CN106780491B

CN106780491B - Initial contour generation method adopted in segmentation of CT pelvic image by GVF method

Info

Publication number: CN106780491B
Application number: CN201710050598.9A
Authority: CN
Inventors: 余辉; 王海均; 于旭耀; 曹玉珍; 孙敬来; 张力新; 安家宝
Original assignee: Tianjin University
Current assignee: Tianjin University
Priority date: 2017-01-23
Filing date: 2017-01-23
Publication date: 2020-03-17
Anticipated expiration: 2037-01-23
Also published as: CN106780491A

Abstract

The invention relates to an initial contour generation method adopted in a Global Volume Function (GVF) method for segmenting a Computed Tomography (CT) pelvic image, which comprises the following steps of: preprocessing a CT image; obtaining a region-of-interest mask; convolving the mask and the initial image to obtain an intermediate image; arranging the intermediate images according to a spatial sequence, selecting a pixel difference value of two adjacent frames of CT images as a characteristic distance, taking the two adjacent frames with the characteristic distance smaller than a specified threshold value as similar frames, and primarily screening the CT sequence to obtain a candidate key frame sequence; performing fine screening on the candidate key frame sequence; the key frame bone contours are interactively labeled.

Description

Initial contour generation method adopted in segmentation of CT pelvic image by GVF method

Technical Field

The invention relates to the field of medical image segmentation, in particular to a method for segmenting bone regions such as a pelvis, a sacrum, a hip bone, an acetabulum and the like in a pelvis CT image.

Background

The medical image segmentation is the basis of medical image analysis and processing, and the accuracy of medical image segmentation directly influences the judgment of doctors on the disease conditions and the selection of surgical schemes. CT has been widely used for diagnosis of various diseases because CT images have a high resolution and can clearly display the characteristics of anatomical structures and lesion tissue regions. The pelvic fracture is one of the factors causing morbidity and mortality, and for the displacement fracture, the fracture range, the crushing degree, the soft tissue damage degree and the like can be accurately and quickly determined, so that reference can be provided for the selection of a treatment mode and the condition after healing. Secondly, for the cases of pelvic dysplasia caused by congenital or acquired, poliomyelitis, hereditary and other reasons, the functional reestablishment and the deformity correction depend on accurate early diagnosis and timely treatment, and the CT has a very important meaning for pelvic anatomical structure description before and after the operation, the formulation of an operation scheme and the effect evaluation after the operation is completed.

Among the bone CT image segmentation methods, the most commonly used segmentation method is a segmentation method based on gray scale information, wherein the threshold method is a typical method, but it is difficult to select an appropriate threshold during the use process due to non-uniformity of bone density, narrow connection between the femoral head and the acetabulum, weak marginality caused by pathological changes, and the like. In addition, classification and clustering methods in machine vision are also used in segmentation, and the method has good robustness to noise, but the segmentation effect depends on the number and types of samples, and the segmentation algorithm has limitation due to large individual difference among patients. At present, a great deal of research is focused on statistical shape model segmentation methods, such as snake model and GVF model^[1]The method comprises the following steps of (Gradient Vector connected Snake Model), level set-based segmentation Model and the like, wherein the research of the segmentation method mainly aims at the aspects of automatic selection of marking points, construction of a Model with less training set, improvement of the Model, combination with other methods and the like, a large amount of manual processing is needed to give prior information before segmentation is realized, the final segmentation effect depends on the accuracy and the integrity of the prior information, and due to the fact that individuation difference among patients is large, the prior information needs to be added to improve the segmentation effect, the method is large in workload, the effect cannot be guaranteed at the early stage, and the method is not suitable for being directly used by a hospital. Due to the GVF model^[2]Two problems which are difficult to solve by the traditional Snack model are well solved: 1. for the initial contourAre very sensitive; 2. the desired effect cannot be achieved when the concave portion of the image is divided. At present, a great deal of research is carried out on segmenting images based on a GVF model, but the GVF model still has the defects of sensitivity to initial contours and long operation time. Therefore, if a more accurate initial contour can be obtained and then the GVF model is used for carrying out bone CT image segmentation, the curve deformation range is greatly reduced, the iteration times are reduced, and the method has important influences on the acceleration of the operation speed and the improvement of the segmentation precision.

Reference documents:

[1]Wu Bingrong；Xie Mei；Li Guo；Gao Jingjing.Medical Image SegmentationBased on GVF Snake Model；Intell igent Computation Technology and Automation；2009:637-640.

