PermissionError: [Errno 13] Permission denied: '/home/$USER$/nnUNet/nnUNet_raw_data_base/nnUNet_cropped_data'

[hoangnambui2301]

Hi everyone,

I'm trying to install and run the models on my inferences. This problem popped up just right when I tried to set up the paths (I haven't even created the nnUNet_cropped_data folder!). This error also pops up whenever I use other commands (nnUNet_print_available_pretrained_models or nnUNet_convert_decathlon_task).

I even wrote down the paths into ~/.bashrc file and sourced it.

Also, here is my folder structure. I just followed the instruction so don't think there is any problem here.

By the way, I'm trying to run the model on WSL Ubuntu.

Thanks for the help.

[mehnaz1985]

Hi, I am facing the same problem. however, earlier I could make successfully train with one given dataset.

[mehnaz1985]

@hoangnambui2301 could you solve the problem?

[FabianIsensee]

nnU-Net is trying to create this folder and you do not seem to have permission to create it. Please pick a path where you are allowed to write to

[mehnaz1985]

Thanks. I was trying to run in AWS platform. I have set the path in the bash and now the problem is solved.

On Tue, Aug 30, 2022, 7:57 PM Fabian Isensee @.***> wrote:

nnU-Net is trying to create this folder and you do not seem to have permission to create it. Please pick a path where you are allowed to write to

— Reply to this email directly, view it on GitHub https://github.com/MIC-DKFZ/nnUNet/issues/1130#issuecomment-1231441953, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP2WSD66TRF2EYGRQJ3AX2TV3XLKLANCNFSM56AXWXOA . You are receiving this because you commented.Message ID: @.***>

[sten2lu]

Hi @mehnaz1985 and @hoangnambui2301,

Since this issue has already been discussed and there has been no recent activity, we will close this issue in 2 weeks (Monday 14th of August). If your described issue happens to persist, please answer here so that we can solve it together.

Best, Carsten

[mehnaz1985]

Sure!

Mehnaz Tabassum

On Mon, Jul 31, 2023 at 6:39 PM sten2lu @.***> wrote:

Hi @mehnaz1985 https://github.com/mehnaz1985 and @hoangnambui2301 https://github.com/hoangnambui2301,

Since this issue has already been discussed and there has been no recent activity, we will close this issue in 2 weeks (Monday 14th of August). If your described issue happens to persist, please answer here so that we can solve it together.

Best, Carsten

— Reply to this email directly, view it on GitHub https://github.com/MIC-DKFZ/nnUNet/issues/1130#issuecomment-1657924946, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP2WSD4CLQULYHB5J5ZHKA3XS5VNVANCNFSM56AXWXOA . You are receiving this because you were mentioned.Message ID: @.***>