CN112184617B - Spine MRI image key point detection method based on deep learning - Google Patents
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Abstract
The invention is called a spine MRI image key point detection method based on deep learning. The invention discloses a spine MRI image key point detection method based on deep learning, which comprises the steps of firstly detecting and positioning vertebrae in a spine MRI image by utilizing a deep target detection network, identifying S1 (sacrum 1) as positioned vertebrae, and then filtering false positive detection results and judging fine grain labels of all the vertebrae by combining with the structural information of the vertebrae. And then, respectively detecting six key points of the upper and lower boundaries UA, UM, UP, LA, LM and LP of each vertebra by using a key point detection network, determining and correcting the key point positions of each vertebra by combining edge information, and finally, developing interactive visual MRI spine image key point automatic labeling software. The method can automatically extract the key points of the spine MRI image, and has great application value in the aspects of medical image analysis, auxiliary medical treatment and the like.
Description
Technical Field
The invention belongs to the field of computer vision and artificial intelligence, and particularly relates to a spine MRI image key point detection method based on deep learning.
Background
Artificial intelligence technology has been used in the medical field in recent years, where computer vision has a great potential for medical image analysis. Aiming at the detection of the key points of the spine MRI image, the detection of the key points of the prior spine MRI image mostly depends on the manual labeling of experts. The manual labeling efficiency is low, the subjective influence of experts is large, and the manual labeling method is particularly not suitable for the condition of large-scale data processing and analysis. Most of the current methods for detecting by using artificial intelligence technology use image bottom layer characteristics, for example Harr characteristics in paper (Ebrahimi S, Angelini E, Gajny L, et al. lumbar spine porsterer detector in X-ray using Haar-based features [ C ]//2016IEEE 13th international symposium on biological imaging (ISBI). IEEE,2016: 180-. The invention realizes a more robust and accurate spine MRI image key point detection method by establishing a high-quality data set and utilizing the excellent learning ability of deep learning.
Disclosure of Invention
The invention is realized by the following technical scheme: a spine MRI image key point detection method based on deep learning comprises the following steps:
the method comprises the following steps: inputting the spine MRI image into a trained target detection network to obtain the position information of each vertebra and whether the position information is a coarse-grained label of S1;
step two: and D, filtering false positive detection results and identifying fine-grained labels of the vertebrae by using all vertebrae obtained in the step one and the positioned S1 position and combining the physiological structure information of the vertebrae.
Step three: cutting out the vertebrae and the peripheral part area thereof obtained by detection in the step two, and inputting the cut vertebrae and the peripheral part area into a trained key point detection network to detect the position information of six key points which are counted by the upper and lower boundaries UA, UM, UP, LA, LM and LP of each vertebra.
Step four: and C, segmenting the vertebrae obtained in the step two by using the trained segmentation network to obtain edge information, and correcting the position information of the key points obtained in the step three according to the edge information obtained in the step four to obtain a final key point prediction result.
Further, in the first step, the coarse-grained labels of the vertebrae are S1 and NS1 (where S1 refers to sacral 1, NS1 is all other vertebrae except sacral 1), and the target detection network is YOLOv 3.
Further, the third step is realized by the following substeps.
1) Using the detected S1 as positioned vertebrae, the height of the center of each vertebra on the image is calculated and the detected vertebrae are sorted according to the centroid height.
2) According to the physiological structure information of the human spine, corresponding fine-grained labels such as S1, L5, L4, L3, L2, L1, T12 and T11 are assigned to each detected vertebra from bottom to top.
3) This false positive target is filtered by calculating the aspect ratio of the vertebrae and the upper side edge height and depending on whether the threshold requirement is met.
Further, the aspect ratio threshold is 1.6 and the upper edge height threshold is 5.
Further, the fourth step is specifically:
(4.1) constructing a vertebral margin segmentation network: the vertebral margin segmentation network is comprised of a down-sampling portion and an up-sampling portion. The structure of the down-sampling part is resnet50 with a full connection layer removed, the up-sampling part is composed of up-sampling convolution blocks of corresponding four stages, and the structure of the up-sampling convolution blocks is upsampling- > conv- > bn- > relu.
(4.2) training a vertebral edge segmentation network: firstly, establishing a coarse-grained segmentation data set by using the key point marking information to pre-train the vertebra edge segmentation network, and then establishing an accurate fine-grained segmentation data set to further train the segmentation network.
And (4.3) after the segmentation result is obtained, further correcting the segmentation result by utilizing the characteristics of the CRF and the larger gradient of the edge image so as to obtain more accurate edge segmentation information.
Further, the step (4.3) is specifically:
(4.3.1) making an extension line of the connection line of the two key points, obtaining vertebra edge information by utilizing the vertebra edge segmentation network, and taking the farthest intersection point of the extension line and the vertebra edge as the coordinate of the corrected key point.
(4.3.2) obtaining a final key point prediction result by combining the label obtained in the second step;
the method has the advantages that the method realizes the key point detection of the spine MRI image by utilizing the deep learning technology, avoids complicated manual labeling and reduces the burden of doctors. Compared with the manual labeling of experts, the method can avoid the influence of subjective factors of doctors, can process large-scale data in batch, and provides data basis for further spine MRI image analysis.
