Adjust Label after resampling medical volume

Question

Odo Luo 2022-11-14

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链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1850568-adjust-label-after-resampling-medical-volume

评论： Odo Luo 2022-11-21

采纳的回答： Harsha

在 MATLAB Online 中打开

I resampled a medical volume (nifti) following these instructions:

https://de.mathworks.com/help/medical-imaging/ref/medicalvolume.resample.html

ctFile=medicalVolume('E:\git\maskRCNN\norm\LD\case_00167.nii.gz');
targetVoxelSize=[3.11 1.59  1.59];
ratios = targetVoxelSize ./ ctFile.VoxelSpacing;
origSize = size(ctFile.Voxels);
newSize = round(origSize ./ ratios);
origRef = ctFile.VolumeGeometry;
origMapping = intrinsicToWorldMapping(origRef);
tform = origMapping.A;
newMapping4by4 = tform.* [ratios([2 1 3]) 1];
newMapping = affinetform3d(newMapping4by4);
newRef = medicalref3d(newSize,newMapping);
newRef = orient(newRef,origRef.PatientCoordinateSystem);
newCTFile = resample(ctFile,newRef,Method='linear');
write(newCTFile,"E:\git\maskRCNN\norm\LD\case_00167");

ctFile is an image with Voxels 512x512,103 , taken from the kits19 challenge (https://github.com/neheller/kits19/tree/master/data)

However, the label (also a nifti file) that marked a organ on the original image (ctFile), does not mark the same area on the new, resampled image (newCTFile). I assume I need to tranform the label too. How do I do that?

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cr 2022-11-14

Please consider providing more information like data sizes, code etc for community to be able to understand and possibly answer.

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Answer 1

Harsha 2022-11-18

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链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1850568-adjust-label-after-resampling-medical-volume#answer_1103358

Hi Odo Luo

Consider the Labels Nifti files also as a medical volume and apply all the transformations(that are performed on the CT file) as given in the link mentioned by you.