RtStruct saved from nifti appears rotated.

[rtdicomexplorer]

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]

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]

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 < ***@***.***>:

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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 — Reply to this email directly, view it on GitHub <#102 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASXTWLKSHMKUTCILVANCUS3YSOFAXAVCNFSM6AAAAABB5BB4ZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZSGE2TMMBZG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[awtkns]

Tagging @carluri @qurit-frizi for visibility. Unfortunately @asim-shrestha and I are no longer maintainers of this project.

[FabianHoerst]

Is there a fix?

[rtdicomexplorer]

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? — Reply to this email directly, view it on GitHub <#102 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASXTWLPUGCUFN22DNNR3YZTZGBSXFAVCNFSM6AAAAABB5BB4ZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJSGU4TSNZXGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>