CASToR 2.0.1用户指南：PET图像重建软件

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CASToR（Customizable and Advanced Software for Tomographic Reconstruction）是一款专注于核医学成像，特别是基于正电子发射断层扫描（PET）图像重建的开源C++软件。此用户手册提供了CASToR的基本功能、架构、安装方法以及如何开始使用它的详细步骤。 CASToR的主要特点在于其高度可定制化和先进的算法支持。它涵盖了迭代优化算法和分析算法，同时也允许用户根据需求添加其他可能的重建算法类型。这使得CASToR在处理PET图像时具有灵活性和高效性，能够适应不同的研究和临床应用。 CASToR的架构分为几个关键部分，包括迭代优化算法，如代数重建技术（ART）或最大似然期望值最大化（MLEM），以及分析算法，如滤波反投影（FBP）。此外，还有其他可能的算法类型，可以根据研究需求进行选择或开发。软件的安装过程考虑到了不同操作系统的兼容性，包括32位和64位系统，以及对数据精度的调整。在Unix系统上，提供了使用Makefile和CMake两种编译方式。对于Windows系统，CASToR可以使用Visual Studio直接编译，或者使用MinGW进行跨平台编译。同时，也提供了静态二进制文件供用户直接使用。在开始使用CASToR时，用户需要了解其主要执行文件`castor-recon`，它可以用于执行重建任务。手册中还包含了基准测试的说明，以便用户评估CASToR的性能。为了使用自己的数据集，用户需要了解如何正确输入数据，并能读取CASToR重建后的图像。在与扫描仪系统的集成方面，CASToR特别支持PET系统的集成。它可以使用通用几何文件（.geom）或预计算的查找表文件（.lut）来适应特定的PET扫描仪。这样，CASToR就能够根据不同的硬件配置进行精确的图像重建。总而言之，CASToR作为一款强大的图像重建工具，为核医学成像提供了全面的解决方案。无论是研究者还是临床工作者，都可以通过这个开源平台实现定制化的图像处理，提升PET图像的质量和分析效率。通过深入理解这个用户手册，用户将能够有效地利用CASToR的功能，进行高质量的图像重建工作。

3 CASToR installation

CASToR source code is available on the CASToR website at castor-project.org, once you complete

the short registration form (castor-project.org/form/castor-registration-form). Do not hesitate to

subscribe to the mailing-list in order to receive information about new versions of the platform and

follow the CASToR community. In addition, if you are interested in contributing as a developer

in the CASToR platform, please ﬁll in the required ﬁelds in the subscription form. Once the

CASToR collaboration will be ready to open the project for external contributions, you will be

contacted with details on how to proceed. In the meantime, if you already developed something

that may be interesting for others, please let us know on the mailing list.

3.1 Operating systems: 32 bits VS 64 bits

If run on 64 bits systems, any dataﬁle can be read and used whatever its size, even if its size exceeds

the size of the memory, thanks to dataﬁle mapping. However, if run on 32 bits systems, it is not

possible to process dataﬁles bigger than 2 GB, whatever the size of the memory.

3.2 Computation and data precision

In CASToR, the precision of ﬂoating point numbers can be customized. This is implemented through

the use of macro deﬁnitions interpreted by the pre-processor of the compiler, deﬁning the type of

diﬀerent variables throughout the code, as follows:



FLTNB: General ﬂoating-point precision (input/intermediary/output image matrices and some

ﬂoating point operations).



HPFLTNB: Higher ﬂoating-point precision for sensitive computations that require at least

double precision (projector implementation, random number generators, etc).



FLTNBDATA: Precision of the ﬂoating point variables read or written into CASToR dataﬁles.



FLTNBLUT: Precision of the ﬂoating point variables read or written into CASToR scanner

LUT elements.

The types of these macros are deﬁned in the include/management/gVariables.hh and are all set

to ﬂoat simple precision by default expect for HPFLTNB which is set to double precision. They can

be changed to double or long double precision as desired, assuming that the operating system and

the compiler are both able to take these types into account (see https://en.wikipedia.org/wiki/

Long_double). When any of these deﬁnitions is changed, the code needs to be entirely recompiled.

