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See The original page where exchange of Atlas State was started
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Work resumed at the end of 2006 with a focus on setting up an Atlas Server that can be used in conjunction with the API for atlas exchange. This outlines the step by step plans of the group.
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Overview:
Work resumed at the end of 2006 with a focus on setting up an Atlas Server that can be used in conjunction with the API for atlas exchange. This outlines the step by step plans of the group.
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Synopsis of intitial work plans from a meeting 1/14/07 between Willy, and UCLA:
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Synopsis of intitial work plans:
Meeting 1/14/07 between Willy, and UCLA:
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- Immediate:
- Willy will give Allan the origin and define the coordinates of SA in relation to the mouse looking at you
- Allan will generate the transformations between the atlases and give Willy a transformation for a single Paxinos slice on Tuesday
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- Willy will give Steve the source code for testing access to the server
- Steve and Heng will begin testing the atlas web-services API sent by Willy and Willy will send basic documentation and a test application for accessing this service
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Synopsis of follow up meeting 1/18/07 between Willy, Drexel, and UCLA:
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Synopsis of follow up meeting 1/18/07:
Willy, Drexel, and UCLA:
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- There was still some confusion about the coordinates used by the three systems, so to clarify, we went through them all together:
- Confirmed that all three systems have the brain situated in the coordinate frame in pretty much the same manner (NT Y coordinate may be 5 at Bregma, but it still increases going down into the brain)
- It’s a little unclear if the coronal planes used in SmartAtlas? are with the animal facing towards us or away from us, but it probably shouldn’t make too much of a difference for how we’ll likely handle the interactions
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Webservice created by Willy Wong for transformations:
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Webservice for transformations:
Created by Willy Wong
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See The original page where exchange of Atlas State was started
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2D transformations from MRI to Paxinos2001:
Below are the transformations in Montreal Neurological Institute XFM format. The transformations take into account that the origin in the images aligned is defined in the images. That is, you will need the images as well. They are included. Though the transformations are in 3 dimensions, I have edited them to two. I was not able to get the full affine transformation nor the thin plate splines to work in 2D.
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2D transformations from Paxinos 2001 to MRI:
Below are the transformations in Montreal Neurological Institute XFM format. The XFM files are text files that can be read in any text editor. Though the transformations are in 3 dimensions, I have edited them to two. I was not able to get the full affine transformation nor the thin plate splines to work in 2D. This transformations are in world coordinates (not voxel coordinates), so in order to use them, you will need the step sizes and starts contained in the mnc file header. If you can't read these mnc files, we've put the relevant information from them below the file download link.
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Since the transformation is in world coordinates and works off the Paxinos coordinate system, I expect that simply applying the transformation matrix to Paxinos coordinates should yield the appropriate location in the 2D MRI image. We will have to repeat this for every plate; tedious, but doable.
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-- AllanMackenzieGraham - 01 Feb 2007
This transformation is in World Coordinates, so in order to use them, you will need the step sizes and starts contained in the mnc file header. if you can't read these mnc files, we've put the relevant information from them below the file download link.
XFMs are text files.
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I used the MNI MINC Tools to align the images and manipulate the transformations. They tools can be downloaded at:
http://www.bic.mni.mcgill.ca/software/distribution/
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Since the transformation is in world coordinates and works off the Paxinos coordinate system, we would use these numbers to apply the matrix to our atlas to put it into the SA paxinos atlas space. He's working on the inverse transformation now.
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The transformations were produced as follows:
- Created a 3D volume from the Paxinos mouse brain atlas plates by scanning in the delineations and spacing them with blank planes.
- Aligned MRI volume to Paxinos volume using Register to calculate a full-affine transformation (12 parameter) by picking fiducial points and Mincresample to apply the transformation and resample into the same voxel space as the Paxinos volume.
- Separated both volumes in to their component 2D image with Minctoimage and selected Paxinos image closest to bregma (0.02) and corresponding MRI image.
- Aligned MRI image to Paxinos image using Register to calculate a rigid body (6 parameter) and a 9 parameter transformation by picking fiducial points and Mincresample to apply the transformation (already in the same voxel space as the Paxinos image).
- Manually edited the transformations to remove Z dimension transformations with Xfm2param and Param2xfm.
- Inverted transformations so that they convert coordinates from Paxinos atlas to MRI, rather than the other way around, with Xfminvert.