Drawings
FIG. 1 is a schematic diagram of key points detected in the present invention.
Fig. 2 is an overall flow chart of the present invention.
Fig. 3 is a schematic diagram of key point correction according to the present invention.
Detailed Description
The present invention is described in detail below with reference to the accompanying drawings.
Referring to fig. 1, the data sets of the training network in the invention are self-built data sets, the key points of the spine are marked by doctors and experts, and the detected key points are six key points in total of the upper and lower boundaries UA, UM, UP, LA, LM and LP of each vertebra. The basic flow of model training is as follows:
1. spinal MRI images are collected and a portion of the images are randomly extracted as an initial data set.
2. And marking or correcting the data set, and training the model by using the marked data set.
3. And predicting the newly acquired spine MRI image by using the trained model, and adding the newly acquired spine MRI image into the data set.
4. And (5) repeating the steps 2 and 3 until the model accuracy meets the use requirement.
The target detection network depicted in fig. 2 is preferably YOLOv3, and the method classifies the vertebrae into two categories of S1 and NS1 (sacral 1 and non-sacral 1) according to whether the vertebrae are S1 or not as coarse-grained label information in the training process. And constructing a data set of the training detection network from the original data set, calculating a bounding box of each vertebra according to the key point labels of the vertebra, and training the YOLOv3 network by using the coarse-grained class labels.
After obtaining the position of the vertebra in the MRI image of the vertebra and whether the coarse-grained category information is S1, the method filters the prediction result of false positive and determines the category to which each vertebra belongs by using the structural information of the vertebra, specifically: using S1 as the positioned vertebrae, the heights of the centers of the respective vertebrae on the image are calculated and the detected vertebrae are sorted according to the height of the centroid. And then, according to the physiological structure information of the human spine, corresponding labels such as S1, L5, L4, L3, L2, L1, T12 and T11 are allocated to each detected vertebra from bottom to top. The method filters the targets by calculating the aspect ratio of the vertebrae and whether the central height meets the threshold requirement, and the aspect ratio of the vertebrae can be calculated according to the target detection result.
The keypoint detection Network depicted in fig. 2 is preferably a U-shaped Network or a Stacked Hourglass Network (Stacked Hourglass Network), the training data is a thermodynamic diagram corresponding to the vertebra image and the surrounding partial images cut out from the original image and the keypoints, and an online hard sample mining method is utilized in the training process of the keypoint detection Network.
Certain errors exist in the original data labeling process, and the errors can cause certain errors of the spine edges at the positions of the labeled key points. The method utilizes the edge information of the spine to further correct the detected key point result. Firstly, training a U-shaped deep convolutional neural network as a vertebra edge segmentation network for segmenting vertebra edges, wherein the vertebra edge segmentation network is composed of a down-sampling part and an up-sampling part. The structure of the down-sampling part is Resnet50 with a full connection layer removed, the up-sampling part is composed of up-sampling convolution blocks of corresponding four stages, and the structure of the up-sampling convolution blocks is upsampling- > conv- > bn- > relu. In order to improve the precision of the vertebra edge segmentation network, the method firstly establishes a coarse-grained segmentation data set by using the key point marking information to pre-train the vertebra edge segmentation network, and then establishes an accurate fine-grained segmentation data set to further train the segmentation network. The method further corrects the segmentation result by using the characteristic of the conditional random field CRF and the larger gradient of the edge image to obtain more accurate edge segmentation information. After the vertebra edge information is obtained by using the vertebra edge segmentation network, the method corrects the detected key points by using the edge information, and as shown in fig. 3, the method takes the extension line to the vertebra edge along the connection line of UA-LA, UM-LM and UP-LP, and takes the farthest intersection point of the extension line and the vertebra edge as the corrected coordinates of UA, LA, UM, LM, UP and LP. In order to improve the efficiency of the data set manufacturing process and facilitate the use of medical personnel, the method is developed into interactive visual automatic detection labeling software.
After the network training is completed, the method can be applied to the whole spine MRI image key point detection process, and according to the technical scheme set forth by the invention, the method needs to complete the following steps aiming at the spine MRI image key point detection process:
the method comprises the following steps: inputting the MRI image of the spine into a trained target detection network YOLOv3(Redmon J, Farhadi A. Yolov3: An unknown actual [ J ]. arXiv preprint arXiv:1804.02767,2018.), and obtaining the position information of each vertebra and whether the position information is a coarse-grained label of S1;
step two: and D, filtering false positive detection results and identifying fine-grained labels of the vertebrae by using all vertebrae obtained in the step one and the positioned S1 position and combining the physiological structure information of the vertebrae.
1) Using the detected S1 as positioned vertebrae, the height of the center of each vertebra on the image is calculated and the detected vertebrae are sorted according to the centroid height.
