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Bug 3206 - Tissue confusion in BEM headmodel tutorial

Reported 2016-11-07 16:41:00 +0100
Modified 2019-08-10 12:33:05 +0200
Product: FieldTrip
Component: documentation
Version: unspecified
Hardware: PC
Operating System: Windows
Importance: P5 normal
Assigned to:
Depends on:
See also:

Jens Klinzing - 2016-11-07 16:41:09 +0100

In the BEM tutorial the output of the segmentation is chosen as cfg.output = {'brain','skull','scalp'}; segmentedmri = ft_volumesegment(cfg, mri); Consequently, the order of tissues in the later output of ft_prepare_mesh is also brain, skull, scalp. From Figure 4 onwards, however, the tutorial assumes the scalp to be represented in vol.bnd(1) and the brain in vol.bnd(3), while its actually the other way around. This should affect the code for Figure 4, Figure 5, and the electrode alignment. I wasn't sure enough to edit it directly in the tutorial (dipoli doesn't run on our server), just tell me if I'm correct and I can do the edits.

Robert Oostenveld - 2016-11-07 17:05:08 +0100

(In reply to Jens Klinzing from comment #0) hmm, I recall that there is some reordering of the surfaces. The order is also different for the different MEB methods. So after vol = ft_prepare_headmodel(cfg, bnd); it could very well be that the order has changed. So unless you can show otherwise, I assume that the tutorial is actually correct. You may want to add a warning that the user should check the order, e.g. in the wiki CMS here goes the warning text.

Jens Klinzing - 2016-11-07 17:18:50 +0100

(In reply to Robert Oostenveld from comment #1) Thanks, I added the warning.

Robert Oostenveld - 2016-11-07 17:21:37 +0100


Robert Oostenveld - 2019-08-10 12:33:05 +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 on