Generated Segmentations do not follow image geometry

[FabianIsensee]

I would expect outputs to follow the image geometry (spacing etc) unless specified otherwise. However the segmentations are always saved in 1x1x1 spacing. This is likely due to a bug in preprocess which overwrites the original affine of the image with the resampled one in this line, so that the postprocessing function cannot resample back

SynthSeg/SynthSeg/predict_synthseg.py

Line 451 in 2a2aa3b

im, aff = edit_volumes.resample_volume(im, aff, im_res)

Later when the postprocess function tried to resample back to the original image affine, it receives the preprocessed instead of the original affine

Best,
Fabian

[BenBillot]

Hi again,

no it's not a bug, this was the intended behaviour (at least at the time of creation of this repo), just because a lot of analysis is performed at 1x1x1mm.

I agree that there should be a flag to disable this behaviour and to preserve the input geometry. We actually added this feature a while ago on the Freesurfer version, where you can simply use the --keepgeom flag.

I also wanted to add this feature to the github version, but that's about when I lost access to my original github account...

if you want to fix this thing directly in the code, you'll still have to resample the images to be 1x1x1 (because that's the training resolution of the network), but then you can resample them back to the original res. See here how we implemented it for the freesurfer version: https://github.com/freesurfer/freesurfer/blob/dev/mri_synthseg/mri_synthseg

Hope this helps!
Benjamin