handling more than one image belonging to one patient

[dilekozkan]

Hi!
The point I don't understand is that how UNet supports png.
I have more than one png file belonging to a patient. should I leave them separately, or collect all the files of a patient into nii.gz?
which one true? (one modality OCT - duke dataset)

[dilekozkan]

@FabianIsensee (thanks in advance, happy new years!!)
for the details:
I am using Duke OCT dataset. we have one modality. Actually 61 scans are obtained for each patient. But since there is no significant difference in consecutive images, doctors created a label for every 5 slices. 11 slices are annotated for 10 patients. (so 110 images and 110 labels are shared)
We have separate png slice files for each patient.
Should I convert this to a nii.gz format (not exactly a consecutive CT though?)
or should I let nnUnet treat each slice of each patient as a separate sample

Duke Dataset Reference:
P. P. Srinivasan, L.A. Kim, P.S. Mettu, S.W. Cousins, G.M. Comer, J.A. Izatt, and S. Farsiu,
"Fully automated detection of diabetic macular edema and dry age-related macular degeneration from optical coherence tomography images",BioMedical Optics Express,5(10), pp. 3568-3577, 2014