Frequently Asked Questions
1. What are the differences among the image volume formats that MBAT supports?
MBAT requires image volumes with 3 attributes:
1. voxel size dimension (e.g. 256 x 256 x 256).
2. step size, the measured distance between two adjacent voxels in mm (e.g. 0.5x 0.5x 0.5).
The two attributes described above determine the actual measured size of the image volume ( 12.8 x 12.8 x 12.8 in the above example).
3. To overlay multiple volumes, the volume should also have a reference point, or "origin" 0.0, 0.0, 0.0 point. This location is dependent on the coordinate system one uses. One way is to define the bregma as the origin.
Analyze image volumes only have the first two attributes defined. Another compatible file format called Nifti contains all three (in fact, it can contain a complete transformation matrix for shifting, rotating and scaling, but MBAT only use the shifting and scaling information). The ImageJ generated stacked Tiff file format only contains the first two attributes. MINC file format has all three attributes.
Without this third attribute, MBAT can load volumes with the center of the volume as the origin, with the top left corner of the volume as the origin, or it can try to fit the new volume into the currently displayed space. You also can create a DuffKeg / Atlas file that include a reference point and load it in instead. Please refer to the MBAT manual for more information.
2. What is the best way to scale and translate an MRI image so that it properly coincides with the atlas?
If you have a stacked tiff from ImageJ, save it out in an Analyze format. You can then generate an analyze image header (*.hdr) with the desired voxel size and step size using the AIR "makeaheader" tool.
For the volume origin, MBAT can load volumes with center of the volume as the origin, top left corner as the origin, or try to fit the new volume into the current displayed space. Or one can create a DuffKeg / Atlas file that would include the 3rd attribute and load it instead. Please refer to the MBAT manual to see the exact format.
3. What is the best way to rotate my data volume relative to the atlas by a small arbitrary angle?
For extensive information on ways to rotate your data volume relative to the atlas we would like to refer you to the AIR site. The Automated Image Registration (AIR) package is primarily designed to solve several different registration problems that arise in tomographic data sets. The AIR package includes automated routines for aligning and reslicing tomographic image data. In addition, a number of utility routines and error checking routines are provided. The AIR library can be used to easily incorporate automated image registration into site specific programs adapted to your particular needs. Please follow this link to visit the AIR site.