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Bug 2604 - document coordinate system for mouse anatomical models

Reported 2014-06-05 21:53:00 +0200
Modified 2019-08-10 12:30:52 +0200
Product: FieldTrip
Component: documentation
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P5 normal
Assigned to: Chung Ki Lee
Depends on:
See also:

Robert Oostenveld - 2014-06-05 21:53:41 +0200

we need to decide and define the coordinate system for the mouse models. This is required for all 3D models, i.e. - electrode locations - geometrical description of the volume conduction model - anatomical MRI - volumetric atlas It seems to make sense to use lambda and bregma as fiducials, just like how AC and PC are used, or NAS/LPA/RPA are used in

Robert Oostenveld - 2014-06-15 10:10:53 +0200

given the PPT that Chung Ki sent, I have just added the section here and here Different coordinate systems can coexist, the only relevant point for us regarding documentation and tools is that we are consistent in naming and using them. Also for the human EEG and MEG different coordinate systems coexist. @Chung Ki: can you check that the two definitions are factually correct?

Robert Oostenveld - 2014-06-15 10:16:52 +0200

Created attachment 634 PPT that I received from Chung Ki by email on 14 June Note that I converted the PPT to PDF, otherwise it was to large to attach

Robert Oostenveld - 2014-06-15 10:32:51 +0200

(In reply to Robert Oostenveld from comment #2) If I look at and compare it with I see that they are different The 2nd is from which is directly under the responsibility of Allen Institute. The 1st is a modified version of it, processed by Rembrandt Bakker (a colleague of mine at the Donders in Nijmegen). Allen Inst. seems again a bit ambiguous w.r.t. positive and negative directions, whereas Rembrandt made the directions explicit. So my feeling is that the possible ambiguous situation regarding the two should be documented as well.

Robert Oostenveld - 2014-06-16 16:32:23 +0200

On it is visible how positive and negative relate to bregma. Positive is anterior of bregma, negative is posterior. This is consistent with the definition of the Y axis in, which is: The origin of the coordinate system is at the Bregma point. The Y-axis points from posterior (-) to anterior (+). It also means that within slice the X and Z axis are visible. The interpretation used by scalablebrainatlas is that: The X-axis points from left (-) to right (+). The Z-axis points from inferior (-) to superior (+). This means that the scalablebrainatlas coordinate system is consistent with that of the allen institute.

Robert Oostenveld - 2014-06-16 16:56:31 +0200

@Chung Ki: please download and explore

Robert Oostenveld - 2014-06-16 16:59:09 +0200

The coordinate system specified for Paxinos-Franklin mouse coordinate system is still not 100%$ confirmed. The x, y, z labels were taken from which does not pertain to the specific atlas at hand.

Robert Oostenveld - 2014-06-16 17:09:02 +0200

The paper goes with the software in the previous comment. It defines Anterioposterior positions as Z-values but does not specify X and Y directions.

Robert Oostenveld - 2014-06-16 17:12:09 +0200

(In reply to Robert Oostenveld from comment #7) wikipedia specifies latero-lateral (x) dorso-ventral (y) rostro-caudal (z) -> this is consistent with AP The x and y do make most sense like this, also in the mouse brain, so lets keep the definition at this.

Robert Oostenveld - 2014-06-16 17:18:02 +0200

Regarding the Allen inst. coordinate system: bregma is along the y-axis, is lambda also along the y-axis? To be checked.

Robert Oostenveld - 2014-06-17 14:20:05 +0200

(In reply to Robert Oostenveld from comment #9) I looked at their software, which avoids the whole complexity altogether by not showing any labels.

Robert Oostenveld - 2014-06-17 17:26:40 +0200

ft_determine_coordsys now knows how the paxinos x/y/z mapping is defined mac011> svn commit utilities/ft_determine_coordsys.m Sending utilities/ft_determine_coordsys.m Transmitting file data . Committed revision 9635.

Robert Oostenveld - 2014-07-04 13:51:39 +0200

the two important coordinate systems have now been documented.

Robert Oostenveld - 2019-08-10 12:30:52 +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