This digital three-dimensional MRI atlas of
the zebra finch brain is available to the scientific community.
Detailed description of this atlas can be found in the accompanying
paper, when using this data-set in a publication of your own, please cite the following paper:
Poirier C., Vellema, M.,
Verhoye, M., Van Meir, V., Wild, J.M., Balthazart, J., Van Der
Linden, A. (2008). A three-dimensional MRI atlas of the
zebra finch brain in stereotaxic coordinates. NeuroImage,
in press. (doi:10.1016/j.neuroimage.2008.01.069).
The present web page mainly contains
information about how to visualize the data in MRIcro
environment (a free software).
we would like to keep track of who uses the atlas for our
strictly internal documentation purposes, we kindly ask you not
to re-distribute the datasets yourself but instead to refer
interested scientists to this website.
The MRI atlas data (16-bit int)
and delineation data (8-bit int) are provided in Raw data (file_name.raw), Amira
format (file_name.am) and in Analyze format (file_name.img and file_name.hdr).
Important note: Analyze files (.img
and .hdr) must be saved in the same directory.
Name of the files:
MRI brain data: atlas
MRI brain data in skull format: atlas_for_skull
CT skull data: skull
Delineation data in skull format:
To download the data, click the link underneath.
Data are available here.
MRI Data description
Resolution: 0.08*0.08*0.08 (mm)
Sequence: Spin Echo sequence
(TE/TR: 30/3000 ms), 4 averages
CT Data description
Dimensions: 300*300*512 (pixels)
Resolution: 0.08*0.08*0.08 (mm)
Definition of the stereotaxic frame
This frame was defined by the
symmetrical axis of the brain and the base of the brain on the mid-sagittal
slice tilted by 10 degrees.
The Origin was defined as the
crossing point between the mid-sagittal plane and the Commissura Posterior.
I- Visualization of the atlas dataset with MRIcro
MRIcro at http://www.sph.sc.edu/comd/rorden/mricro.html and install it
menu, Open image…[Analyse or VoxBo]
file named atlas.hdr. A horizontal view should be displayed on the right
contrast by dragging over the image while depressing the RIGHT mouse button.
the Slice Viewer section (left panel, purple spot in fig. 1) the icon
representing the three orthogonal views. The coronal view is now displayed on
the top/ left corner, the sagittal view is on the top/right corner and the
horizontal view in the bottom/left corner of the right panel.
Press on the
LR/RL icon (orange spot in fig. 1) to select SPM2 default orientation. After
this manipulation, the left hemisphere will be represented on the left side of
the coronal and horizontal views (neurological orientation). This means that now,
you look at the coronal view from the back.
II- Reading of relative coordinates
In the Slice
Viewer section, select the voxel with the following coordinates: X = 132, Y =
120, Z = 128. These coordinates are expressed in voxels. Then press the red
cross button (yellow spot in fig. 1). The red cross should target what we have
chosen as the origin of the atlas: the intersection of the posterior commisura
and the mid-sagittal plane.
To read the
coordinates related to the origin, adjust the origin in the Header Information
section (grey spot in fig. 1) to X = 125; Y = 120; Z = 128. Then press on the
icon positioned on the left side of the red cross icon (blue spot in fig. 1).
Coordinates relative to the origin will be displayed on the bottom right corner.
They are now of 0, 0, 0 since the red cross is positioned at the origin. What
you see on your screen should correspond to figure 1.
When you open
the atlas dataset, voxel size is automatically expressed in the Header
Information section in hundreds of microns (0.8 *0.8*0.8). Adjust the voxel size
to 80*80*80 (the new unit will be now microns). Now if you click on one voxel of
one view, the 3 orthogonal slices containing this voxel will be displayed.
Relative coordinates will be automatically adjusted and will be expressed in
microns (and not in mm as written on the screen). The first number corresponds
to the X value, the second one to the Y value and the third one to the Z value.
The X axis corresponds to the left/right axis (with positive values for the
right side), the Y axis corresponds to the rostral/caudal axis (with positive
values for the rostral side) and the Z axis corresponds to the dorsal/ventral
axis (with positive values for dorsal side). Absolute coordinates, expressed in
voxels in the Slice Viewer section will also be automatically adjusted.