### First-Time Development Setup Script

Source: https://github.com/brainsia/brainstools/blob/main/Documentation/AI/git-commits.md

Run this script once after cloning the repository to install necessary Git hooks for local validation.

```bash
./Utilities/SetupForDevelopment.sh
```

--------------------------------

### Run Developer Setup Script

Source: https://github.com/brainsia/brainstools/blob/main/github/CONTRIBUTING.md

Execute the setup script to prepare your work tree and configure Git aliases for development.

```sh
   $ ./Utilities/SetupForDevelopment.sh
```

--------------------------------

### Running Example on OSX

Source: https://github.com/brainsia/brainstools/blob/main/AutoWorkup/README.md

An example command to run `singleSession.py` on an OSX system, setting environment variables and specifying script parameters.

```sh
env="OSX"

NamicBuild="/Shared/sinapse/scratch/eunyokim/src/NamicExternal/build_OSX_20150619/"
export PATH=$NamicBuild/bin:$PATH
export PYTHONPATH=$NamicBuild/SimpleITK-build/Wrapping/:$NamicBuild/BRAINSTools/AutoWorkup/:$NamicBuild/NIPYPE:$PYTHONPATH

wfrun="local"

python $NamicBuild/BRAINSTools/AutoWorkup/singleSession.py \
      --wfrun $wfrun \
      --workphase atlas-based-reference \
      --pe ${env} \
      --ExperimentConfig ./KIDsHD.config \
      --use-sentinal \
      all

```

--------------------------------

### Setup for Developer Workflow

Source: https://github.com/brainsia/brainstools/blob/main/docs/index.md

Run the setup script to configure Git hooks, remotes, and establish the recommended developer workflow for BRAINSTools.

```bash
cd BRAINSTools
bash ./Utilities/SetupForDevelopment.sh
```

--------------------------------

### Setup and Build BRAINSTools (macOS)

Source: https://github.com/brainsia/brainstools/blob/main/README.md

Steps to clone the BRAINSTools repository, run the setup script, configure with CMake, and build the project on macOS. Includes commands for finding the number of CPU threads.

```sh
mkdir brains
cd brains
git clone http://github.com/BRAINSIa/BRAINSTools.git

cd BRAINSTools
./Utilities/SetupForDevelopment.sh
cd ..

mkdir build
cd build
cmake ../BRAINSTools

## NOTE: To configure options in the cmake GUI, use:
##     ccmake ../BRAINSTools
## instead
make -j${NUMOFTHREADS} -k

## NOTE: To find the number of threads from the OSX terminal, use:
##    sysctl -n hw.ncpu
```

--------------------------------

### Clone and Set Up BRAINSTools

Source: https://github.com/brainsia/brainstools/blob/main/Documentation/AI/building.md

Initial steps to clone the repository and set up development environment with git hooks. This is a one-time setup.

```bash
git clone https://github.com/BRAINSia/BRAINSTools.git
cd BRAINSTools
./Utilities/SetupForDevelopment.sh   # install git hooks; required once
```

--------------------------------

### BRAINSTools Install Layout

Source: https://github.com/brainsia/brainstools/blob/main/Documentation/AI/building.md

Illustrates the directory structure of a typical BRAINSTools installation, showing the locations of executables, libraries, and headers.

```text
BRAINSTools-build/BRAINSTools-Release-5.8.0/   ← CMAKE_INSTALL_PREFIX
├── bin/          ← compiled tool executables
├── lib/          ← shared libraries
│   └── cmake/    ← CMake config files
└── include/      ← public headers
```

--------------------------------

### Install CMake and Build BRAINSTools (Linux Debian/Ubuntu)

Source: https://github.com/brainsia/brainstools/blob/main/README.md

Instructions for building BRAINSTools on a fresh Linux Debian/Ubuntu install, including installing a specific CMake version from binaries and compiling the project.

```sh
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install git python2.7
python2.7-dev g++ freeglut3-dev
```

```sh
# You can find the URL of the latest CMake binary by
# * Go to www.cmake.org/download in a browser
# * Hover over the desired 'Binary distribution' for your operating
#     system
# * Right-click and select 'Copy Link Address' for the file ending in
#     "tar.gz"
URL=http://www.cmake.org/files/v3.2/cmake-3.2.1-Linux-x86_64.tar.gz
wget ${URL}
# Decompress the file
tar -xzvf cmake-3.2.1-Linux-x86_64.tar.gz
# Add the binary to your PATH environment variable
export PATH=${PWD}/cmake-3.2.1-Linux-x86_64/bin:${PATH}
```

```sh
git clone https://github.com/BRAINSia/BRAINSTools.git
mkdir build
cd build
CC=/usr/bin/gcc-4.8 \
CXX=/usr/bin/g++-4.8 \
cmake ../BRAINSTools \
make -j${NUMOFTHREADS} -k
:warning: You can find the number of threads on your system in Ubuntu with `lscpu`
```

--------------------------------

### AutoWorkup Configuration Examples

Source: https://context7.com/brainsia/brainstools/llms.txt

Examples of input CSV and INI configuration files for the AutoWorkup pipeline. The CSV lists MRI sessions, and the INI file specifies experiment parameters and Nipype settings.

```csv
"projectA","111","session001","{'T1-30':['data/sub-111/t1.nii.gz'],'T2-30':['data/sub-111/t2.nii.gz']}"
"projectA","112","session002","{'T1-30':['data/sub-112/t1.nii.gz','data/sub-112/t1_rep.nii.gz'],'T2-30':['data/sub-112/t2.nii.gz']}"
```

```ini
[EXPERIMENT]
SESSION_DB_BASE=./bawInputList.csv
SESSION_DB_TEMP=%(SESSION_DB_BASE)s
BASE_OUTPUT_DIR=./experiment_results
EXPERIMENT_BASE=20240101_base
WORKFLOW_COMPONENTS_BASE=['denoise','landmark','auxlmk','tissue_classify','warp_atlas_to_subject']
ATLAS_PATH=/path/to/Atlas/Atlas_20131115

[NIPYPE]
GLOBAL_DATA_SINK_REWRITE=False

[OSX]
QUEUE=-q all
_BRAINSTOOLS_BIN_DIR=/path/to/BRAINSTools-build/bin
APPEND_PATH=%(_BRAINSTOOLS_BIN_DIR)s
```