[2]Chen,L.,et al.,Segmentation of the Pelvic Bone Using a GeneralizedGradient Vector Convolution Field Snake Model.JOURNAL OF MEDICAL IMAGING ANDHEALTH INFORMATICS,2015.5(7):p.1482-1487.

disclosure of Invention

The invention aims to provide a method for quickly generating an initial contour for a segmentation algorithm for bone CT image segmentation by using a GVF model. According to the invention, by utilizing the characteristic of temporal and spatial continuity of bone morphology among CT sequences, key frames are extracted from CT sequence slices, an interactive marking method is used in the key frames, so that a doctor can mark, correct and confirm the pelvis edge contour extracted by a marked watershed algorithm in the key frames, and the marked contour obtained in the key frames is further used as an initial value of a GVF model of the pelvis contour of an adjacent frame. The technical scheme is as follows:

step 1: CT image preprocessing

Windowing processing, denoising, artifact and CT table non-body area removing and image cutting operation are carried out on the CT image, so that the image size of the CT image sequence is kept consistent after preprocessing, and the relative position of the body area is kept unchanged. For convenience of description, the cropped image is referred to as an initial image.

Step 2: obtaining candidate key frame sequence by preliminary screening

Carrying out mean value filtering, spot removal and morphological processing on the initial image to obtain an approximate region of bone distribution, and taking the region as a region of interest to obtain a region of interest mask; convolving the mask and the initial image to obtain an intermediate image; arranging the intermediate images according to a spatial sequence, selecting a pixel difference value of two adjacent frames of CT images as a characteristic distance, taking the two adjacent frames with the characteristic distance smaller than a specified threshold value as similar frames, and primarily screening the CT sequence to obtain a candidate key frame sequence.

And step 3: fine screening of candidate key frame sequences

Calculating the number of interested areas, a normalized correlation coefficient and a mutual information quantity characteristic of the candidate key frame sequence, taking adjacent candidate key frames with the same number of the interested areas as similar frames, judging whether the adjacent candidate key frames are the similar frames or not by comparing the normalized correlation coefficient and the mutual information quantity characteristic with the corresponding specified threshold value, and further screening to obtain the target key frame sequence.

And 4, step 4: interactive labeling of key frame bone contours

For a key frame in a target key frame sequence, firstly, skeleton extraction is carried out on a key frame interesting region to obtain a mark point, an initial contour is generated by utilizing a watershed algorithm based on the mark point, the initial contour is displayed, a doctor judges whether the key frame interesting region accords with a medical anatomical structure, if the key frame interesting region does not accord with the medical anatomical structure, the mark point is manually added or deleted to correct the initial contour, topology information is perfected, so that a contour curve of a CT image bone region in the target key frame sequence is obtained, and a bone contour mark of the key frame is used as an initial contour of a sequence CT image for further segmenting the same patient.

The invention provides an initial contour generation method adopted in a GVF method-based CT pelvis image segmentation, which adopts an autonomous design algorithm to determine a key frame in a CT sequence, and takes a bone contour mark of the key frame interactively confirmed by a doctor as a pelvis initial contour of a GVF model of an adjacent frame. The invention can greatly reduce the number of CT images needing doctor interactive labeling (only about 5-10% of key frames in the labeled full-sequence CT images need to be confirmed), and can reduce the image processing time and labor intensity by using the labeled contour obtained in the key frames as the initial value of the adjacent frame pelvis contour GVF model.

Drawings

FIG. 1: flow chart of method for rapidly extracting pelvis outline of sequence CT image based on key frame mark

FIG. 2: initial image display

FIG. 3: candidate key frame extraction flow chart

FIG. 4: target set extraction flow chart

Fig. 5(a) (b): respectively labeling contours of adjacent key frames

FIG. 6: automatic segmentation result of a certain CT image between two adjacent key frames in FIG. 5

Detailed Description

Considering that the existing hospital uses manual marking of the pelvis region to make a surgical plan and the number of CT sequences of one patient is large, the time for manually marking a single CT image clinically takes about 15 minutes, so the manual segmentation of the pelvis region takes long time and is high in pressure. Because the shooting distance in the serial CT slices is small, the bone morphological characteristics between two adjacent frames are not changed greatly, and the serial CT slices have high similarity, by utilizing the characteristic, key frames are extracted from the CT serial slices, the data volume needing to be segmented is greatly reduced through the step, the initial contour of the serial CT image of the same patient is further segmented through marking and drawing of bone edge contours in a very small number of key frames by a doctor, and a foundation is laid for rapidly segmenting the CT pelvis image by adopting a GVF method. The invention and its application scenarios will now be further described with reference to the embodiments and the accompanying drawings:

step 1: CT image preprocessing

For one example of a patient with pelvic fracture, 540 CT sequences were obtained in a flat scan at 1mm intervals, each CT size was 512x512, and only image portions were extracted for each DICOM file. The windowing processing is carried out on the image part, wherein the window level is 900, the window width is 600, namely c is 900, w is 600, the data in the image is converted according to the formula (1), and the data is compressed to 256 gray levels:

where f is the displayed bitmap gray scale value, x is the image data, w is the window width, and c is the window level.

