help > RE: Brain extraction in MRIcrogl
Jul 19, 2021  09:07 PM | Chris Rorden
RE: Brain extraction in MRIcrogl
The View/ExtractBrain menu item will call FSL's BET Brain Extraction Tool. This should handle NIfTi spatial orientations fine.
However, be aware that some FSL tools will flip the way images are stored on disk to ensure a negative determinant. These flips are stored in the NIfTI header, but can confuse tools that ignore the NIfTI SForm/QForm:

The View/RemoveHaze should also preserve spatial orientation, though disk order may be changed for RAS storage. Again, the modification is stored in the SForm/QForm, so it is lossless.

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severus Jul 19, 2021
RE: Brain extraction in MRIcrogl
Chris Rorden Jul 19, 2021
severus Jul 19, 2021
Chris Rorden Jul 20, 2021
severus Jul 20, 2021