--------------------------------

### Install BRAINS Build Scripts

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSCommonLib/CMakeLists.txt

Globally finds and configures build scripts from the BuildScripts directory and installs them. Use this to ensure common build utilities are available.

```cmake
file(GLOB BRAINSBUILD_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "BuildScripts/*")
foreach(BUILDFILE ${BRAINSBUILD_FILES})
  #message(STATUS "${BUILDFILE} ${CMAKE_CURRENT_BINARY_DIR}/${BUILDFILE}")
  configure_file(${BUILDFILE} ${CMAKE_CURRENT_BINARY_DIR}/${BUILDFILE} @ONLY IMMEDIATE)
endforeach()
install(FILES ${BRAINSBUILD_FILES}
  DESTINATION ${BRAINSTools_CLI_INSTALL_ARCHIVE_DESTINATION}/BuildScripts COMPONENT Development)
```

--------------------------------

### Example Input List File (bawInputList.csv)

Source: https://github.com/brainsia/brainstools/blob/main/AutoWorkup/README.md

Defines the input MRI data for the pipeline. Each line specifies project, subject, session, and a dictionary of T1 and T2 scan paths. Ensure MRISessionName is unique.

```python
"projectName","subjectName","MRISessionName","{'T1-30':[t1 repeated scans list],'T2-30':[t2 repeated scans list]}"
"projectA","111","12345611","{'T1-30':['somewhere/T1_filename.nii.gz'],'T2-30':['somewhere/T2_COR.nii.gz']}"
"projectB","112","12345614","{'T1-30':['somewhere/T1_filename.nii.gz', 'somewhere/T1_COR_REP1.nii.gz'],'T2-30':['somewhere/T2_COR.nii.gz']}"
"projectA","111","12345698","{'T1-30':['somewhere/T1_COR.nii.gz', 'somewhere/T1_COR_REP1.nii.gz'],'T2-30':['somewhere/T2_COR.nii.gz']}"
```

--------------------------------

### Create New Topic Branch from Origin Release

Source: https://github.com/brainsia/brainstools/blob/main/github/CONTRIBUTING.md

Start a new topic branch from 'origin/release' for fixes on the release branch. Use a 'release-' prefix for the topic name.

```sh
   $ git checkout -b my-topic origin/release
```

--------------------------------

### Commit Message Format Example

Source: https://github.com/brainsia/brainstools/blob/main/Documentation/AI/style.md

Follow this format for commit messages, including a prefix, a brief subject line, and an optional longer explanation.

```text
PREFIX: Brief description

Longer explanation if needed. Describe *what* changed and *why*.
```

--------------------------------

### Clean Build BRAINSTools (Linux RedHat 6)

Source: https://github.com/brainsia/brainstools/blob/main/README.md

Example session for a clean build of BRAINSTools on Linux RedHat 6, including specific GCC/G++ versions and CMake configuration options.

```sh
mkdir ~/src/mytester
cd ~/src/mytester
git clone https://github.com/BRAINSia/BRAINSTools.git

cd BRAINSTools/
bash ./Utilities/SetupForDevelopment.sh

mkdir -p ../BRAINSTools-build
cd ../BRAINSTools-build/
CC=/usr/bin/gcc-4.2 CXX=/usr/bin/g++-4.2 ccmake ../BRAINSTools \
    -DUSE_BRAINSConstellationDetector:BOOL=ON \
    -DUSE_BRAINSABC:BOOL=ON

make -j${NUMOFTHREADS} -k

## NOTE: The fetching of data still has problems with parallel builds, so we need to restart it at least
#        once
make
```

--------------------------------

### BRAINSConstellationDetector Landmark Comparison Test Setup

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/TestSuite/CMakeLists.txt

Sets up a test for BRAINSConstellationDetector focused on landmark comparison. It generates aligned landmarks and a verification script.

```cmake
set(BCDTestName BCDTestForLandmarkCompare)
  ExternalData_add_test( ${BRAINSTools_ExternalData_DATA_MANAGEMENT_TARGET} NAME ${BCDTestName}
    COMMAND ${LAUNCH_EXE} $<TARGET_FILE:BRAINSConstellationDetectorTestDriver>
    BRAINSConstellationDetectorTest
    --inputVolume DATA{${TestData_DIR}/T1.nii.gz}
    --LLSModel DATA{${TestData_DIR}/Transforms_h5/LLSModel_50Lmks.${XFRM_EXT}}
    --inputTemplateModel DATA{${TestData_DIR}/T1_50Lmks.mdl}
    --outputVolume ${CMAKE_CURRENT_BINARY_DIR}/${BCDTestName}_aligned.nrrd
    --outputLandmarksInACPCAlignedSpace ${CMAKE_CURRENT_BINARY_DIR}/${BCDTestName}_ACPCSpace_aligned.fcsv
    --outputLandmarksInInputSpace ${CMAKE_CURRENT_BINARY_DIR}/${BCDTestName}_InputSpace_aligned.fcsv
    --outputVerificationScript ${CMAKE_CURRENT_BINARY_DIR}/${BCDTestName}_aligned.sh
    )
  set_tests_properties(${BCDTestName} PROPERTIES TIMEOUT 9876 PROCESSORS ${_brainstools_test_nproc})
```

