title: ÐÐµÐ¹ÑÐ¾ÑÐµÑÐµÐ²Ð°Ñ ÑÐµÐ³Ð¼ÐµÐ½ÑÐ°ÑÐ¸Ñ ÐÐ Ð¢-Ð¸Ð·Ð¾Ð±ÑÐ°Ð¶ÐµÐ½Ð¸Ð¹ Ð³Ð¾Ð»Ð¾Ð²Ð½Ð¾Ð³Ð¾ Ð¼Ð¾Ð·Ð³Ð° ÑÐµÐ»Ð¾Ð²ÐµÐºÐ°
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Neural network segmentation of MRI images of the human brain
Creators: name: ÐÑÐ¸Ð²Ð¾ÑÐµÐµÐ², ÐÑÑÑÐ¼
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2023
Subjects: ÐÐ Ð¢
ÐÐ Ð¢-Ð¸Ð·Ð¾Ð±ÑÐ°Ð¶ÐµÐ½Ð¸Ñ
Ð³Ð¾Ð»Ð¾Ð²Ð½Ð¾Ð¹ Ð¼Ð¾Ð·Ð³
ÑÐµÐ³Ð¼ÐµÐ½ÑÐ°ÑÐ¸Ñ
FreeSurfer
FastSurfer
FastSurferCNN
Ð½ÐµÐ¹ÑÐ¾Ð½Ð½ÑÐµ ÑÐµÑÐ¸
ÐºÐ¾ÑÑÑÐ¸ÑÐ¸ÐµÐ½Ñ Ð¿Ð¾Ð´Ð¾Ð±Ð¸Ñ ÐÐ°Ð¹ÑÐ°
MRI
MRI images
human brain
segmentation
neural networks
Dice similarity coefficient

description: ÐÐ°Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð¿Ð¾ÑÐ²ÑÑÐµÐ½Ð° Ð¸ÑÑÐ»ÐµÐ´Ð¾Ð²Ð°Ð½Ð¸Ñ ÑÐ¾ÑÐ½Ð¾ÑÑÐ¸ Ð½ÐµÐ¹ÑÐ¾ÑÐµÑÐµÐ²Ð¾Ð¹ ÑÐµÐ³Ð¼ÐµÐ½ÑÐ°ÑÐ¸Ð¸ ÐÐ Ð¢-Ð¸Ð·Ð¾Ð±ÑÐ°Ð¶ÐµÐ½Ð¸Ð¹ Ð³Ð¾Ð»Ð¾Ð²Ð½Ð¾Ð³Ð¾ Ð¼Ð¾Ð·Ð³Ð° ÑÐµÐ»Ð¾Ð²ÐµÐºÐ° Ñ Ð¿Ð¾Ð¼Ð¾ÑÑÑ FastSurfer. ÐÐ²ÑÐ¾Ð¼Ð°ÑÐ¸ÑÐµÑÐºÐ°Ñ ÑÐµÐ³Ð¼ÐµÐ½ÑÐ°ÑÐ¸Ñ â Ð»ÑÑÑÐ¸Ð¹ ÑÐ¿Ð¾ÑÐ¾Ð± Ð¾Ð±ÑÐ°Ð±Ð¾ÑÐºÐ¸ Ð¸Ð·Ð¾Ð±ÑÐ°Ð¶ÐµÐ½Ð¸Ð¹ Ð´Ð»Ñ Ð²ÑÐ´ÐµÐ»ÐµÐ½Ð¸Ñ Ð¸Ð½ÑÐµÑÐµÑÑÑÑÐ¸Ñ ÑÑÑÑÐºÑÑÑ, Ð½Ð¾ Ð¸Ð·-Ð·Ð° Ð½Ð°Ð»Ð¸ÑÐ¸Ñ Ð²ÑÑÐ¸ÑÐ»Ð¸ÑÐµÐ»ÑÐ½Ð¾ ÑÐ»Ð¾Ð¶Ð½ÑÑ ÑÐ°Ð³Ð¾Ð² Ð¿ÑÐ¾ÑÐµÑÑ Ð¼Ð¾Ð¶ÐµÑ Ð·Ð°Ð½Ð¸Ð¼Ð°ÑÑ Ð¿ÑÐ¾Ð´Ð¾Ð»Ð¶Ð¸ÑÐµÐ»ÑÐ½Ð¾Ðµ Ð²ÑÐµÐ¼Ñ, Ð½ÐµÐ´Ð¾Ð¿ÑÑÑÐ¸Ð¼Ð¾Ðµ Ð´Ð»Ñ Ð¼Ð°ÑÑÑÐ°Ð±Ð½ÑÑ Ð¸ÑÑÐ»ÐµÐ´Ð¾Ð²Ð°Ð½Ð¸Ð¹, Ð³ÐµÐ½ÐµÑÐ¸ÑÑÑÑÐ¸Ñ Ð±Ð¾Ð»ÑÑÐ¸Ðµ Ð¾Ð±ÑÑÐ¼Ñ Ð´Ð°Ð½Ð½ÑÑ. ÐÐ»Ñ ÑÑÐºÐ¾ÑÐµÐ½Ð¸Ñ Ð¼Ð¾Ð¶Ð½Ð¾ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°ÑÑ Ð½ÐµÐ¹ÑÐ¾Ð½Ð½ÑÐµ ÑÐµÑÐ¸. FastSurferCNN â Ð½ÐµÐ¹ÑÐ¾Ð½Ð½Ð°Ñ ÑÐµÑÑ Ð² ÑÐ¾ÑÑÐ°Ð²Ðµ Ð¿Ð°ÐºÐµÑÐ° FastSurfer, Ð¾Ð±ÑÑÐµÐ½Ð½Ð°Ñ Ð½Ð° ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐ°Ñ ÑÐµÐ³Ð¼ÐµÐ½ÑÐ°ÑÐ¸Ð¸ ÐÐ Ð¢-Ð¸Ð·Ð¾Ð±ÑÐ°Ð¶ÐµÐ½Ð¸Ð¹ ÐºÐ¾Ð½Ð²ÐµÐ¹ÐµÑÐ¾Ð¼ recon-all Ð¸Ð· Ð¿Ð°ÐºÐµÑÐ° FreeSurfer. Ð ÐµÐ·ÑÐ»ÑÑÐ°ÑÑ FastSurferCNN Ð´Ð¾Ð»Ð¶Ð½Ñ Ð±ÑÑÑ ÑÐ¾ÑÐ½ÑÐ¼Ð¸. Ð Ð´Ð°Ð½Ð½Ð¾Ð¹ ÑÐ°Ð±Ð¾ÑÐµ Ð¾ÑÑÑÐµÑÑÐ²Ð»ÑÐµÑÑÑ ÑÑÐ°Ð²Ð½ÐµÐ½Ð¸Ðµ ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐ¾Ð² ÑÐµÐ³Ð¼ÐµÐ½ÑÐ°ÑÐ¸Ð¸ FastSurferCNN Ñ ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐ°Ð¼Ð¸ recon-all, Ð¿ÑÐ¸Ð½ÑÑÑÐ¼Ð¸ Ð·Ð° ÑÑÐ°Ð»Ð¾Ð½Ð½ÑÐµ. ÐÐµÑÑÐ¸ÐºÐ¾Ð¹ Ð´Ð»Ñ Ð¾ÑÐµÐ½ÐºÐ¸ ÐºÐ°ÑÐµÑÑÐ²Ð° ÑÐµÐ³Ð¼ÐµÐ½ÑÐ°ÑÐ¸Ð¸ Ð²ÑÐ±ÑÐ°Ð½ ÐºÐ¾ÑÑÑÐ¸ÑÐ¸ÐµÐ½Ñ Ð¿Ð¾Ð´Ð¾Ð±Ð¸Ñ ÐÐ°Ð¹ÑÐ°. ÐÐ° Ð¾ÑÐ½Ð¾Ð²Ðµ Ð¿Ð¾Ð»ÑÑÐµÐ½Ð½ÑÑ Ð´Ð°Ð½Ð½ÑÑ Ð¸ Ð¸Ñ ÑÑÐ°ÑÐ¸ÑÑÐ¸ÑÐµÑÐºÐ¾Ð¹ Ð¾Ð±ÑÐ°Ð±Ð¾ÑÐºÐ¸ ÑÑÑÐ°Ð½Ð¾Ð²Ð»ÐµÐ½Ð¾, ÑÑÐ¾ ÑÑÐ´ Ð¿Ð¾Ð´ÐºÐ¾ÑÐºÐ¾Ð²ÑÑ ÑÑÑÑÐºÑÑÑ (Ð±ÐµÐ»Ð¾Ðµ Ð²ÐµÑÐµÑÑÐ²Ð¾ Ð±Ð¾Ð»ÑÑÐ¸Ñ Ð¿Ð¾Ð»ÑÑÐ°ÑÐ¸Ð¹, ÐºÐ¾ÑÐ° Ð¼Ð¾Ð·Ð¶ÐµÑÐºÐ°) Ð¸Ð¼ÐµÑÑ Ð±Ð¾Ð»ÑÑÐ¸Ðµ Ð²ÐµÑÐ°, Ð² ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐµ ÑÐµÐ³Ð¾ Ð½Ð° Ð¾Ð±Ð¾Ð±ÑÑÐ½Ð½Ð¾Ðµ Ð·Ð½Ð°ÑÐµÐ½Ð¸Ðµ ÐºÐ¾ÑÑÑÐ¸ÑÐ¸ÐµÐ½ÑÐ° ÐÐ°Ð¹ÑÐ° Ð¿ÑÐ¾ÑÐ¸Ðµ ÑÑÑÑÐºÑÑÑÑ ÑÑÑÐµÑÑÐ²ÐµÐ½Ð½Ð¾Ð³Ð¾ Ð²Ð»Ð¸ÑÐ½Ð¸Ñ Ð½Ðµ Ð¾ÐºÐ°Ð·ÑÐ²Ð°ÑÑ. ÐÐ»Ñ ÐºÐ¾ÑÐºÐ¾Ð²ÑÑ ÑÑÑÑÐºÑÑÑ ÑÐ°ÑÐ¿ÑÐµÐ´ÐµÐ»ÐµÐ½Ð¸Ðµ Ð²ÐµÑÐ¾Ð² Ð±Ð¾Ð»ÐµÐµ ÑÐ°Ð²Ð½Ð¾Ð¼ÐµÑÐ½Ð¾Ðµ, Ð¿Ð¾ÑÑÐ¾Ð¼Ñ ÑÐ°ÐºÐ¾Ðµ ÑÑÐ²ÐµÑÐ¶Ð´ÐµÐ½Ð¸Ðµ Ðº Ð½Ð¸Ð¼ Ð½ÐµÐ¿ÑÐ¸Ð¼ÐµÐ½Ð¸Ð¼Ð¾. ÐÐ½Ð°Ð»Ð¸Ð· Ð¾Ð±Ð¾Ð±ÑÑÐ½Ð½ÑÑ Ð·Ð½Ð°ÑÐµÐ½Ð¸Ð¹ ÐºÐ¾ÑÑÑÐ¸ÑÐ¸ÐµÐ½ÑÐ° Ð´Ð»Ñ Ð¿Ð¾Ð´ÐºÐ¾ÑÐºÐ¾Ð²ÑÑ Ð¸ ÐºÐ¾ÑÐºÐ¾Ð²ÑÑ ÑÑÑÑÐºÑÑÑ ÑÐ²Ð¸Ð´ÐµÑÐµÐ»ÑÑÑÐ²ÑÐµÑ Ð¾ Ð»ÑÑÑÐµÐ¹ ÑÐµÐ³Ð¼ÐµÐ½ÑÐ°ÑÐ¸Ð¸ Ð¿Ð¾Ð´ÐºÐ¾ÑÐºÐ¾Ð²ÑÑ ÑÑÑÑÐºÑÑÑ, Ð¾Ð´Ð½Ð°ÐºÐ¾, Ñ Ð¿Ð¾Ð¼Ð¾ÑÑÑ Ð¿ÑÐµÐ´Ð»Ð¾Ð¶ÐµÐ½Ð½Ð¾Ð¹ Ð² ÑÐ°Ð±Ð¾ÑÐµ Ð¼ÐµÑÐ¾Ð´Ð¸ÐºÐ¸ Ð¿Ð¾ÐºÐ°Ð·Ð°Ð½Ð¾, ÑÑÐ¾ FastSurferCNN, Ð½Ð°Ð¾Ð±Ð¾ÑÐ¾Ñ, Ð»ÑÑÑÐµ Ð¾Ð±ÑÐ°Ð±Ð°ÑÑÐ²Ð°ÐµÑ ÐºÐ¾ÑÐºÐ¾Ð²ÑÐµ ÑÑÑÑÐºÑÑÑÑ. ÐÐ° Ð¾ÑÐ½Ð¾Ð²Ðµ ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐ¾Ð² ÑÐ´ÐµÐ»Ð°Ð½ Ð²ÑÐ²Ð¾Ð´ Ð¾ Ð½ÐµÐ¾Ð±ÑÐ¾Ð´Ð¸Ð¼Ð¾ÑÑÐ¸ Ð¿Ð¾Ð²ÑÑÐµÐ½Ð¸Ñ ÑÐ¾ÑÐ½Ð¾ÑÑÐ¸ FastSurferCNN.