2) According to the physiological structure information of the human spine, corresponding fine-grained labels such as S1, L5, L4, L3, L2, L1, T12 and T11 are assigned to each detected vertebra from bottom to top.
3) This false positive target is filtered by calculating the aspect ratio of the vertebrae and the upper lateral margin height and depending on whether the threshold requirement is met. The aspect ratio threshold is 1.6 and the upper edge height threshold is 5.
Step three: cutting out the vertebrae and the peripheral part area thereof obtained by detection in the step two, and inputting the cut vertebrae and the peripheral part area into a trained key point detection network to detect the thermodynamic diagram of six key points of the upper and lower boundaries UA, UM, UP, LA, LM and LP of each vertebra. The method of extracting the coordinates of the key points in the thermodynamic diagram can be adopted by, but not limited to, the methods in the papers (Zhang F, Zhu X, Dai H, et al. distribution-aware correlation representation for human position estimation [ C ]// Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern registration. 2020:7093 and 7102).
Step four: and C, segmenting the vertebrae obtained in the step two by using the trained segmentation network to obtain edge information, and correcting the position information of the key points obtained in the step three according to the edge information obtained in the step four.
1) Obtaining vertebra edge information by using a vertebra edge segmentation network;
2) the method takes an extension line to the edge of the vertebra along a connection line of UA-LA, UM-LM and UP-LP, and takes the farthest intersection point of the extension line and the edge of the vertebra as a corrected coordinate of UA, LA, UM, LM, UP and LP.
3) And outputting a final key point prediction result by combining the label obtained in the step two.
And developing interactive visual MRI spine image key point automatic labeling software based on the process, and calculating the intervertebral disc height index and the lumbar vertebra anterior eminence angle based on the key point detection result.
The main contents of the present invention are described above, and all the equivalent structures or equivalent flow transformations made by the contents of the present specification and the attached drawings, or directly or indirectly applied to other related technical fields, are included in the scope of the present invention.
Claims (4)
1. A spine MRI image key point detection method based on deep learning is characterized by comprising the following steps:
the method comprises the following steps: inputting the spine MRI image into a trained target detection network to obtain the position information of each vertebra and whether the position information is a coarse-grained label of S1; s1 refers to sacral 1;
step two: filtering false positive detection results by using all vertebrae obtained in the step one and the positioned S1 position in combination with the physiological structure information of the vertebra and identifying fine-grained labels to which the vertebrae belong;
step three: cutting out the vertebrae and the peripheral part area thereof obtained by detection in the step two, and inputting the cut vertebrae and the peripheral part area into a trained key point detection network to detect the position information of six key points which are counted by the upper boundary UA, UM, UP, LA, LM and LP of each vertebra;
step four: utilizing a trained segmentation network to segment the vertebrae obtained in the step two to obtain edge information, and correcting the position information of the key points obtained in the step three according to the obtained edge information to obtain a final key point prediction result, wherein the method specifically comprises the following steps:
(4.1) constructing a vertebral margin segmentation network: the vertebra edge segmentation network consists of a down-sampling part and an up-sampling part; the down-sampling part is structured by removing resnet50 of a full connection layer, the up-sampling part is composed of up-sampling convolution blocks of corresponding four stages, and the up-sampling convolution blocks are structured by upsampling- > conv- > bn- > relu;
(4.2) training a vertebral edge segmentation network: firstly, establishing a coarse-grained segmentation data set by using key point marking information to pre-train a vertebra edge segmentation network, and then establishing an accurate fine-grained segmentation data set to further train the segmentation network;
(4.3) after the segmentation result is obtained, further correcting the segmentation result by using the conditional random field and the characteristic of larger image gradient at the edge so as to obtain more accurate edge segmentation information; the method specifically comprises the following steps:
(4.3.1) making an extension line of a connecting line of the two key points, obtaining vertebra edge information by utilizing a vertebra edge segmentation network, and taking a farthest intersection point of the extension line and the vertebra edge as a corrected key point coordinate;
and (4.3.2) outputting a final key point prediction result by combining the label obtained in the step two.
2. The deep learning based spine MRI image keypoint detection method according to claim 1, wherein in the first step, the coarse-grained labels of the vertebrae are S1 and NS1, wherein S1 refers to sacral 1, NS1 refers to all other vertebrae except sacral 1, and the target detection network is YOLOv 3.
3. The spine MRI image key point detection method based on deep learning according to claim 1, wherein the second step is realized by the following sub-steps:
(2.1) using the detected S1 as positioned vertebrae, calculating the heights of the centers of the respective vertebrae on the image and sorting the detected vertebrae according to the height of the centroid;
(2.2) according to the physiological structure information of the human spine, allocating corresponding S1, L5, L4, L3, L2, L1, T12 and T11 fine-grained labels to each detected vertebra from bottom to top in sequence;
(2.3) filtering false positive objects by calculating the aspect ratio and upper lateral margin height of the vertebrae and depending on whether the threshold requirement is met.
4. The deep learning based spine MRI image key point detection method according to claim 3, wherein the aspect ratio threshold is 1.6 and the upper side edge height threshold is 5.
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