Note also that the memory requirements of the CASToR program will double with the use of double

precision compared to ﬂoat precision.

3.3 CASToR conﬁguration folder

The CASToR programs may use a bunch of conﬁguration ﬁles, for scanners, default module’s con-

ﬁgurations, isotopes database, etc. In the CASToR source tree, there is a folder named conﬁg, which

contains all these conﬁguration ﬁles. For instance, a dataﬁle is linked to a scanner description; this

scanner description, either based on a geometrical ﬁle or a LUT ﬁle (see section 5), is located in

the conﬁg/scanner sub-folder. There is also one sub-folder per type of modules (e.g. projector,

convolver, etc). And ﬁnally, there is a conﬁg/misc folder containing miscellaneous conﬁguration

ﬁles, such as isotopes’ database with their associated half-life and branching ratio.

When running CASToR, the conﬁguration folder is localized by the CASTOR CONFIG envi-

ronment variable. If the code was compiled using the CMake tools (see sub-sections 3.4.2 and 3.5.1),

this variable has been hard-linked to the executable during the compilation. If the code was com-

piled using the provided Makeﬁle (see sub-section 3.4.1), this variable is read dynamically from the

CASTOR CONFIG environment variable; so this variable must exist during run-time and point to

the absolute path of the conﬁg directory. If the code is cross-compiled from a 64-bits Unix system

for Windows systems (see sub-section 3.5.2), then the environment variable is also hard-linked dur-

ing compilation. If the environment variable does not exist during the compilation, a compilation

error will occur on purpose, specifying that you must set it. Note that the value of this environ-

ment variable for cross-compilation should contain the path of the conﬁguration folder under the

Windows system that will be used for execution. This path can use ”/” instead of ”\” but must

not be provided within ”double quotes”. Finally, whatever the value of the CASTOR CONFIG

environment variable and whether it was hard-linked during the compilation or not, the path to the

conﬁguration folder can be overloaded by using the -conf command-line option.

3.4 Unix systems

There are two alternatives to compile the code: using the provided Makeﬁle or the CMake tools. If

you do not link CASToR to external libraries, we recommend using the standard Makeﬁle as it is

quite straightforward.

3.4.1 Compile CASToR on Unix systems using the provided Makeﬁle

1. Get the CASToR source code

2. Conﬁgure the compilation using the following environment variables considered during the

compilation (export CASTOR XXX = ):



CASTOR CONFIG: Set to the absolute path of the CASToR conﬁguration directory (i.e.

the conﬁg directory inside the source tree)



CASTOR MPI: Set to 1 to build CASToR with MPI (required for multiprocessing / par-

allel computing at the dataﬁle level)



CASTOR OMP: Set to 1 to build CASToR with OpenMP (required for multithreading /

parallel computing at the event level)



CASTOR ROOT: Set to 1 to build CASToR with ROOT library (for dataﬁle conversion

using root. In case of issues with compilation using ROOT, check the root-conﬁg -libs

and root-conﬁg -cﬂags variables are correctly initialized.)



CASTOR SIMD: Set to 1 to build CASToR with SIMD optimization options from the

compiler (CASToR does not include any speciﬁc vector programming)



CASTOR VERBOSE: Set to 1 to output maximum information during reconstruction,

mainly used for debugging



CASTOR DEBUG: Set to 1 to activate many additional checks inside primitive functions

of the code, mainly used for debugging as it can slow down the execution

3. Run make to compile the CASToR code (you can use the ’-j X’ option of Makeﬁle to use X

threads during the compilation). It will create binaries for the main reconstruction program

(castor-recon) and for each utility (section 8) into the bin directory.

4. (optional) Add CASToR to your environment using one of the following command lines:

- bash or zsh:

export PATH=$PATH:/path/to/CASToR/bin

- tcsh

setenv PATH ${PATH}:$/path/to/CASToR/bin

3.4.2 Compile CASToR on Unix systems using CMake

1. Install CMake: www.cmake.org

2. Get the CASToR source code

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