help > Brain extraction in MRIcrogl
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Jul 19, 2021  08:07 PM | severus
Brain extraction in MRIcrogl
2 questions:
- when extracting brain in mricrogl does it maintain the left/right orientation or can this get lost e.g in MRIcro
- when displaying a 3D render and the 2D image side by side is it possible to display the crosshairs on the render and yoke the 2? This would really make such a huge difference!

Thanks in advance!
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.
Jul 19, 2021  11:07 PM | severus
RE: Brain extraction in MRIcrogl
That’s great, thank you so much. Could you please advise whether it is possible to display crosshairs on the 3D render on mricroGL and to yoke with the 2D slices? Thank you so much,
Jul 20, 2021  03:07 PM | Chris Rorden
RE: Brain extraction in MRIcrogl
You should try out the pre-release
this includes a new feature
specifically, choose View/Multiplanar(A+C+S+R) to see four views simultaneously: the axial, coronal, sagittal and rendering. Clicking on the rendering will show you the corresponding location on the 2D slices.
Attachment: mprR.jpg
Jul 20, 2021  10:07 PM | severus
RE: Brain extraction in MRIcrogl
Amazing, thank you so much