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rawtominc -zyx -xstep 0.01818 -ystep 0.01818 -zstep 0.01818 -xstart -5.50854 -ystart -1.21806 -zstart 0.02 -input NorAtlasBregma?.img NorAtlasBregma?.mnc 1 500 606
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rawtominc -zyx -xstep 0.01818 -ystep 0.01818 -zstep 0.01818 -xstart -5.50854 -ystart -1.21806 -zstart 0.02 -input PaxinosBregma?.img PaxinosBregma?.mnc 1 500 606
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- X dimension 606
- Y dimension 500
- Z dimension 1
- X step 0.01818
- Y step 0.01818
- Z step 0.01818
- X start -5.50854
- Y start -1.21806
- Z start 0.02
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- Bregma6.xfm: 6 (3 translations + 3 rotations) parameter transformation in XFM format
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- Pax2MRI6.xfm: Rigid body transformation (6 parameters, 3 translations and 3 rotations) aligning Paxinos atlas to MRI
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- Bregma9a.xfm: 9 (3 translations + 3 rotations + 3 scales) parameter transformation in XFM format
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- Pax2MRI9.xfm: 9 parameter transformation (3 translations, 3 rotations, and 3 scales) aligning Paxinos atlas to MRI
-- AllanMackenzieGraham - 01 Feb 2007
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| META FILEATTACHMENT | NorAtlasBregma?.mnc | attr="" comment="MRI image in MNC format" date="1170361441" path="NorAtlasBregma.mnc" size="304868" user="amg" version="1.1" |
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| META FILEATTACHMENT | PaxinosBregma?.mnc | attr="" comment="Paxinos Atlas image in MNC format" date="1170361476" path="PaxinosBregma.mnc" size="304868" user="amg" version="1.1" |
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| META FILEATTACHMENT | Bregma6.xfm | attr="" comment="6 (3 translations + 3 rotations) parameter transformation in XFM format" date="1170361535" path="Bregma6.xfm" size="249" user="amg" version="1.1" |
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| META FILEATTACHMENT | Bregma9a.xfm | attr="" comment="9 (3 translations + 3 rotations + 3 scales) parameter transformation in XFM format" date="1170361590" path="Bregma9a.xfm" size="191" user="amg" version="1.1" |
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| META FILEATTACHMENT | Pax2MRI6.xfm | attr="" comment="Rigid body transformation (6 parameters, 3 translations and 3 rotations) aligning Paxinos atlas to MRI" date="1170372475" path="Pax2MRI6.xfm" size="194" user="amg" version="1.1" |
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| META FILEATTACHMENT | Pax2MRI9.xfm | attr="" comment="9 parameter transformation (3 translations, 3 rotations, and 3 scales) aligning Paxinos atlas to MRI" date="1170372515" path="Pax2MRI9.xfm" size="192" user="amg" version="1.1" |
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See The original page where exchange of Atlas State was started
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Below are the transformations in Montreal Neurological Institute XFM format. The transformations take into account that the origin in the images aligned is defined in the images. That is, you will need the images as well. They are included. Though the transformations are in 3 dimensions, I have edited them to two. I was not able to get the full affine transformation nor the thin plate splines to work in 2D.
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<
< |
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-- AllanMackenzieGraham - 01 Feb 2007
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>
> |
This transformation is in World Coordinates, so in order to use them, you will need the step sizes and starts contained in the mnc file header. if you can't read these mnc files, we've put the relevant information from them below the file download link.
XFMs are text files.
Since the transformation is in world coordinates and works off the Paxinos coordinate system, we would use these numbers to apply the matrix to our atlas to put it into the SA paxinos atlas space. He's working on the inverse transformation now.
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rawtominc -zyx -xstep 0.01818 -ystep 0.01818 -zstep 0.01818 -xstart -5.50854 -ystart -1.21806 -zstart 0.02 -input NorAtlasBregma?.img NorAtlasBregma?.mnc 1 500 606
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rawtominc -zyx -xstep 0.01818 -ystep 0.01818 -zstep 0.01818 -xstart -5.50854 -ystart -1.21806 -zstart 0.02 -input PaxinosBregma?.img PaxinosBregma?.mnc 1 500 606
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- Bregma6.xfm: 6 (3 translations + 3 rotations) parameter transformation in XFM format
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