Hi all,
QSIPrep generates two segmentation maps as final outputs: *dseg.nii.gz and *aseg_dseg.nii.gz. I have two questions:
- Are these segmentation outputs used by QSIRecon?
- Are they used for any other downstream processes?
The reason I’m asking is that in *dseg.nii.gz, the white matter regions appear very restricted—some tracts are clearly missing. Could this be due to SynthSeg applying stricter criteria for white matter?
Additionally, I noticed several mislabels in *aseg_dseg.nii.gz, particularly around the brain’s outer layer. Is this expected? The major cortical areas seem correct, but the outer layer looks somewhat fragmented (looks like confetti!).
Are these results expected? My team is deciding whether to keep these segmentation maps or use our own existing methods. Any insights would be appreciated!