Machine for fMRI video analysis

2023 January 2 TEGARA Co., Ltd. Research workstation, R & D PC configuration example (Tegsys)

A customer involved in research in the field of brain science asked us for a machine for analyzing videos acquired by functional magnetic resonance imaging (fMRI).
Your requirements are as follows.

・Image analysis using MATLAB, Python, Fiji, etc. is assumed.
・Since Parallel Computing is used in MATLAB, CPU performance is emphasized.
・Since the capacity of a single data is about 4 GB, memory capacity is also important.
・In addition, SPM and CONN are also used on a daily basis.
・Deep Learning is not assumed.
・The OS is Windows 10.
・The budget is about 200 million yen.

Based on the information you provided, we proposed the following configuration.

【Main Specifications】

CPU Xeon Gold 6326 (2.90GHz 16 cores) x2
memory 512GB REG ECC
Storage 1 1TB M.2 SSD
Storage 2 7.68TB SSD U.2
Video Nvidia T1000
network On Board (1000Base-T X2)
Housing + power supply Tower type housing + 850W
OS Microsoft Windows 10 Pro 64 bit

Considering CPU performance and memory capacity, it has a 3-CPU configuration with 2rd generation Xeon Scalable.

Considering the balance with the OS, we chose a CPU with 32 cores and 64 threads.
When Windows 10 recognizes more than 64 logical cores (threads), it creates a group of logical cores called a processor group.As a general rule, applications that are not explicitly designed to cross processor groups cannot parallelize across processor groups, and MATLAB is subject to this limitation.Therefore, even if more than 64 logical cores are installed, there will be situations where they cannot be fully utilized.

reference:maxNumCompThreads (MathWorks) *Jumps to an external site

As a countermeasure to this situation, there is a method of disabling Hyperthreading and using only physical cores, and a method of changing the OS to Windows 11.
In Windows 11, the mechanism of processor groups has changed, and applications can access all logical cores regardless of the number of logical cores installed.
If there is no problem in terms of operation method, etc., please consider it as an option.

reference:Processor Group (Microsoft) *Jumps to an external site

The configuration of this case study is based on the conditions given by the customer.
Please feel free to contact us even if you are considering different conditions from what is posted.

■FAQ

・What is MATLAB?
MATLAB is software for numerical analysis used in data analysis, algorithm development, and model creation in a wide range of fields such as engineering, science, and economics, and is also the name of the programming language used internally.

reference:MATLAB (MathWorks) *Jumps to an external site

・What is Python?
Python is an object-oriented programming language copyrighted by the Python Software Foundation (PSF).Its programming syntax is simple, so it is highly readable, and it also features a wide variety of components such as libraries and frameworks that are suitable for different purposes.A popular language for programming beginners to advanced users.

reference:Python *Jumps to an external site

TEGAKARI
2020.12.11
[Feature article] Why is the programming language Python so popular? - Python programming...
https://www.tegakari.net/2020/12/sp-python
 What makes Python popular? Python is an object-oriented programming language copyrighted by the Python Software Foundation (PSF). ...

・What is Fiji?
Fiji is open source image processing software.It comes bundled with a number of plugins suitable for scientific image analysis.

reference:Fiji *Jumps to an external site

・What is a processor group?
Restrictions for stable CPU operation.
A way to limit resources so that no one process uses all of the CPU.

 

・What is SPM?
SPM (Statistical parametric mapping) is software that supports the analysis of functional neuroimaging data. It is distributed as free software written in MATLAB.

reference:SPM (University College London) *Jumps to an external site

・What is CONN?
CONN is a MATLAB-based cross-platform imaging software for calculating, displaying, and analyzing functional connectivity in fMRI.

reference:CONN toolbox *Jumps to an external site

 

 

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Machine for fMRI video analysis

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