--------------------------------

### Create New Topic Branch from Origin Master

Source: https://github.com/brainsia/brainstools/blob/main/github/CONTRIBUTING.md

Start a new topic branch from the latest 'origin/master' for new feature development.

```sh
   $ git checkout -b my-topic origin/master
```

--------------------------------

### Build BRAINSTools with LLVM 10

Source: https://github.com/brainsia/brainstools/blob/main/Utilities/build_configs/README.md

Use this script to set up the build environment and compile BRAINSTools using LLVM 10 in RelWithDebInfo mode. Ensure you have Git, CMake, and Ninja installed.

```bash
mkdir -p src
cd src
git clone git@github.com:BRAINSia/BRAINSTools.git
mkdir -p BRAINSTools-llvm10-RelWithDebInfo
cmake \
    -G Ninja \
    -S BRAINSTools \
    -B BRAINSTools-RelWithDebInfo \
    -C BRAINSTools/Utilities/build_configs/Darwin/BRAINSTools-llvm10-RelWithDebInfo.cmake

cd BRAINSTools-llvm10-RelWithDebInfo
ninja

```

--------------------------------

### Add Test Executable and Link Libraries

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSCommonLib/TestLargestForegroundFilledMaskImageFilter/CMakeLists.txt

Defines the test executable name, adds the source file, and links the necessary library. This is a standard setup for creating test executables in CMake.

```cmake
set(TestName TestLargestForegroundFilledMaskImageFilter)

add_executable(${TestName} ${TestName}.cxx)
target_link_libraries(${TestName} PRIVATE BRAINSCommonLib)
set_target_properties(${TestName} PROPERTIES FOLDER ${MODULE_FOLDER})
```

--------------------------------

### Configure and Build BRAINSTools (Phase I Superbuild)

Source: https://github.com/brainsia/brainstools/blob/main/Documentation/AI/building.md

Configures the project for a two-phase superbuild and then builds it. Phase I fetches dependencies, and Phase II builds the tools.

```bash
mkdir ../BRAINSTools-build
cd ../BRAINSTools-build
cmake ../BRAINSTools \
  -DCMAKE_BUILD_TYPE=Release \
  -DBRAINSTools_SUPERBUILD=ON

make -j$(nproc)
```

--------------------------------

### Add Dependency for External Data Installation

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSPosteriorToContinuousClass/TestSuite/CMakeLists.txt

Ensures that the reference atlas data is installed before the test driver is built, by adding a dependency on the InstallReferenceAtlas target.

```cmake
if(TARGET InstallReferenceAtlas)
  add_dependencies(BRAINSPosteriorToContinuousClassTestDriver InstallReferenceAtlas) ## Needed to ensure data is installed
endif()
```

--------------------------------

### Build Configuration (Old Method)

Source: https://github.com/brainsia/brainstools/blob/main/AutoWorkup/README.md

Use this INI configuration if NAMICExternal was built without an Anaconda environment.

```INI
############## A -- if you built NAMICExternal without anaconda env (old) ###########
_BRAINSTOOLS_BIN_DIR=%(_BUILD_DIR)s/bin
_SIMPLEITK_PYTHON_LIB=%(_BUILD_DIR)s/lib
_SIMPLEITK_PACKAGE_DIR=%(_BUILD_DIR)s/SimpleITK-build/Wrapping
_NIPYPE_PACKAGE_DIR=%(_BUILD_DIR)s/NIPYPE
############## -- You should not need to modify below here. ###########
APPEND_PYTHONPATH=%(_NIPYPE_PACKAGE_DIR)s:%(_SIMPLEITK_PYTHON_LIB)s:%(_SIMPLEITK_PACKAGE_DIR)s
APPEND_PATH=%(_BRAINSTOOLS_BIN_DIR)s:%(_SIMPLEITK_PYTHON_LIB)s:%(_GRAPHVIZ_BIN)s
############## end of OSX specification ##############
```

--------------------------------

### Install BRAINS Test Data

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSCommonLib/CMakeLists.txt

Recursively finds SHA512 checksum files in the TestData directory, configures them, and installs them. This is used to ensure test data integrity.

```cmake
file(GLOB_RECURSE BRAINSTEST_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}/TestData" "*.sha512")
set(TESTFILES_TO_INSTALL "")
foreach(TESTFILE ${BRAINSTEST_FILES})
  #message(STATUS "### ${TESTFILE} ${CMAKE_CURRENT_BINARY_DIR}/TestData/${TESTFILE}")
  configure_file("TestData/${TESTFILE}" ${CMAKE_CURRENT_BINARY_DIR}/TestData/${TESTFILE} @ONLY IMMEDIATE)
  list(APPEND TESTFILES_TO_INSTALL "TestData/${TESTFILE}")
endforeach()
install(FILES ${TESTFILES_TO_INSTALL}
  DESTINATION ${BRAINSTools_CLI_INSTALL_ARCHIVE_DESTINATION}/TestData COMPONENT Development)
```

--------------------------------

### Build Simple CLP Programs

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/landmarkStatistics/CMakeLists.txt

Sets up simple CLP programs using the StandardBRAINSBuildMacro, specifying target libraries for common functionality.

```cmake
set(PROGS_LIST_2
  GenerateAverageLmkFile
  )

foreach(prog ${PROGS_LIST_2})
    StandardBRAINSBuildMacro(NAME ${prog}
     TARGET_LIBRARIES landmarksConstellationCOMMONLIB BRAINSCommonLib)
endforeach()
```

--------------------------------

### singleSession.py Options

Source: https://github.com/brainsia/brainstools/blob/main/AutoWorkup/README.md

Detailed explanation of the available command-line options for the `singleSession.py` script.

```sh
 Options:
  -h, --help            Show this help and exit
  -v, --version         Print the version and exit
  --rewrite-datasinks   Turn on the Nipype option to overwrite all files in the 'results' directory
  --use-sentinal        Use the t1_average file as a marker to determine if session needs to be run
  --dry-run             Do not submit jobs, but print diagnostics about which jobs would be run
  --pe ENV              The processing environment to use from configuration file
  --wfrun PLUGIN        The name of the workflow plugin option (default: 'local', 'SGE','SGEGraph', 'local4')
  --workphase WORKPHASE The type of processing to be done [atlas-based-reference|subject-based-reference]
  --ExperimentConfig FILE   The configuration file
```

