Comments (2)
@stelatopalova you need nnUNetV1 to generate the pickle files, nnUNetV2 generates .json files. If you run the install script scripts/install.sh
, it should install the correct version:
3D-TransUNet/scripts/install.sh
Line 13 in 190fe40
Alternatively, you can install nnunet v1 in a separate env, and run preprocessing commands from there. The confusion I think is because on the nnUNet github repo the default is to install v2. Then, you can run a command similar to:
nnUNet_plan_and_preprocess -t 501
,
or if you want a particular planner for 2d/3d setups for example:
nnUNet_plan_and_preprocess -t 501 -pl2d ExperimentPlanner2D_v21 -pl3d None
, (this will create planner only for a 2D setup) or you can add/remove pl2d/pl3d flags and set them appropriately etc.
You need to make sure that you have previously exported all the right environment variables, they have the same names as in scripts/train.sh
Hope this helps
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@dimitar10 Thank you for your help! The confusion came because I was following the readme file of 3D-TransUNet and the link of the preprocessing goes to nnunetv2. I now have the preprocessing files I need.
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