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jackyko1991 / vnet-tensorflow

Implementation of vnet in tensorflow for medical image segmentation
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Requested region is (at least partially) outside the largest possible region. #19

Open pangda72 opened 3 years ago

pangda72 commented 3 years ago

Hi，@jackyko1991 Thank you for sharing such a great repo.I'm using this repo to segment medical grayscale images on a private dataset,but my segmentation target is very small, so I follow your notes in the NiftiDataset3D.py,replacing RandomCrop()with ConfidenceCrop2 in the image preprocessing section.But I got a problem:

RuntimeError: Exception thrown in SimpleITK RegionOfInterestImageFilter_Execute: D:\a\1\sitk-build\ITK\Modules\Core\Common\src\itkDataObject.cxx:393: Requested region is (at least partially) outside the largest possible region.

I have also looked up some information, but I still don't know how to solve it.Could you give me some help?

BTW,My segmentation goal is small,the results were poor: the DICE score was low. I don't know how to improve it, Could you give me some hints?

Looking forward to your reply. Thanks in advance. Best.

jackyko1991 commented 3 years ago

Dear Panda,

I think you may first check if all the images and labels have the same header information, i.e. both images and labels have the same spacing, direction and origin. Otherwise similar errors may be reported.

Regards, Jacky

On Fri, 29 Oct 2021 at 20:14, panda @.***> wrote:

@.*** https://github.com/jackyko1991 Thank you for sharing such a great repo.I'm using this repo to segment medical grayscale images on a private dataset,but my segmentation target is very small, so I follow your notes in the NiftiDataset.py,replacing RandomCrop()with ConfidenceCrop2 in the image preprocessing section.But I got a problem:

RuntimeError: Exception thrown in SimpleITK RegionOfInterestImageFilter_Execute: D:\a\1\sitk-build\ITK\Modules\Core\Common\src\itkDataObject.cxx:393: Requested region is (at least partially) outside the largest possible region.

I have also looked up some information, but I still don't know how to solve it.Could you give me some help?

Looking forward to your reply. Thanks in advance. Best.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/jackyko1991/vnet-tensorflow/issues/19, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC4BUBYXT6ZRCGCWFCDHPR3UJKF2XANCNFSM5G7GCSRA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

pangda72 commented 3 years ago

Dear Panda, I think you may first check if all the images and labels have the same header information, i.e. both images and labels have the same spacing, direction and origin. Otherwise similar errors may be reported. Regards, Jacky … On Fri, 29 Oct 2021 at 20:14, panda @.> wrote: @. https://github.com/jackyko1991 Thank you for sharing such a great repo.I'm using this repo to segment medical grayscale images on a private dataset,but my segmentation target is very small, so I follow your notes in the NiftiDataset.py,replacing RandomCrop()with ConfidenceCrop2 in the image preprocessing section.But I got a problem: RuntimeError: Exception thrown in SimpleITK RegionOfInterestImageFilter_Execute: D:\a\1\sitk-build\ITK\Modules\Core\Common\src\itkDataObject.cxx:393: Requested region is (at least partially) outside the largest possible region. I have also looked up some information, but I still don't know how to solve it.Could you give me some help? Looking forward to your reply. Thanks in advance. Best. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#19>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC4BUBYXT6ZRCGCWFCDHPR3UJKF2XANCNFSM5G7GCSRA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Dear jackyko1991 Thank you for your advice.I'm going to try. This repo has helped me a lot. Thank you very much indeed.

Best.