--------------------------------

### Build Configuration (Newer Method)

Source: https://github.com/brainsia/brainstools/blob/main/AutoWorkup/README.md

Use this INI configuration if NAMICExternal was built with an Anaconda environment.

```INI
############## -- -- if you built NAMICExternal with anaconda env (newer)  ###########
_BRAINSTOOLS_BIN_DIR=%(_BUILD_DIR)s/bin
############## -- You should not need to modify below here. ###########
APPEND_PYTHONPATH=
APPEND_PATH=%(_BRAINSTOOLS_BIN_DIR)s:%(_GRAPHVIZ_BIN)s
############## end of OSX specification ##############
```

--------------------------------

### BRAINSConstellationDetector Test Driver Command

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/TestSuite/CMakeLists.txt

Example of invoking the BRAINSConstellationDetectorTestDriver executable with various input parameters for testing purposes.

```cmake
BRAINSConstellationDetectorTest
    --inputVolume DATA{${TestData_DIR}/T1.nii.gz}
    --outputVolume ${CMAKE_CURRENT_BINARY_DIR}/${BCDTestName}_aligned.nrrd
    --inputTemplateModel DATA{${TestData_DIR}/T1_50Lmks.mdl}
    --LLSModel DATA{${TestData_DIR}/Transforms_h5/LLSModel_50Lmks.${XFRM_EXT}})
```

--------------------------------

### Migrate from DWIConvert to dcm2niix

Source: https://github.com/brainsia/brainstools/blob/main/DWIConvert/README.md

Replace DWIConvert command-line invocations with the equivalent dcm2niix command. Install dcm2niix from its GitHub repository.

```bash
# Before (DWIConvert)
DWIConvert --inputDicomDirectory /path/to/dicoms --outputVolume out.nii.gz

# After (dcm2niix)
dcm2niix -o /path/to/output /path/to/dicoms
```

--------------------------------

### Create Input List from Denoised Images

Source: https://github.com/brainsia/brainstools/wiki/BCD-Manual-Corrections

Generates a text file containing paths to denoised NIfTI images, used as input for BCD processing.

```bash
find /Shared/johnsonhj/HDNI/Neuromorphometrics/2012Subscription/Data -name "*_UNM_denoised.nii.gz" >> inputFiles.txt
```

--------------------------------

### Clone and Build BRAINSTools

Source: https://context7.com/brainsia/brainstools/llms.txt

Steps to clone the BRAINSTools repository, set up development environment, and configure/build the project using CMake. Includes instructions for both initial build and iterating on source code.

```bash
# Clone repository
git clone https://github.com/BRAINSia/BRAINSTools.git
cd BRAINSTools

# Install git hooks (required once per clone)
./Utilities/SetupForDevelopment.sh

# Configure and build (out-of-source, Release recommended)
mkdir ../BRAINSTools-build && cd ../BRAINSTools-build
cmake ../BRAINSTools \
  -DCMAKE_BUILD_TYPE=Release \
  -DBRAINSTools_SUPERBUILD=ON

# Build — Phase I fetches deps, Phase II compiles all tools
make -j$(nproc)

# Install layout after build:
# BRAINSTools-build/BRAINSTools-Release-5.8.0/bin/   ← executables
# BRAINSTools-build/BRAINSTools-Release-5.8.0/lib/   ← shared libraries
# BRAINSTools-build/BRAINSTools-Release-5.8.0/include/

# Iterate on BRAINSTools source without rebuilding deps (Phase II only)
cd BRAINSTools-build/BRAINSTools-Release-EPRelease-build
make -j$(nproc)
```

--------------------------------

### Program List and Build Macro

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSLabelStats/CMakeLists.txt

Sets the list of programs to build and applies standard build macros for each.

```cmake
set(ALL_PROGS_LIST
  BRAINSLabelStats
  )

foreach(prog ${ALL_PROGS_LIST})
  StandardBRAINSBuildMacro(NAME ${prog} TARGET_LIBRARIES BRAINSCommonLib ${BRAINSLabelStats_ITK_LIBRARIES})
endforeach()
```

--------------------------------

### Update Local Master Branch

Source: https://github.com/brainsia/brainstools/blob/main/github/CONTRIBUTING.md

Ensure your local master branch is up-to-date with the remote repository before starting new work.

```sh
   $ git checkout master
   $ git pullall
```

--------------------------------

### Project and Include Directories

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSDeface/CMakeLists.txt

Defines the project name and sets the binary directory for include files.

```cmake
project(BRAINSDeface)

#include_directories(${CMAKE_CURRENT_BINARY_DIR})
```

--------------------------------

### Checkout BRAINSConstellationDetector Source Code

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/README.md

Use SVN to download the source files from the NITRC repository. Ensure you have an SVN client installed.

```bash
svn checkout https://www.nitrc.org/svn/brainscdetector/branches/wei-lu/MedicalSliceViewer
```

--------------------------------

### Build Test Executable for landmarksConstellationTrainingDefinitionIO

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/TestSuite/CMakeLists.txt

Defines a test executable for landmarksConstellationTrainingDefinitionIO and links it with required libraries.

```cmake
add_executable(TestlandmarksConstellationTrainingDefinitionIO TestlandmarksConstellationTrainingDefinitionIO.cxx)
target_link_libraries(TestlandmarksConstellationTrainingDefinitionIO PRIVATE BRAINSCommonLib ${BRAINSConstellationDetector_ITK_LIBRARIES}
  ${VTK_LIBRARIES})
set_target_properties(TestlandmarksConstellationTrainingDefinitionIO PROPERTIES FOLDER ${MODULE_FOLDER})
```

