Segment MR brain images using the Segm program. The software provides advanced segmentation capabilities that enable accurate analysis of brain images.
Segm is a program designed to segment MR images of the brain, created by the Brain Behavior Laboratory at the University of Pennsylvania. Specifically, it includes BrainMask, Kmean_3Dseg, and AdpKmean_3Dseg_Ebeta, which were initially developed by Michelle Yan for use with specific MR imaging protocols from the lab. These tools are intended for quantitative analysis of MRI volume images to automatically segment tissue types in human brains.
While these programs have been effective for the imaging protocols they were designed for, they are not adaptable to other protocols. This means that they are not recommended for new image analysis applications. While there may be changes to fix bugs or support data interchange with newer programs, no major updates are expected. Instead, the Brain Behavior Laboratory recommends using their newer toolkit, BBLimage, for new applications.
A unique feature of Segm is that images files are read and written in big-endian order, regardless of the native architecture. This is because most image files at the lab have been generated and stored on the Sparc workstation. Thus, it was more straightforward to have programs on all other platforms read and write this format than to constantly convert data files.
Users interested in Segm should note that it has been compiled and tested successfully on Red Hat Linux 6.2 for Intel and Solaris 2.7 for Sparc. However, fixes for other machines and operating systems are welcome. The installation process for Segm is straightforward as well, involving unpacking the tar file, running configure, compiling with make, and installing with make install. As the shared library for Segm is installed in a specific directory, users may need to modify search paths to ensure it is found by other programs.
Overall, users interested in segmenting MR images of brains may find Segm a useful tool, but should keep in mind its limitations and the availability of other, newer options like BBLimage.
While these programs have been effective for the imaging protocols they were designed for, they are not adaptable to other protocols. This means that they are not recommended for new image analysis applications. While there may be changes to fix bugs or support data interchange with newer programs, no major updates are expected. Instead, the Brain Behavior Laboratory recommends using their newer toolkit, BBLimage, for new applications.
A unique feature of Segm is that images files are read and written in big-endian order, regardless of the native architecture. This is because most image files at the lab have been generated and stored on the Sparc workstation. Thus, it was more straightforward to have programs on all other platforms read and write this format than to constantly convert data files.
Users interested in Segm should note that it has been compiled and tested successfully on Red Hat Linux 6.2 for Intel and Solaris 2.7 for Sparc. However, fixes for other machines and operating systems are welcome. The installation process for Segm is straightforward as well, involving unpacking the tar file, running configure, compiling with make, and installing with make install. As the shared library for Segm is installed in a specific directory, users may need to modify search paths to ensure it is found by other programs.
Overall, users interested in segmenting MR images of brains may find Segm a useful tool, but should keep in mind its limitations and the availability of other, newer options like BBLimage.
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