data conversion file for MyoPS data

[mehrnia]

I'm in real need of dataset_conversion.py file for a MyoPS2020 dataset. I tried several trials of nnunet1 and nnunetv2 and did not get any output. Usually I get errors in dataset integrity part. If you face any difficulty accessong the dataset, pls feel free to ask me Best, Mehri

[Karol-G]

Hello Mehri,

Thank you for reaching out and utilizing nnU-Net for your work. To better assist you, could you please provide a more detailed description of the issues you are encountering? Specifically, it would help to understand exactly what error you receive. Please report the command line output here including the error message.

Additionally, could you share your dataset.json file along with the exact preprocessing, training, and inference commands you used? This information will allow us to replicate the issue and provide more targeted support.

Looking forward to your response.

Best regards, Karol Gotkowski

[mehrnia]

Hi Karol, thank you for reaching out to me. "MyoPS" has 3 channels. I don't have json file as it's part of creat dataset from "dataset conversion" in nnunetv2. As instance: if not os.path.exists('nnUNet_raw') and not os.path.exists( 'nnUNet_preprocessed'): from nnunetv2.dataset_conversion.Dataset027_ACDC import Create_ACDC I need create MyoPS.

Best Regards Mehri Mehrnia

On Mon, May 13, 2024 at 4:10 AM Karol Gotkowski @.***> wrote:

Hello Mehri,

Thank you for reaching out and utilizing nnU-Net for your work. To better assist you, could you please provide a more detailed description of the issues you are encountering? Specifically, it would help to understand exactly what error you receive. Please report the command line output here including the error message.

Additionally, could you share your dataset.json file along with the exact preprocessing, training, and inference commands you used? This information will allow us to replicate the issue and provide more targeted support.

Looking forward to your response.

Best regards, Karol Gotkowski

— Reply to this email directly, view it on GitHub https://github.com/MIC-DKFZ/nnUNet/issues/2170#issuecomment-2107047343, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAUWETMCOJZ2OZFPTXVWB3ZCB7P5AVCNFSM6AAAAABHNVVRK2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBXGA2DOMZUGM . You are receiving this because you authored the thread.Message ID: @.***>

[mehrnia]

Speaking of which, can you introduce me which dataset of those provided one has 3 or 4 channels?

Best Regards Mehri Mehrnia

On Tue, May 14, 2024 at 4:17 PM Chicago Girl @.***> wrote:

Hi Karol, thank you for reaching out to me. "MyoPS" has 3 channels. I don't have json file as it's part of creat dataset from "dataset conversion" in nnunetv2. As instance: if not os.path.exists('nnUNet_raw') and not os.path.exists( 'nnUNet_preprocessed'): from nnunetv2.dataset_conversion.Dataset027_ACDC import Create_ACDC I need create MyoPS.

Best Regards Mehri Mehrnia

On Mon, May 13, 2024 at 4:10 AM Karol Gotkowski @.***> wrote:

Hello Mehri,

Thank you for reaching out and utilizing nnU-Net for your work. To better assist you, could you please provide a more detailed description of the issues you are encountering? Specifically, it would help to understand exactly what error you receive. Please report the command line output here including the error message.

Additionally, could you share your dataset.json file along with the exact preprocessing, training, and inference commands you used? This information will allow us to replicate the issue and provide more targeted support.

Looking forward to your response.

Best regards, Karol Gotkowski

— Reply to this email directly, view it on GitHub https://github.com/MIC-DKFZ/nnUNet/issues/2170#issuecomment-2107047343, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAUWETMCOJZ2OZFPTXVWB3ZCB7P5AVCNFSM6AAAAABHNVVRK2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBXGA2DOMZUGM . You are receiving this because you authored the thread.Message ID: @.***>

[Karol-G]

My apologies but I am unable to understand you. Please spend more time on formulating your request only then I will be able to help you.

[mehrnia]

hi, this is my dataset file:

Best Regards Mehri Mehrnia

On Wed, May 15, 2024 at 4:59 AM Karol Gotkowski @.***> wrote:

My apologies but I am unable to understand you. Please spend more time on formulating your request only then I will be able to help you.

— Reply to this email directly, view it on GitHub https://github.com/MIC-DKFZ/nnUNet/issues/2170#issuecomment-2112083223, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAUWETQL7DELKKDBNURVBLZCMWYDAVCNFSM6AAAAABHNVVRK2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJSGA4DGMRSGM . You are receiving this because you authored the thread.Message ID: @.***>