No, we're aligning on other programs using this convention, we won't change it.
It might be that my computer is too old, but even if the segmentation is really fast (<60min), then the importation is also taking ~1hour. It seems that the nearest neighbour search step is taking a lot of time.
Indeed, this is terrible, but it will get faster soon.
The CAT developers are working on a new version of CAT12 that will include much faster algorithms to project the FSAverage atlases to the subject space.
When using the overlay option to display segmentation over MRI, it's actually hard to see the anatomical MRI under the segmentation. And the transparency cursor doesn't change anything.
It's the transparency slider in the panel Data options that you should adjust.
also, for my personal knowledge, do you think it could be possible to refine this segmentation using an additional T2 image ?
Quick question, what is the surface used for the cortex ?
I'm sorry, I'm not sure what you're asking for here. Can you be more specific?