Pierre-Louis Benveniste
Pierre-Louis Benveniste
Thanks for the feedback @joshuacwnewton ! 😃
Hi ! Can you explain what installation you did to get this ?
I am having the same problem so I looked at the code and it seems that in the latest version of nnunetv2, the trainer is not built the same way....
Thanks for the solution @SergioRodLla ! It worked for me as well.
Eventhough, I don't have a correct spinal cord segmentation (WM/GM) for this image, I solved the problem of failing inference. The problem came from the image header (even though I...
Here is the result with `sct_deepseg -i thor_3d_10.nii.gz -task seg_mice_sc`  The result with `sct_deepseg -i thor_3d_10_mul.nii.gz -task seg_mice_sc` (on the multiplied by -1 image) 
FInally, the model `seg_mice_gm` doesn't segment anything on both the image and the image multiplied by -1.
You're right sct_image -transpose would have been easier!
I also tried changing the resolution to try human segmentation models. (resolution was changed from [1,0.001,0.001] to [10,0.01,0.01] (in mm). The `seg_exvivo_gm-wm_t2` created empty masks on the image. However, on...
@jcohenadad Are there other investigations that you have in mind?