MBATForum < MouseBIRN

---++Mouse BIRN Atlasing Toolkit (MBAT) Forum
Please feel free to post to the Mouse BIRN MBAT forum.  You must have an account to post to this space.  2/07
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---++++General information
   * Visit the [[MouseBIRNFAQ][Mouse BIRN FAQs page for general information]]
   * Also, visit the MBAT page for more information or to download the software and data
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---++++Documentation
   * Download the MBAT user's manual:  [[%PUBURL%/%WEB%/MBAT/MBAT_v1.1_beta_tutorial.pdf][MBAT_v1.1_beta_tutorial.pdf]]: Users documentation
   * [[FileFormats][File formats supported by MBAT]]
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---++++User's Questions
---+++++What are the differences among the image volume formats that MBAT supports?
In MBAT, it requires image volumes with 3 attributes:

1. voxel size of the dimension (i.e. 256 x 256 x 256).<br/>
2. step size, the measured distance between two adjacent voxels (i.e. 0.5x 0.5x 0.5) in mm.

The above two attributes determine the actual measured the size of the image volume ( 12.8 x 12.8 x 12.8 in the above example).

3. To overlay multiple volumes, volume should also have a reference point, or "origin" for 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(tm) image volumes only have the first two information defined.  A compatible format called [[http://nifti.nimh.nih.gov/][Nifti]] contains all three (in fact, it can contain a complete transformation matrix for shifting, rotation and scaling, but MBAT only use the shifting and scaling information).  !ImageJ generated stacked Tiff only contains the first two information.  MINC format has all three information.

Without this third information, 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 you 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.

---+++++What is the way to scale and translate an MRI image so that it properly coincides with the atlas?
If one has stacked tiff from !ImageJ, save it out to Analyze format.  Then one can generate an analyze image header (*.hdr) with desired voxel size and step size using "makeaheader" tool from [[http://air.bmap.ucla.edu/AIR5][AIR]].

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.

---+++++What is the best way to rotate my data volume relative to the atlas by a small arbitrary angle?
Use the [[http://air.bmap.ucla.edu/AIR5][AIR]] tools.

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---++++Feature Requests


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