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MIC-DKFZ / HD-BET

MRI brain extraction tool
Apache License 2.0
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SimpleITK==2.0.2 #25

Open patricio-astudillo opened 2 years ago

patricio-astudillo commented 2 years ago

Dear @FabianIsensee,

if I use versions higher than 2.0.2, I receive the following error: ITK only supports orthonormal direction cosines. No orthonormal definition found. This is also mentioned in (https://github.com/MIC-DKFZ/nnDetection/issues/24).

Could please undo your change in the requirement.txt file please? I have corrected this in the past and now I receive the same errors as before.

If you want I can push this change also, but this seems a bit back and forth to me.

Best regards, Patricio

FabianIsensee commented 2 years ago

Hi, can you please specify what dataset you are having problems with? I just upgraded my SimpleITK to SimpleITK==2.1.1 and have not had any problems with the commands I tested. Best, Fabian

patricio-astudillo commented 2 years ago

Hey Fabian, It is a private dataset from a hospital. However, I don't think it is dataset related. However, I don't want to block updating any versions of SimpleITK but I also want to make sure that others do not run into the same troubles that I have had. How shall I proceed to investigate this? I can do a pip show to list all my versions and provide an overview of my system (os, etc...)? Thanks in advance for your help, Patricio

Op do 20 jan. 2022 om 08:33 schreef Fabian Isensee @.***

:

Hi, can you please specify what dataset you are having problems with? I just upgraded my SimpleITK to SimpleITK==2.1.1 and have not had any problems with the commands I tested. Best, Fabian

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Xtaltec commented 2 years ago

Had the same issue with a private dataset and it was solved by downgrading to SimpleITK 2.0.2.

machur commented 1 year ago

We've encountered the same problem on a private dataset. Only couple of MR studies were affected for hundreds that were processing. It doesn't seem like an easy case to reproduce, especially considering the fact that all failed cases looked quite "orthogonal" by visual inspection. It's probably some corner case of affine matrix processing by SimpleITK.

machur commented 1 year ago

@patricio-astudillo I upgraded SimpleITK from 2.1.1.2 to 2.2.1 and it has worked with the new version.

FabianIsensee commented 1 year ago

SimpleITK has changes the way it works with geometries. It's unfortunate and causes quite a few issues. Changing the SimpleITK version will resolve this, thanks @machur