Problem with seg_sc_epi (nnUNetTrainer)

SCT
1

Hi guys, I’m currently working on a M1Pro Macbook Pro Sonoma 14.6.1.

I tried to install SCT 6.4 and it seems to work standalone, but when I try to segment an EPI acquisition with the related task (seg_sc_epi) it seems that there is some type of installation(?) error with nnUNet, can it be the case? (see screenshot)
I tried to reinstall the task and even the full package but the error persists.
Can you help me solve it?

CleanShot 2024-08-28 at 16.21.57@2x
CleanShot 2024-08-28 at 16.21.57@2x3180×762 234 KB

Thanks for your time and your help.
Alberto

2

Dear @albfin_98

Thank you very much for reporting this error. This is a bug with how we have packaged the EPI model. We will fix this ASAP.

In the meantime, you can fix this issue locally by performing the following steps:

  • Navigate to the folder ‘/Users/albertofinora/spinalcordtoolbox/data/deepseg_models/model_seg_sc_epi_nnunet/’
  • Create a new folder inside of this folder called ‘nnUNetTrainer’
  • Move all of the model’s files into this new folder except the file ‘source.json’, which should be left alone.

After doing this, the error should go away. If you encounter any more issues, please feel free to let us know and we will be happy to assist further. :slight_smile:

Kind regards,
Joshua

3

Dear Joshua,

with this fix now it works.

Thanks a lot for your help.

Alberto