Those who are involved in neuroimaging analysis have surely experienced spending an inordinate amount of time setting up a system environment before analyzing data. Still, they are lucky in the sense that they have managed to set it up: how many researchers struggle in vain, giving up before they are able to analyze their data? Setting up a system environment should not be a rite of passage into "neuroimaginghood." With Lin4Neuro in one's hand, one can access neuroimaging software packages easily and immediately focus on analyzing data. This approach will also benefit developers of software packages since the pre-installation of software will give many potential users opportunities to try them.
As an application of Lin4Neuro, we compared the processing time of intensity inhomogeneity correction under different system conditions. Surprisingly, the results showed that the USB-boot live Linux system is as capable as the hard-disk-installed Linux system. This means that one is able to achieve a versatile Linux environment for neuroimaging analyses by simply booting Lin4Neuro from a USB flash drive, omitting complicated procedures for installing and configuring Linux and Linux-based neuroimaging software packages. In addition, the current study also demonstrated the possibility of utilizing virtualization. Although full use of hardware power cannot be achieved, virtualization may provide a practical solution for realizing a neuroimaging Linux environment on a Windows PC. Thus, using live Linux or virtualization software, one does not have to prepare new hardware but can make the best use of one's current hardware.
It is noteworthy that many neuroimaging software packages have command-line utilities. This makes the combining of functions of different software packages easy, and the processing of images automatic. Providing a common analytical platform with Lin4Neuro facilitates such integrative protocols across packages. In the future, we plan to incorporate Nipype into this system, which will provide an environment that encourages interactive exploration of algorithms from different packages, eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages.
Recently, multi-center studies have become increasing common. Accordingly, quality control of imaging data is gaining much more importance. For example, Alzheimer's disease Neuroimaging Initiative (ADNI) standardized the MRI protocol, post-acquisition corrections, and phantom-based monitoring of all scanners across sites and platforms [35
]. Lin4Neuro provides a practical means of sharing the analysis environment across sites. Once this system is installed on a hard disk, one can customize the environment and re-create distributable copies. By doing so, each center can share a neuroimaging analysis environment for specific research. Moreover, one can replicate the image processing protocols easily by sharing the scripts which describe how images are processed. From a different perspective, it should also be noted that Lin4Neuro on a USB flash drive can serve as an installer for a Linux operating system and Linux-based neuroimaging software packages. With a slight modification of the BIOS (Basic Input/Output System) settings to enable booting from the USB flash disk, one can easily realize an optimized Linux environment for neuroimaging analyses on a new personal computer.
With the interdisciplinary development of neuroimaging research, not only neuroscientists but also many researchers from different fields are participating in neuroimaging research. Thus, it is becoming more important to establish a platform in which one can easily access various neuroimaging analysis software packages. Lin4Neuro could be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis.
In the current release, we limited the software packages incorporated into the system to only those that are frequently used. However, there are many software packages which are redistributable on the internet. Recently, a website named NITRC (The Neuroimaging Informatics Tools and Resources Clearinghouse) has been established and is open to public, enabling us to find many useful neuroimaging software packages [36
]. In the future, it might be possible to include a wide variety of redistributable software packages based on information from NTIRC. Though we cannot include commercial software packages or software packages that require license keys, installing Lin4Neuro on a hard disk will enable the user to install any Linux-based software packages. Specifically, SPM, one of the most influential neuroimaging software packages, which is a freeware package itself but dependent on Matlab, is currently excluded from Lin4Neuro. However, since a standalone SPM which does not a require MATLAB license is under development [38
], hopefully it may be included in Lin4Neuro in a future release.
As our system includes many well-known software packages, some may argue that the contributions of this study are not original. However, the genuine originality of our study lies in the creation of a unique and integrative neuroimaging environment. In this respect, Lin4Neuro plays a role as a portal for neuroimaging software packages and keeps researchers from getting lost in vast amounts of information. Lin4Neuro is available on the Internet [39
]. Since this system has an interactive nature, we hope that, through interaction among users, Lin4Neuro will become more sophisticated and easier to use, and consequently contribute to the further development of the neuroimaging field.