Auto3DSeg for Multi-Modal/Phase Input

[moonforsun]

[Update on 01/03/2023]: The solution is using 4D data preparation. Project-MONAI/MONAI#5592 (comment)

I am interested in how to get the auto3dseg work for the multi-phase/modal images as input.
I can run the Task04_Hippocampus example but failed on my own multi-phase data.
My failure issue can be found here: Project-MONAI/MONAI#5592.

[KumoLiu]

Hi @moonforsun, from the error message, It looks like you didn't prepare your data properly. Could you please prepare your data referring to this JSON file?
https://github.com/Project-MONAI/tutorials/blob/main/auto3dseg/tasks/msd/Task04_Hippocampus/msd_task04_hippocampus_folds.json
Hope it can help you, thanks!

[moonforsun]

[Update on 01/03/2023]: The answer is: Preparing the data in a 4D nifty can be the solution for this. Project-MONAI/MONAI#5592 (comment)

@KumoLiu Thank you for your reply. Yes, the issue here is indeed due to the JSON. The reason is that I have multiple phase data for each case.

Single phase/modality data that can be run in current Auto3DSeg version:
{
"testing": [
{
"image": "imagesTs/hippocampus_267.nii.gz"
},
{
"image": "imagesTs/hippocampus_379.nii.gz"
},
...
}

Multiple phase/modality data that has the issue as in Project-MONAI/MONAI#5592:
{
"testing": [
{
"image": ["imagesTs/phase1.nii.gz", "imagesTs/phase2.nii.gz"]
},
{
"image": ["imagesTs/phase1.nii.gz", "imagesTs/phase2.nii.gz"]
},
...
}

Any suggestion of how should I prepare JSON for multiple phase data? Or any idea to support the multiple phase data as input for the Auto3DSeg?

[KumoLiu]

Hi @moonforsun, seems we didn't have an example about multiple modalities in auto3dseg. A simple way to do that is to concat modalities in the channel dim like this tutorial.
Thanks!

[moonforsun]

Preparing the data in a 4D nifty can be the solution for this. Thank you @KumoLiu for your nice reference to the tutorial.