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MRtrix3 / mrtrix3

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density
http://www.mrtrix.org
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How to modify orientation when doing segmentation of MRI image #1255

Open ishtar83 opened 6 years ago

ishtar83 commented 6 years ago

Hi all! I am new to MRview-MRtrix and am trying to use it to identify brain structures in a non model animal. So I am having some issues with placing the 3 orthogonal views in an orientation which is the best for detecting the structures I am interested in. The software always presents me with the same 3 orthogonal orientations, and even if I change the orientation with the "omega" green tool which moves the camera in plane, when I then click on the screen to trace structures borders (with the "Edit" tool), the orientations go back to the original view, in which is hard to detect structures. Is there any way by which I can fix the orientation of the 3 orthogonal views in my preferred one and still be able to work (trace structure) on my preferred orientation?

Thanks a lot! Gabriella

Lestropie commented 6 years ago

Hi Gabriella,

The GUI is very intentionally designed so that the moment you attempt to perform any drawing operation on a ROI, the view camera automatically "snaps" to the axes of the ROI on which you are drawing. This guarantees that any single drawing operation is constrained to a single slice of the ROI.

We have attempted to support 3D brushes and drawing ROIs at arbitrary viewing angles in the past. But it has typically led to more confusion than satisfaction. There is a bit of discussion you can read in #10 and #155, as well as a somewhat-related feature request in #1208.

Permitting off-axis ROI drawing turns out to open up a very big can of worms from a technical perspective. While it might be theoretically possible, I don't think anyone here is particularly motivated to pursue it given how much difficulty it has caused for us in the past. Of course, if you can make a strong case for its importance, you might be able to sway someone's mind...

Cheers Rob