--------------------------------

### Build All Programs

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/src/CMakeLists.txt

Defines a list of programs to be built and then iterates through this list, using a macro to build each program. This macro likely handles common build steps for executables.

```cmake
set(ALL_PROGS_LIST
  BRAINSConstellationModeler
  BRAINSLinearModelerEPCA
  BRAINSConstellationDetector
  BRAINSAlignMSP
  BRAINSClipInferior
  BRAINSTrimForegroundInDirection
  BRAINSLmkTransform
  BRAINSTransformFromFiducials
  BRAINSEyeDetector
  insertMidACPCpoint
  fcsv_to_hdf5
  landmarksConstellationAligner
  landmarksConstellationWeights
  BinaryMaskEditorBasedOnLandmarks
  BRAINSConstellationLandmarksTransform
  )
foreach(prog ${ALL_PROGS_LIST})
  StandardBRAINSBuildMacro(NAME ${prog} TARGET_LIBRARIES landmarksConstellationCOMMONLIB ${VTK_LIBRARIES})
endforeach()
```

--------------------------------

### BRAINSFit Test with Initial Transform

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSFit/TestSuite/CMakeLists.txt

Configures a BRAINSFit test case using an initial transform, suitable for scenarios where a starting point is known.

```cmake
set(BRAINSFitTestName BRAINSFitTest_ScaleSkewVersorScaleNoMasks)
ExternalData_add_test( ${BRAINSTools_ExternalData_DATA_MANAGEMENT_TARGET} NAME ${BRAINSFitTestName}
  COMMAND ${LAUNCH_EXE} $<TARGET_FILE:BRAINSFitTestDriver>
  --compare DATA{${TestData_DIR}/${BRAINSFitTestName}.result.nii.gz}
            ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.test.nii.gz
  --compareIntensityTolerance 9
  --compareRadiusTolerance 0
  --compareNumberOfPixelsTolerance 1000
  BRAINSFitTest
  --costMetric MMI
  --failureExitCode -1 --writeTransformOnFailure
  --numberOfIterations 2500
  --numberOfHistogramBins 200
  --samplingPercentage 0.3
  --translationScale 250
  --minimumStepLength 0.001
  --outputVolumePixelType uchar
  --transformType ScaleSkewVersor3D
  --initialTransform DATA{${TestData_DIR}/Transforms_h5/Initializer_0.05_${BRAINSFitTestName}.${XFRM_EXT}}
  --fixedVolume DATA{${TestData_DIR}/test.nii.gz}
  --movingVolume DATA{${TestData_DIR}/scale.test.nii.gz}
  --outputVolume ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.test.nii.gz
  --outputTransform ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.${XFRM_EXT}
)
```

--------------------------------

### ITK Object Creation and Pipeline

Source: https://github.com/brainsia/brainstools/blob/main/Documentation/AI/conventions.md

Use the factory method `New()` for object creation and `SmartPointer` for managing object lifetimes. `Update()` triggers execution, and parameters changed after `Update()` require another call to `Update()`.

```cpp
// Factory method returns SmartPointer — never use new/delete
auto filter = FilterType::New();
filter->SetInput(image);
filter->Update();   // Lazy: nothing runs until here
auto output = filter->GetOutput();

// Parameters changed after Update() require another Update()
filter->SetRadius(3);
filter->Update();
```

--------------------------------

### Configure GTRACTCommon Include Directories

Source: https://github.com/brainsia/brainstools/blob/main/GTRACT/Common/CMakeLists.txt

Sets public include directories for the GTRACTCommon library, including the binary directory and the current source directory.

```cmake
target_include_directories(GTRACTCommon PUBLIC
  ${GTRACT_BINARY_DIR}
  ${CMAKE_CURRENT_SOURCE_DIR}
)
```

--------------------------------

### Import necessary libraries for DWI processing

Source: https://github.com/brainsia/brainstools/blob/main/DWIConvert/TestSuite/DWI_ProcessingTest.ipynb

Imports essential libraries for handling neuroimaging data, DTI models, and plotting. Ensure these are installed before running.

```python
from dipy.data import get_data
import nibabel as nib
from dipy.io import read_bvals_bvecs
from dipy.core.gradients import gradient_table
from dipy.reconst.dti import TensorModel
from dipy.reconst.dti import fractional_anisotropy
from dipy.reconst.dti import color_fa

%matplotlib inline
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import numpy as np
```

--------------------------------

### Slicer Execution Model (SEM) CLI Pattern

Source: https://github.com/brainsia/brainstools/blob/main/Documentation/AI/conventions.md

Tools often expose a Command Line Interface (CLI) through an XML descriptor. The `main()` function is typically minimal, using the `PARSE_ARGS` macro to handle argument parsing based on the SEM XML specification.

```cpp
// ToolName.cxx
#include "ToolNameCLP.h"   // generated by SEM from ToolName.xml
int main(int argc, char * argv[]) {
  PARSE_ARGS;              // SEM macro: parses argc/argv using the XML spec
  // ... call into BRAINSToolNameHelper or itk filters
  return EXIT_SUCCESS;
}
```

--------------------------------

### Test Case: Output Resampled Volume

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/TestSuite/CMakeLists.txt

Initiates a test case for BRAINSConstellationDetector focusing on the output of the resampled volume. This setup is part of a larger test configuration.

```cmake
set(BCDTestName BCDTest_T1_outputResampledVolume)
ExternalData_add_test( ${BRAINSTools_ExternalData_DATA_MANAGEMENT_TARGET} NAME ${BCDTestName}
  COMMAND ${LAUNCH_EXE} $<TARGET_FILE:BRAINSConstellationDetectorTestDriver>

