MouseBIRN.MBATForum (r1.1 vs. r1.5)
Diffs

 <<O>>  Difference Topic MBATForum (r1.5 - 22 Jun 2007 - JylBoline)

META TOPICPARENT MBAT

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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  • Also, visit the MBAT page for more information or to download the software and data

Documentation

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<		 Download the MBAT user's manual: MBAT_v1.1_beta_tutorial.pdf: Users documentation
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User's Questions

What are the differences among the image volume formats that MBAT supports?

 <<O>>  Difference Topic MBATForum (r1.4 - 20 Feb 2007 - JylBoline)

META TOPICPARENT MBAT

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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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.

Changed:
<
<		 Analyze(tm) image volumes only have the first two information defined. A compatible format called 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.
>
>		 Analyze(tm) image volumes only have the first two information defined. A compatible format called 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.

Changed:
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<		 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.
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>		 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?
Changed:
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<		 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 AIR.
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>		 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 AIR.

Changed:
<
<		 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.
>
>		 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 AIR tools.

 <<O>>  Difference Topic MBATForum (r1.3 - 20 Feb 2007 - HengYuan)

META TOPICPARENT MBAT

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
Line: 12 to 12

 Download the MBAT user's manual: MBAT_v1.1_beta_tutorial.pdf: Users documentation

User's Questions

Added:
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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).
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 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 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 AIR tools.

User's Feedback


 <<O>>  Difference Topic MBATForum (r1.2 - 08 Feb 2007 - JylBoline)

META TOPICPARENT MBAT
Changed:
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<		 Visit the Mouse BIRN FAQs page for general information
>
>

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

General information

Documentation

Download the MBAT user's manual: MBAT_v1.1_beta_tutorial.pdf: Users documentation

User's Questions


Changed:
<
<		 Please feel free to post to the Mouse BIRN MBAT forum. You must have an account to post to this space.
>
>

User's Feedback


Changed:
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<		 2/07
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Feature Requests



 <<O>>  Difference Topic MBATForum (r1.1 - 05 Feb 2007 - JylBoline)
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Added:
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META TOPICPARENT MBAT
Visit the Mouse BIRN FAQs page for general information

Please feel free to post to the Mouse BIRN MBAT forum. You must have an account to post to this space.

2/07


Topic: MBATForum . { View | Diffs | r1.5 | > | r1.4 | > | r1.3 | More }

Revision r1.1 - 05 Feb 2007 - 18:17 - JylBoline
Revision r1.5 - 22 Jun 2007 - 23:06 - JylBoline