search

EmotionCognitionLab / flywheel

Scripts and gears for use with flywheel.io
1 stars 2 forks source link

SuperBet2 does not work on fast spin echo data #58

Closed md06451 closed 1 week ago

md06451 commented 1 month ago

Hi Noah I tried, SuperBet2 on fast spin echo (FSE) data but it fails (see fsl-superbet2_Try_SkullStrip_FSE) INstead it works on whole brain data: https://uscdni.flywheel.io/#/projects/6615ba1626fa7095f409418d/sessions/66870c0cf7cdcb78af9494c3?subjectTab=session&tab=analyses https://uscdni.flywheel.io/#/projects/6615ba1626fa7095f409418d/sessions/67172c5469393b5ba92a8ad8?subjectTab=session&tab=data

on my machine bet works for FSE data.

noah10 commented 1 month ago

Can you try BET2 on your machine and see if that works for FSE data? That will help me know whether we should install a BET gear or ask Flywheel to make the BET2 gear work with FSE data.

md06451 commented 1 month ago

Hi Noah, I tried and bet2 works. However, I just noticed that bet (but not bet2) has -Z option which allows to deal with scans that have small FOV. this seems to work better with my data-to-skull strip FSE

noah10 commented 1 month ago

OK - so it sounds like you'd rather have a BET gear than have the BET2 gear work with FSE data?

md06451 commented 1 month ago

yes I think so

md06451 commented 1 week ago

@noah10 I manage to find a way out from skull-stripping the data. So this step will not be necessary. I will close the issue