After windowing the image, it is converted into BMP format, and the effect before and after windowing is shown in fig. 2. Carrying out binarization processing on the BMP image according to the formula (2),

filling the holes in the binary image by using morphological operation; according to experience, a body region and a CT table can be distinguished according to the area size of a connected domain, so that the areas of the connected domains in a binary image are sequenced, the region with the largest area is set as 1, the rest regions are set as 0, a mask image is obtained, and the size Rect (x, y, width, height) of an adjacent rectangle of the region with the largest area is simultaneously obtained; and (3) convolving the obtained mask image with the BMP image to remove the interference of a CT table, an artifact and the like, only keeping a body area in the image at the moment, and setting the rest areas as 0.

Considering that the body area of the patient does not change much when CT scanning is performed, in order to reduce the data amount and simultaneously save the body area information, the adjacent Rectangle Rect (x, y, width, height) is extended by 10 pixels in each of the four directions of the upper direction, the lower direction, the left direction, the right direction to obtain the Rectangle Rect (x, y, width, height), and then the image is cut with reference to the Rectangle Rect (x, y, width, height), and the original image is regenerated, wherein the original image is shown in fig. 3, and the size of the original image is 436x240 in this example. Thereafter, all CT images are cropped according to this rectangle, ensuring that the relative position of the body region in adjacent CT images remains unchanged.

Step 2: key frame extraction

This step includes two parts, namely, the preliminary screening to obtain the candidate key frame sequence and the fine screening to obtain the target key frame sequence.

In the primary screening process, firstly, operations such as mean value filtering, speckle removing, morphological processing and the like are carried out on an initial image to obtain an approximate bone distribution area, the area is used as an interested area, an interested area mask is obtained, and the number RoiNumber of the interested areas is recorded. Region of interest mask as shown in fig. 4, the region of interest, i.e. the region to be accurately segmented. The mask is convolved with the initial image to obtain an intermediate image.

Arranging the intermediate images according to a spatial sequence, namely keeping the relative sequence between the CT sequence sets unchanged, selecting the pixel difference value of two adjacent frames of CT images as a characteristic distance to carry out primary screening on the CT sequence, and obtaining a candidate key frame sequence { y₁,y₂,y₃,……,y_l}. Fig. 5 shows a flowchart of a candidate key frame sequence extraction method, and the specific steps are described as follows:

1) CT sequence set { f₁,f₂,f₃,……,f_nFirstly, select the first frame f₁As the current key frame, j is 1, and the current key frame is added into a candidate set;

2) the pixel difference between the next frame image j +1 and the current frame image j is Dif ═ f_j+1-f_jIf the difference value is larger than the specified threshold value, the difference between the two images is considered to be larger, the similarity is lower, and the j +1 frame image is added into the candidate set; if the difference is less than the specified threshold, then the current frame is considered to be summarized f_j+1The j +1 frame is not processed;

3) j is j +1, namely the j +1 th frame image is used as the current key frame, whether the frame is the last frame or not is judged, and if yes, the extraction of the candidate key frame is stopped; if not, the step 2 is continued.

According to the above step flow, candidate key frame sequence { y ] can be obtained₁,y₂,y₃,……,y_lAnd in the example, l is 237, and fine screening is carried out on the basis of the l, so that the target key frame sequence can be obtained.

In the fine screening process, the candidate key frame sequence y is subjected to₁,y₂,y₃,……,y_lSequentially using the number of the interested areas, the normalized correlation coefficient and the mutual information quantity characteristic as a characteristic value for further extracting the key frame, and obtaining a target key frame sequence { k ] by comparing the characteristic value with a set threshold value₁,k₂,k₃,……,k_tExtracting final key frame k in the candidate set₁,k₂,k₃,……,k_tThe algorithm flow is as followsAs shown in fig. 6, the specific steps are described as follows:

1) first, a first frame y is selected₁As a key frame, i is 1, and the frame is added into the target set;

2) judging whether the number of the interested areas of the i +1 th frame image is the same as that of the i frame image, namely RoiNumber (i +1) ═ RoiNumber (i), if the number of the interested areas of the i +1 th frame image is different from that of the interested areas of the i frame image, considering that the similarity between the i +1 th frame image and the current frame image is low, and adding the i +1 th frame image into a target set; if the two are the same, turning to 3);

3) according to the formula

Calculating the mutual information quantity characteristics of two frames of images according to a formula

And calculating the normalized correlation coefficient of the two frames of images, wherein the larger the I value is, the higher the correlation degree of the two frames of images is, the smaller the I value is, the lower the correlation degree of the two frames of images is, and the reverse is true. Therefore, when I (j +1, j) is satisfied>T1 simultaneous R (j +1, j)<Adding the (i +1) th frame into the target set under the condition of T2; when this condition is not satisfied, no processing is performed.