```

--------------------------------

### Define Project and Build Targets

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSMultiModeSegment/CMakeLists.txt

This section defines the main project and iterates through a list of programs to build, applying a standard build macro. It also includes conditional logic for testing.

```cmake
set(ALL_PROGS_LIST
  BRAINSMultiModeSegment
  )
foreach(prog ${ALL_PROGS_LIST})
  StandardBRAINSBuildMacro(NAME ${prog} TARGET_LIBRARIES BRAINSCommonLib )
endforeach()

if(BUILD_TESTING AND NOT BRAINSTools_DISABLE_TESTING)
  #  add_subdirectory(TestSuite)
endif()
```

--------------------------------

### Conditional Test Execution in CMakeLists.txt

Source: https://github.com/brainsia/brainstools/blob/main/docs/index.md

Conditionally add tests based on the BRAINSTools_MAX_TEST_LEVEL variable. This example shows how to add a specific test if the level is greater than 8.

```cmake
if(${BRAINSTools_MAX_TEST_LEVEL} GREATER 8)
  ExternalData_add_test(BRAINSToolsFetchData
    NAME itkResampleInPlaceImageFilterTest
    COMMAND $<TARGET_FILE:itkResampleInPlaceImageFilterTest>
      itkResampleInPlaceImageFilterTest input1 transform1 checkresult
  )
endif()
```

--------------------------------

### Registering Tests in CMakeLists.txt

Source: https://github.com/brainsia/brainstools/blob/main/Documentation/AI/testing.md

Tests are registered within the `TestSuite/CMakeLists.txt` file using CMake commands. This example shows the basic structure for adding a test executable.

```cmake
add_executable(ToolNameTest ToolNameTest.cxx)

target_link_libraries(ToolNameTest PRIVATE
  ITKCommon
  BRAINSCommon
  BRAINSCommon-test
  )

add_test(NAME ToolNameTest
  COMMAND ToolNameTest
  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
  )

# For GoogleTest, use gtest_discover_tests() instead of add_test()
# gtest_discover_tests(ToolNameGTest)

```

--------------------------------

### Build GUI Programs

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/gui/CMakeLists.txt

Iterates through a list of programs to build, using the StandardBRAINSBuildMacro to configure each program with the BRAINSConstellationDetectorGUICOMMONLIB.

```cmake
set(ALL_PROGS_LIST
  BRAINSConstellationDetectorGUI
  )
foreach(prog ${ALL_PROGS_LIST})
  StandardBRAINSBuildMacro(NAME ${prog} TARGET_LIBRARIES BRAINSConstellationDetectorGUICOMMONLIB )
endforeach()
```

--------------------------------

### Portable Shell Scripting: Readlink

Source: https://github.com/brainsia/brainstools/blob/main/Documentation/AI/style.md

Avoid GNU's 'readlink -f'. Use Python for a portable way to resolve symbolic links and get the real path.

```python
import os,sys; print(os.path.realpath(sys.argv[1]))
```

--------------------------------

### Create SR_support Library

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSSuperResolution/EdgeBasedWeightedTV/CMakeLists.txt

Creates a static library named 'SR_support' from specified C++ source files. This library likely contains core functionalities for super-resolution support.

```cmake
add_library(SR_support FFTWUpsample.cpp OpWeightedL2.cpp)
```

--------------------------------

### Add 2D Images and Get Statistics

Source: https://github.com/brainsia/brainstools/blob/main/ImageCalculator/doc/Examples.txt

Adds two 2D images and outputs the result along with various statistics. Ensure input images are compatible with UCHAR type.

```bash
<path to ImageCalculator.exe> -in 2 UpperHalfHundreds.png LowerHalfHundreds.png  -intype UCHAR -outtype UCHAR -add -out AllHundreds.png -Dimensions 2 -statNPX -statMIN -statAVG -statMAX -statVAR -statSUM
```

--------------------------------

### Define Project Programs and Build Macros

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSInitializedControlPoints/CMakeLists.txt

Defines the list of programs to be built for the project and applies a standard build macro for each program. Links against BRAINSCommonLib.

```cmake
set(ALL_PROGS_LIST
  BRAINSInitializedControlPoints
  )
foreach(prog ${ALL_PROGS_LIST})
  StandardBRAINSBuildMacro(NAME ${prog} TARGET_LIBRARIES BRAINSCommonLib )
endforeach()
```

--------------------------------

### BRAINSFit Test: MSEScaleSkewVersorRotationMasks

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSFit/TestSuite/CMakeLists.txt

Configures a BRAINSFit test using the MSE cost metric with a ScaleSkewVersor3D transform and masked volumes. This setup is appropriate for testing registration accuracy with scaling, skewing, and rotation.

```cmake
set(BRAINSFitTestName BRAINSFitTest_MSEScaleSkewVersorRotationMasks)
ExternalData_add_test( ${BRAINSTools_ExternalData_DATA_MANAGEMENT_TARGET} NAME ${BRAINSFitTestName}
  COMMAND ${LAUNCH_EXE} $<TARGET_FILE:BRAINSFitTestDriver>
  --compare DATA{${TestData_DIR}/${BRAINSFitTestName}.result.nii.gz}
            ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.test.nii.gz
  --compareIntensityTolerance 11
  --compareRadiusTolerance 0
  --compareNumberOfPixelsTolerance 1000
  BRAINSFitTest
  --costMetric MSE
  --failureExitCode -1 --writeTransformOnFailure
  --numberOfIterations 2500
  --numberOfHistogramBins 200
  --samplingPercentage 0.5
  --translationScale 250
  --minimumStepLength 0.001
  --outputVolumePixelType uchar
  --transformType ScaleSkewVersor3D
  --initialTransform DATA{${TestData_DIR}/Transforms_h5/BRAINSFitTest_Initializer_RigidRotationNoMasks.${XFRM_EXT}}
)
```

