RtStruct saved from nifti appears rotated.
rtdicomexplorer opened this issue · 5 comments
rtdicomexplorer commented
Hello everyone, I'm trying to export a nii segmentation file in a RTSTRUCT-DICOM file.
The ROIs in DICOM appear rotated.
The dataset I have from https://nbia.cancerimagingarchive.net (CT/ Whole Body).
The CTs with the created RTSTRUCT I have loaded into https://dicom-web-viewer-b4139.web.app/ (they must be in the same folder)
I've attached the screenshots and the nii segmentation file.
vertebre.nii.gz
Anyway,
Great Job
Michel
Nilser3 commented
Hi @rtdicomexplorer
I had the same problem:
- anat_image: DICOM native (RAI orientation)
- brain mask: rtstruct file crated from anat_image.nii.gz (using
dcm2niix
) (I had test different orientations for input)
To explore: #84
I appreciate your comments 😊 @asim-shrestha @awtkns
Best,
Nilser
rtdicomexplorer commented
Hi Nils Laines Medina,
I found a workaround that works for me:
I had to rotate the the mask-data-array more times as below:
mask_dataflip = np.flipud(mask_data)
mask_dataflip2 = np.flip(mask_dataflip)
mask_rtdata = np.rot90(mask_dataflip2)
In my case the Patient had a HFS position.
I will test that also for other cases.
Regards..,
Michel
Am Mi., 7. Feb. 2024 um 15:24 Uhr schrieb Nilser Laines Medina <
***@***.***>:
… Hi @rtdicomexplorer <https://github.com/rtdicomexplorer>
I had the same problem:
- anat_image: DICOM native (RAI orientation)
- brain mask: rtstruct file crated from anat_image.nii.gz (using
dcm2niix) (I had test different orientations for input)
image.png (view on web)
<https://github.com/qurit/rt-utils/assets/77469192/6cd39535-c71b-4c4f-a6dc-5109155d2eda>
To explore: #84 <#84>
I appreciate your comments 😊 @asim-shrestha
<https://github.com/asim-shrestha> @awtkns <https://github.com/awtkns>
Best,
Nilser
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awtkns commented
Tagging @carluri @qurit-frizi for visibility. Unfortunately @asim-shrestha and I are no longer maintainers of this project.
FabianHoerst commented
Is there a fix?
rtdicomexplorer commented
I think that as NIFTI will be saved automatically in RAS orientation..
regards 😉
[image: image.png]
Am Do., 6. Juni 2024 um 15:53 Uhr schrieb Fabian Hörst <
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… Is there a fix?
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