4) if the current frame is the last frame in the candidate set, generating a key frame target set; if not, the step 2 is continued.

Following the above-described process flow, a sequence y of candidate key frames can be selected₁,y₂,y₃,……,y_lIs further screened, thereby obtaining a target key frame sequence k₁,k₂,k₃,……,k_t}. In this example, t is 28. That is, a total of 28 CT images are acquired as a key frame, via step 2. The number of key frames extracted in the two stages of step (2) of the method of the present invention is shown in table 1, and the use time of each stage is shown in table 2.

TABLE 1

TABLE 2

And step 3: interactive labeling of key frame bone contours

For a target key frame sequence k₁,k₂,k₃,……,k_tAnd (4) firstly, skeleton extraction is carried out on the key frame region of interest to obtain mark points, and then an initial contour is automatically generated by utilizing a watershed algorithm based on the mark points. And displaying the initial contour, judging whether the initial contour conforms to the medical anatomical structure by a doctor, and if the initial contour does not conform to the medical anatomical structure, manually adding or deleting the mark points to correct the initial contour and improve topological information so as to obtain a contour curve of a bone region of the CT image in the target key frame sequence. The bone contour markers of the keyframes will serve as initial contours to further segment the sequential CT images of the same patient.

And 4, step 4: bone contour of CT image of each layer is extracted by introducing GVF model

The CT image sequence between key frame i and key frame i +1 uses the standard contour of key frame i as the initial contour. And (3) deforming the initial contour by using a GVF model to obtain a target contour of the sequence CT image of the same patient.

In the GVF model, a curve with energy is defined near an image target, and the curve moves towards the position of the image corresponding to the energy minimum value under the action of internal and external energy, and is represented as x(s) ═ x(s), y (s)), where s ∈ [0,1]Then the curve energy functional may be defined as:

to minimize this energy, the curve should then satisfy the equation:

-α(s)X″(s)+β(s)X″(s)+E_ext(X)＝0 (3)

the target edge can be obtained by solving the minimum value of the equation. In the GVF model, the gradient vector field is defined as V (x, y) — (μ (x, y), V (x, y)), where μ (x, y), V (x, y) is V (x, y), and the energy functional of the image edge contour is expressed as:

wherein (x, y) is the coordinate of any point in the image,

denotes the gradient value at (x, y) and μ is the adjustment factor. According to variational theory, GVF satisfies the euler equation, its decomposition form is:

by this equation, V (x, y) can be obtained as the external force F_extV (x, y), the solution curve x(s) in equation (3) is substituted, and the solution process is a process of moving the initial contour curve to the target edge, i.e. an initial contour deformation process.

And (3) regarding the CT image sequence of the same patient, using the manual contour mark of the key frame as an initial contour, and transforming the initial contour by using the GVF model to obtain the bone segmentation results of all pelvis CT sequence images of the same patient.

Claims

1. A method for generating an initial contour used in a Global Volume Function (GVF) method for segmenting a Computed Tomography (CT) pelvic image comprises the following steps:

step 1: CT image preprocessing

Windowing the CT image, denoising, removing artifacts and a non-body area of a CT table, and cutting the image to ensure that the image size of the CT image sequence is kept consistent after preprocessing, and the relative position of the body area is kept unchanged; for convenience of description, the clipped image is referred to as an initial image;

step 2: obtaining candidate key frame sequence by preliminary screening

Carrying out mean value filtering, spot removal and morphological processing on the initial image to obtain an approximate region of bone distribution, and taking the region as a region of interest to obtain a region of interest mask; convolving the mask and the initial image to obtain an intermediate image; arranging the intermediate images according to a spatial sequence, selecting a pixel difference value of two adjacent frames of CT images as a characteristic distance, taking the two adjacent frames with the characteristic distance smaller than a specified threshold value as similar frames, and primarily screening the CT sequence to obtain a candidate key frame sequence;

and step 3: fine screening of candidate key frame sequences

Calculating the number of interested areas, a normalized correlation coefficient and mutual information quantity characteristics of the candidate key frame sequence, judging whether the adjacent candidate key frames are similar frames or not by comparing the normalized correlation coefficient and the mutual information quantity characteristics with the corresponding specified threshold value for the adjacent candidate key frames with the same number of the interested areas, and further screening to obtain a target key frame sequence;

and 4, step 4: interactive labeling of key frame bone contours