--------------------------------

### Configure Project and Common Library

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSSuperResolution/GenerateEdgeMap/CMakeLists.txt

Configures the project and copies a header file template to the build directory. This is a standard CMake practice for generating configuration headers.

```cmake
project(BRAINSSuperResolution)

#-----------------------------------------------------------------------------
# Dependencies.
#
#-----------------------------------------------------------------------------
# Output directories.
#

configure_file(
  ${CMAKE_CURRENT_SOURCE_DIR}/BRAINSSuperResolutionCommonLib.h.in
  ${CMAKE_CURRENT_BINARY_DIR}/BRAINSSuperResolutionCommonLib.h
  )
```

--------------------------------

### BRAINSFit: Deformable BSpline Registration

Source: https://context7.com/brainsia/brainstools/llms.txt

Example of using BRAINSFit for deformable BSpline registration for fine alignment. Specifies BSpline grid size, maximum displacement, sampling percentage, and cost metric.

```bash
# Deformable BSpline registration (for final fine alignment)
BRAINSFit \
  --fixedVolume  atlas_t1.nii.gz \
  --movingVolume subject_t1_registered.nii.gz \
  --useBSpline \
  --splineGridSize 14,10,12 \
  --maxBSplineDisplacement 0.0 \
  --samplingPercentage 0.1 \
  --costMetric MMI \
  --bsplineTransform bspline_output.h5 \
  --outputVolumePixelType float
```

--------------------------------

### Build GUI Version using CMake (Linux 64-bit)

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/README.md

Build the Qt-based GUI version of the BRAINSConstellationDetector on Linux 64-bit using CMake. Requires Qt libraries version 4.6.2 or higher and CMake version 2.8 or higher.

```bash
mkdir brainscdetector-build
cd brainscdetector-build
cmake –DBUILD_MEDICAL_SLICEVIEWER_GUI=ON –C ../MedicalSliceViewer/InitialCache-Linux64.cmake ../MedicalSliceViewer
```

--------------------------------

### Create FFTWUpsampleTest Executable

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSSuperResolution/EdgeBasedWeightedTV/CMakeLists.txt

Creates an executable named 'FFTWUpsampleTest' from 'FFTWUpsampleTest.cpp'. This executable is likely for testing the FFTW upsampling functionality.

```cmake
add_executable(FFTWUpsampleTest FFTWUpsampleTest.cpp)
```

--------------------------------

### BRAINSFit: Rigid Registration

Source: https://context7.com/brainsia/brainstools/llms.txt

Example of using BRAINSFit for rigid registration (6 DOF) to align a subject's T1-weighted MRI to an atlas T1. Uses center-of-head alignment and specifies sampling percentage.

```bash
# Rigid registration (6 DOF): align subject T1 to atlas T1
BRAINSFit \
  --fixedVolume  atlas_t1.nii.gz \
  --movingVolume subject_t1.nii.gz \
  --useRigid \
  --initializeTransformMode useCenterOfHeadAlign \
  --samplingPercentage 0.05 \
  --linearTransform rigid_output.h5 \
  --outputVolume   subject_t1_registered.nii.gz
```

--------------------------------

### Define Test Driver and Include Directories

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSPosteriorToContinuousClass/TestSuite/CMakeLists.txt

Sets up the test driver executable and specifies the necessary include directories for the BRAINSPosteriorToContinuousClass tests.

```cmake
MakeTestDriverFromSEMTool(BRAINSPosteriorToContinuousClass BRAINSPosteriorToContinuousClassTest.cxx)
target_include_directories(BRAINSPosteriorToContinuousClassTestDriver PRIVATE
  ${BRAINSPosteriorToContinuousClass_SOURCE_DIR}/BRAINSPosteriorToContinuousClass
)
```

--------------------------------

### BRAINSFit Test with Initial Transform and Auto Masking

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSFit/TestSuite/CMakeLists.txt

Configures a BRAINSFit test case with an initial transform and automatic mask processing, suitable for scenarios requiring a specific starting transform and automated mask handling.

```cmake
set(BRAINSFitTestName BRAINSFitTest_ScaleTranslationRescaleHeadMasksInit)
ExternalData_add_test( ${BRAINSTools_ExternalData_DATA_MANAGEMENT_TARGET} NAME ${BRAINSFitTestName}
  COMMAND ${LAUNCH_EXE} $<TARGET_FILE:BRAINSFitTestDriver>
  --compare DATA{${TestData_DIR}/${BRAINSFitTestName}.result.nii.gz}
            ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.test.nii.gz
  --compareIntensityTolerance 7
  --compareRadiusTolerance 0
  --compareNumberOfPixelsTolerance 777
  BRAINSFitTest
  --costMetric MMI
  --failureExitCode -1 --writeTransformOnFailure
  --numberOfIterations 2500
  --numberOfHistogramBins 200
  --samplingPercentage 0.3
  --translationScale 250
  --minimumStepLength 0.001
  --outputVolumePixelType uchar
  --maskProcessingMode ROIAUTO
  --initialTransform DATA{${TestData_DIR}/Transforms_h5/Initializer_BRAINSFitTest_TranslationRescaleHeadMasks.${XFRM_EXT}}
  --transformType ScaleVersor3D
  --fixedVolume DATA{${TestData_DIR}/test.nii.gz}
  --movingVolume DATA{${TestData_DIR}/translation.rescale.test.nii.gz}
  --outputVolume ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.test.nii.gz
  --outputTransform ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.${XFRM_EXT}
)
```

--------------------------------

### INI Configuration File: DEFAULT Section

Source: https://github.com/brainsia/brainstools/blob/main/AutoWorkup/README.md

Sets default parameters for the pipeline, such as mount prefixes and modules.

```ini
[DEFAULT]
MOUNT_PREFIX=
MODULES=
```

