PROJECT_VERSION}${DCCCCORE_VERSION_SUFFIX}")
 
@@ -20,6 +20,7 @@ find_package(onnxruntime CONFIG REQUIRED)
 find_package(tomlplusplus CONFIG REQUIRED)
 find_package(Eigen3 CONFIG REQUIRED)
 find_package(rapidcsv CONFIG REQUIRED)
+find_package(ZLIB REQUIRED)
 
 # Include directories
 # include_directories(${CMAKE_CURRENT_SOURCE_DIR})
@@ -67,6 +68,8 @@ target_sources(DCCCcore PRIVATE
 target_sources(DCCCcore PRIVATE
     core/preprocessing/ImagePreprocessor.h
     core/preprocessing/ImagePreprocessor.cpp
+    core/preprocessing/PetMotionCorrector.h
+    core/preprocessing/PetMotionCorrector.cpp
 )
 
 # Add utility sources
@@ -186,6 +189,8 @@ target_sources(DCCCcore PRIVATE
     spatialNormalizations/adni/AdniPetCoreCLI.cpp
     spatialNormalizations/rigid/RigidCLI.h
     spatialNormalizations/rigid/RigidCLI.cpp
+    spatialNormalizations/pet/PetMotionCorrectionCLI.h
+    spatialNormalizations/pet/PetMotionCorrectionCLI.cpp
 )
 
 # Link libraries
@@ -196,6 +201,7 @@ target_link_libraries(DCCCcore PRIVATE
     tomlplusplus::tomlplusplus
     Eigen3::Eigen
     rapidcsv::rapidcsv
+    ZLIB::ZLIB
 )
 
 # Compile options

localizer/src/README.md

@@ -110,12 +110,27 @@ Perform spatial standardization without metric calculation:
 # ADNI-style processing
 ./DCCCcore adni-pet-core --input pet.nii --output normalized.nii
 
+# Multi-frame PET motion correction and arithmetic mean
+./DCCCcore pet-motion-correct --input dynamic_pet.nii.gz --output averaged_pet.nii.gz
+
+# Optionally retain corrected frames and per-frame rigid motion parameters
+./DCCCcore pet-motion-correct --input dynamic_pet.nii.gz --output averaged_pet.nii.gz \
+  --save-corrected-dynamic corrected.nii.gz --motion-output motion.tsv
+
 # Iterative rigid registration
 ./DCCCcore normalize --input pet.nii --output normalized.nii --iterative
 ./DCCCcore adni-pet-core --input pet.nii --output normalized.nii --iterative
 ./DCCCcore rigid --input pet.nii --output rigid.nii --iterative
 ```
 
+`pet-motion-correct` accepts general 4D `X × Y × Z × N` PET data. It uses frame 0
+as the fixed reference, independently registers every later frame to it with a
+six-degree-of-freedom rigid transform, and writes the arithmetic mean as a 3D
+float NIfTI. A 4D input passed to `adni-pet-core` is automatically motion-corrected
+and averaged before the existing ADNI PET Core pipeline; 3D input follows the
+existing pipeline unchanged. Motion TSV translations are in millimetres and
+Euler rotations are in radians.
+
 #### ADAD Analysis
 Run the ADAD decoupling-based metric:
 

localizer/src/conanfile.py

@@ -4,7 +4,7 @@
 
 class AppConan(ConanFile):
     name = "DCCCcore"
-    version = "4.2.6"
+    version = "4.3.0"
     settings = "os", "arch", "compiler", "build_type"
     generators = "CMakeDeps", "CMakeToolchain"
 
@@ -15,6 +15,7 @@ def requirements(self):
         self.requires("onnxruntime/1.18.1")
         self.requires("tomlplusplus/3.4.0")
         self.requires("rapidcsv/8.84")
+        self.requires("zlib/1.3.2")
         # ---- conflict resolution: choose one Eigen for the whole graph ----
         # If the graph shows ORT wants 3.4.0, prefer:
         self.requires("eigen/3.4.0")

localizer/src/core/config/Version.h

@@ -1,4 +1,4 @@
 #pragma once
 #include <string>
 
-const std::string SOFTWARE_VERSION = "4.2.6";
+const std::string SOFTWARE_VERSION = "4.3.0";