Add option to use SynthSeg as alternative to recon-all
tsalo opened this issue · comments
Is your feature request related to a problem? Please describe.
Given that SynthSeg is much faster than recon-all, and more accurate than FAST, I was thinking that it might be good to provide an option to use it in sMRIPrep.
@mattcieslak has successfully integrated SynthSeg and SynthStrip into QSIPrep. For a normal T1w, he has profiled it as using about 7.5 GB memory. He might have specific recommendations for implementing a workflow in sMRIPrep, if you are interested.
Describe the solution you'd like
A --synthseg parameter that is mutually exclusive with --fs-no-reconall would work well, I think, assuming you don't want to default to SynthSeg when --fs-no-reconall is used.
Describe alternatives you've considered
I'd specifically like to make this an option for ASLPrep, so if the sMRIPrep devs don't think it's a good idea to support SynthSeg in sMRIPrep, I could adapt a workflow from QSIPrep to handle this.
Additional context
None
Sorry, we should discuss this. @oesteban has been integrating synthseg into other workflows, so it seems inevitable that it gets here sooner or later. I'm instinctively conservative here, as plenty of surefire improvements have led to a long series of bug fixes. I think it would be worth thinking about how to "prove" an alternative without a big commitment.
How would this interact with the #280 effort?
Also: #299