--------------------------------

### Configure landmarksConstellationAligner Test

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSConstellationDetector/TestSuite/CMakeLists.txt

Sets up a test for the landmarksConstellationAligner program, defining input and output landmark files for comparison.

```cmake
set(BCDTestName landmarksConstellationAlignerTest) #This test aims to generate the output of the landmarksConstellationAligner to be compared with the baseline file
ExternalData_add_test( ${BRAINSTools_ExternalData_DATA_MANAGEMENT_TARGET} NAME ${BCDTestName}
  COMMAND ${LAUNCH_EXE} $<TARGET_FILE:landmarksConstellationAlignerTestDriver>
  ${BCDTestName}
  --inputLandmarksPaired DATA{${TestData_DIR}/${BCDTestName}_input.fcsv}
  --outputLandmarksPaired ${CMAKE_CURRENT_BINARY_DIR}/${BCDTestName}.fcsv #output of the program
  )
```

--------------------------------

### BRAINSFit Test Driver with GD Cost Metric

Source: https://github.com/brainsia/brainstools/blob/main/BRAINSFit/TestSuite/CMakeLists.txt

Configures and runs the BRAINSFit test driver using the Gradient Difference (GD) cost metric. This setup includes parameters for comparison, iteration, sampling, and transform type.

```cmake
COMMAND ${LAUNCH_EXE} $<TARGET_FILE:BRAINSFitTestDriver> \
    --compare DATA{${TestData_DIR}/test.nii.gz} \
              ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.test.nii.gz \
    --compareIntensityTolerance 9 \
    --compareRadiusTolerance 0 \
    --compareNumberOfPixelsTolerance 1000 \
    BRAINSFitTest \
    --costMetric GD \
    --failureExitCode -1 --writeTransformOnFailure \
    --numberOfIterations 25 \
    --numberOfHistogramBins 200 \
    --samplingPercentage 0.3 \
    --translationScale 250 \
    --minimumStepLength 0.001 \
    --outputVolumePixelType uchar \
    --transformType Rigid --initializeTransformMode useMomentsAlign \
    --fixedVolume DATA{${TestData_DIR}/test.nii.gz} \
    --movingVolume DATA{${TestData_DIR}/test.nii.gz} \
    --outputVolume ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.test.nii.gz \
    --outputTransform ${CMAKE_CURRENT_BINARY_DIR}/${BRAINSFitTestName}.${XFRM_EXT}
```

--------------------------------

### BRAINSTools Commit Message Format

Source: https://context7.com/brainsia/brainstools/llms.txt

Enforces a specific commit message format using a git hook. Subject lines must be ≤78 characters with a mandatory prefix. Includes examples of valid single-line and multi-line commit messages.

```bash
# Valid commit message examples (pass the hook)
git commit -m "ENH: Add robust min/max computation to BRAINSCommonLib"
git commit -m "BUG: Fix segfault in NrrdToFSL when input has zero components"
git commit -m "COMP: Fix unused variable warning in BRAINSFit optimizer path"
git commit -m "DOC: Update building.md with Phase II iteration instructions"
git commit -m "STYLE: Apply clang-format to BRAINSConstellationDetector sources"
git commit -m "PERF: Replace linear scan with binary search in landmark lookup"
```

```bash
# Multi-line with body
git commit -m "$(cat <<'EOF'
BUG: Correct gradient direction sign for coronal DICOM acquisitions

SetDirectionsFromSliceOrder assumed axial acquisition geometry; for
coronal scans the AP cosine is in a different matrix column. This fix
reads the ImageOrientationPatient tag to detect acquisition plane before
assigning axis signs.
EOF
)"
```

```bash
# Prefix reference
# ENH:   New feature or enhancement
# BUG:   Runtime crash or incorrect result
# COMP:  Compiler error or warning fix
# DOC:   Documentation only
# STYLE: Formatting/naming, no logic change
# PERF:  Performance improvement
```

--------------------------------

### Create Build Directory

Source: https://github.com/brainsia/brainstools/blob/main/docs/BRAINSToolsInClion.md

Create a separate build directory outside the source tree to manage build artifacts and SuperBuild files.

```bash
mkdir BRAINSTools-build
cd BRAINSTools-build
```

--------------------------------

### Example Failure Log in BCD

Source: https://github.com/brainsia/brainstools/wiki/Oz-T1-only-sample-failures

This log indicates a failure in the BRAINSConstellationDetector (BCD) during landmark initialization. The error occurs when saving aligned image and zero eye centers landmarks, suggesting an issue with the EMSP.fcsv file format or content.

```text
itk::ExceptionObject (0x7b07b00)
Location: "unknown" 
File: /Shared/pinc/sharedopt/20170302/RHEL7/NEP-intel/BRAINSTools/BRAINSConstellationDetector/src/landmarksConstellationDetector.cxx
Line: 1475
Description: itk::ERROR: EMSP aligned image and zero eye centers landmarks are written to 
./. Use GUI corrector to correct the landmarks in.EMSP.fcsvINITIAL LMKS: EMSP.fcsvFOR IMAGE: Image (0x7b08790)
  RTTI typeinfo:   itk::Image<short, 3u>
  Reference Count: 2
  Modified Time: 12892440
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 12892430
  UpdateMTime: 12892439
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 256, 256]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 256, 256]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 256, 256]
  Spacing: [1, 1, 1]
  Origin: [-127.5, -127.5, -127.5]
  Direction: 
1 0 0
0 1 0
0 0 1

  IndexToPointMatrix: 
1 0 0
0 1 0
0 0 1

  PointToIndexMatrix: 
1 0 0
0 1 0
0 0 1

  Inverse Direction: 
1 0 0
0 1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x7b07b90)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, short>
      Reference Count: 1
      Modified Time: 12892437
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7b110d0
      Container manages memory: true
      Size: 16777216
      Capacity: 16777216
IN DIR: ./
```