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Bug 2604 - document coordinate system for mouse anatomical models
| Status | CLOSED FIXED |
| 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 |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: | http://bugzilla.fcdonders.nl/show_bug.cgi?id=2602http://bugzilla.fcdonders.nl/show_bug.cgi?id=2635 |
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 http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined
Robert Oostenveld - 2014-06-15 10:10:53 +0200
given the PPT that Chung Ki sent, I have just added the section here http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined?&#details_on_the_paxinos-franklin_mouse_coordinate_system and here http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined?&#details_on_the_allen_institute_mouse_coordinate_system 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 http://scalablebrainatlas.incf.org/main/coronal3d.php?template=ABA12& and compare it with http://mouse.brain-map.org/experiment/siv/?imageId=102162303 I see that they are different The 2nd is from http://mouse.brain-map.org 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 http://mouse.brain-map.org/experiment/siv/?imageId=102162303 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 http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined?&#details_on_the_allen_institute_mouse_coordinate_system, 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 http://software.incf.org/software/atlas3d/screenshots
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 http://en.wikipedia.org/wiki/Stereotactic_surgery which does not pertain to the specific atlas at hand.
Robert Oostenveld - 2014-06-16 17:09:02 +0200
The paper http://journal.frontiersin.org/Journal/10.3389/neuro.11.004.2007/full 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.