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rcuocolo / PROSTATEx_masks

Lesion and prostate masks for the PROSTATEx training dataset, after a lesion-by-lesion quality check.
https://rcuocolo.github.io/PROSTATEx_masks/
Creative Commons Attribution 4.0 International
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number of slices in masks is not always the same as number of slices in the scan #8

Closed harisgavranovic closed 3 years ago

harisgavranovic commented 3 years ago

For example, for the patient ProstateX-0003, based on the data in the image_list.csv we should regard the following directory : /ProstateX-0003/10-17-2011-MC prostaat kliniek detectie-mc MCPROSKL30-03010/3-t2tsetra-30967/

We have in total 21 DICOM files there. On the other hand the masks have only 19 slices.

I would expect the same number of slices.

There are several other patients having such differences (They are small but it looks important for me.).

Thank you very much for your help.

rcuocolo commented 3 years ago

You are correct, the masks and DICOM files must have the same geometry, including number of slices. Regarding the example you provided, the 3-t2tsetra-30967 folder is correct and I can confirm it has 21 slices. However, the ProstateX-0003.nii.gz mask in the repository (as well as the "_pz" and "_tz" equivalents) also should have 21 slices. I would advise to try downloading the masks again and check if the masks for this patient still present 19 slices or the correct number (21). Let me know if the issue persists.

rcuocolo commented 3 years ago

You are correct, the names in the PROSTATEx gland and zonal masks are not entirely consistent. I will fix them in the next days and update the repository. Regarding the issue of the number of slices in the ProstateX-0003 case masks, I am unsure how to proceed. On my end, the dimensions are correct (21 slices, not 19). Maybe it could be useful if another user could confirm this issue.

harisgavranovic commented 3 years ago

Dear Renato,

There is probably a misunderstandings here: you have 19 slices in the MRI scans and 21 (as you are saying) in masks.

Can you check this please.

Best regards, Haris

On Fri, Mar 26, 2021 at 4:44 PM Renato Cuocolo @.***> wrote:

You are correct, the names in the PROSTATEx gland and zonal masks are not entirely consistent. I will fix them in the next days and update the repository. Regarding the issue of the number of slices in the ProstateX-0003 case masks, I am unsure how to proceed. On my end, the dimensions are correct (21 slices, not 19). Maybe it could be useful if another user could confirm this issue.

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rcuocolo commented 3 years ago

Regarding the case used as an example (ProstateX-0003), in the DICOM files I see that sequence 3 (the axial T2) has 21 files/slices. I will send you the files in question via email.

rcuocolo commented 3 years ago

The naming issues for some cases (mostly in the 80-100 range) should also be fixed. The correct files have been uploaded to the repository.