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Bug 2707 - implement ft_volumerealign based on fiducial clicking in 3D skin surface mesh

Reported 2014-09-27 12:18:00 +0200
Modified 2019-08-10 12:29:06 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P5 normal
Assigned to:
Depends on:
See also:

Robert Oostenveld - 2014-09-27 12:18:40 +0200

this is the code we now use, it results in a 3D MRI slice view in which the ears are difficult to make sense of. It would be much easier if it were based on a 3D rendering. cfg = []; cfg.method = 'interactive'; cfg.coordsys = 'neuromag'; [mri_realigned] = ft_volumerealign(cfg, mri);

Tzvetan Popov - 2014-09-27 20:29:17 +0200

Would you be able to see the vitamin E markers then?

Jan-Mathijs Schoffelen - 2014-10-28 16:44:41 +0100

It seems that Robert has implemented this, correct?

Robert Oostenveld - 2014-10-29 10:13:19 +0100

added cfg.viewmode=ortho|surface to allow fiducials to be clicked on head surface (see Also overhauled the general documentation, removing the already obsolete landmark method (which is now a special case of fiducial). mac011> svn commit Sending ft_electroderealign.m Sending ft_volumerealign.m Transmitting file data .. Committed revision 9928. @Tzvetan: you might or might not see the vitamin E markers, as they will not be reliably segmented and converted to the surface mesh. The surface method is especially useful if there are no markers, and you have to click on specific points of the ears.

Robert Oostenveld - 2014-10-29 10:15:46 +0100

Jan-Mathijs, could you review the updated help of ft_volumerealign?

Jan-Mathijs Schoffelen - 2014-10-29 10:27:56 +0100

Sure. Done.

Robert Oostenveld - 2019-08-10 12:29:06 +0200

This closes a whole series of bugs that have been resolved (either FIXED/WONTFIX/INVALID) for quite some time. If you disagree, please file a new issue describing the issue on