description: The given work is devoted to the study of the accuracy of neural network segmentation of MRI images of the human brain using FastSurfer. Automatic segmentation is the best way to process images for processing structures of interest, but due to the presence of computationally intensive steps, the process can take a long time, which is unacceptable for large-scale studies that generate large amounts of data. Neural networks can be used to speed up the process. FastSurferCNN is a neural network as part of the FastSurfer package, trained on the results of segmentation of MRI images by the recon-all pipeline from the FreeSurfer package. FastSurferCNN results should be accurate. In this work, the FastSurferCNN segmentation results are compared with the recon-all results taken as reference. The metric for assessing the quality of segmentation is the Dice similarity coefficient. Based on the obtained data and their statistical processing, it was found that a number of subcortical structures (the white matter of the large cerebral hemispheres, the cerebellar cortex) have large weights, as a result of which other structures with small weights do not significantly affect the generalized value of the Dice coefficient. However, for cortical structures, the distribution of weights is more uniform, so this statement does not apply to them. The analysis of generalized coefficient values for subcortical and cortical structures indicates better segmentation of subcortical structures, however, using the methodology proposed in the work, it is shown that FastSurferCNN, on the contrary, processes cortical structures better. Based on the general estimates, it is concluded that edits need to be made to the FastSurferCNN architecture in order to increase the accuracy of segmentation.