Comments (6)
你好,对于第一个问题,索引超出160可能是由于裁剪的patch尺寸不为160,160,96。你可以输出尺寸大小进行检查。此外,3Dircadb标签只做了门静脉与肝静脉分割,且血管标签值应都设为1。在3_graph_liver.py注释部分可以将图结构可视化显示以保证正确。第二个问题直接像你说的一样更改路径便可以。
from livervesselwithgraph.
作者您好,感谢您百忙之中的答复!
我用代码检查打印了F:\Code\Liver_vessel\pre_data\val下的case3、case6、case8、case12、case13、case16文件夹中的所有如case12_patch001_cenertline.nii.gz、case12_patch001_img.nii.gz、case12_patch001_seg.nii.gz文件的尺寸,确定了文件尺寸均为(160,160,96),为什么执行3_graph_liver.py时graph_val文件夹下只生成了cae12相应文件,之后刚打印case13信息时:
********** Time: 25.777490854263306 **********
F:\Code\Liver_vessel\pre_data\val\case13\case13_patch001_img.nii.gz
case13_patch001 start 紧接着报错:
F:\Code\LiverVesselWithGraph\3_graph_liver.py:83: RuntimeWarning: invalid value encountered in divide
temp = np.around(temp / count).astype(int) Traceback (most recent call last):
File "F:\Code\LiverVesselWithGraph\3_graph_liver.py", line 193, in
graph = graph_construct(img_paths[idx], seg_paths[idx], size=12, edge_dist_thresh=20,save_dir=save_dir)
File "F:\Code\LiverVesselWithGraph\3_graph_liver.py", line 103, in graph_construct
if speed[graph.nodes[n]['x'], graph.nodes[n]['y'], graph.nodes[n]['z']] == 0:
IndexError: index -2147483636 is out of bounds for axis 0 with size 160
有关标签问题,在3Dircadb中,20个患者均含有portalvein标签,对于venacava和venoussystem每个患者只含有其中之一,因此,在做肝脏血管分割任务时,我合并了portalvein+(venacava/venoussystem)作为label(参考了noisy lables are useful MTCL这篇论文的方法)有一个困惑是:您的答复中“血管标签值应都设为1”的操作在哪里完成,在项目中还没有发现,不同于MSD task8数据集,3Dircadb中没有json文件标明lable=1
恳请作者百忙之中帮忙排查下是哪里的问题,应该如何解决,不胜感激!
from livervesselwithgraph.
你用itk-snap等软件打开3Dircadb数据的标签的时候可以显示标签的值,而把lable设为1则表明将肝静脉与门静脉看做一类用于分割
from livervesselwithgraph.
作者您好,已经确定了文件尺寸均为(160,160,96),为什么只有val下的case12下的每个patch.nii.gz可以在graph_val文件夹下生成对应gpickle文件,其他文件夹均报错if speed[graph.nodes[n]['x'], graph.nodes[n]['y'], graph.nodes[n]['z']] == 0:
IndexError: index -2147483636 is out of bounds for axis 0 with size 160 是否与graph = graph_construct(img_paths[idx], seg_paths[idx], size=12, edge_dist_thresh=20,save_dir=save_dir)的设置有关呢?
from livervesselwithgraph.
这个设置一般不会影响,你可以加我一下qq:924710446
from livervesselwithgraph.
作者您好,执行preprogress.py后,生成的大部分case中的patch_image.nii.gz文件用itk-snap打开后,图像看的不清晰或一片白色,与原始图像相差甚远,这是什么原因造成的呢,期待并感谢您百忙之中的答复
from livervesselwithgraph.
Related Issues (2)
- 3Dircadb数据集的artery HOT 4
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