BrainVisa Talairach

Questions about BrainVisa usage and installation

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Blessy
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BrainVisa Talairach

Post by Blessy »

Is there a scaling of the brain that is done for talairaching? I read that BrainVisa uses the 3 points AC, PC, IH and a bounding box for talairaching, what is this bounding box?
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riviere
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Re: BrainVisa Talairach

Post by riviere »

Hi,
Yes, 3 scaling factors are applied along the Talairach referential axes, to make the brain match the bounding box of a "standard Talairach" brain.
Denis
Blessy
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Re: BrainVisa Talairach

Post by Blessy »

Thanks Denis. So BrainVisa uses a standard talairach base template to do the scaling. I want to recreate/output the talairached brain from BrainVisa to use in my group analysis, I wanted to know where these scaling values are stored. The .trm file only contains the translation and rotation values.
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riviere
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Re: BrainVisa Talairach

Post by riviere »

Hi,
The scaling factors are included in the .trm matrix. The 3x3 part is not limited to a rotation, but may include shearing and scaling, it's a full affine transformation matrix. However in most cases the scaling factors are close to 1. so they are maybe not really visible when looking at the .trm.
Denis
Blessy
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Re: BrainVisa Talairach

Post by Blessy »

Hi,
After running my data throught the analysis pipeline, I have a 4x3 *.trm matrix. I want to apply the transformation matrix to the Raw T1 MRI image to generate talairach T1MRI for each subject. I did the following

/tools/brainvisa/bin/AimsResample -i study2.ima -m TALAIRACH-ACPC.trm -o transformed.ima

But there is only half the brain in the output, given below is my matrix (TALAIRACH-ACPC.trm)
-155.187960 -118.471694 -89.659727
1.270859 0.059891 -0.112749
-0.040245 1.126839 0.144882
0.115250 -0.152473 1.217995

How do I get the whole brain tranformed output?
denghien
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Re: BrainVisa Talairach

Post by denghien »

Hi,

The .trm file seems correct (the command line too). Is it created by the anatomical pipeline in BrainVISA ?
The first line of the .trm file is just coordinates for a translation.
I'm wondering if the problem will be rather with the visualization in Anatomist. It would be a problem with referential of your image or windows (which contains your image).
Have you ever handled referential system in Anatomist ?
Do you use Anatomist to visualize data ? otherwise, which software do you use ?

Isa
Blessy
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Re: BrainVisa Talairach

Post by Blessy »

Yes, the .trm file is created by the anatomical pipeline in BrainVisa.

The Raw T1 MRI image I am using is 256x256x120 matrix ( or 256x256x144mm). When I played with the translation values in the .trm file (and applied AimsResample) I was able to get a fuller brain (though still looks shifted). I am using AFNI to view the file.

I guess my question is, how do I modify the .trm file to get the AC in the center of the talairach brain, so I can view it in other software as well?
Also what is the bounding box limits set for talairaching? is it the following?
intercommisure - 23mm
front to AC- 70mm
PC to back- 79mm
AC to top - 74mm
AC to left or right - 68mm
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Jean-Francois Mangin
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Re: BrainVisa Talairach

Post by Jean-Francois Mangin »

Yes your problem is that our Talairach system puts CA at the origine I guess,
leading to negative coordinates for the left of the volume, which can not be handled by our
resampling command. The solution is to add a translation as you did.

Otherwise, if you open the transformation window of Anatomist, which is dealing with
all the referentials and transformations used in Anatomist, you may find a transformation
from our Talairach referential to the MNI space. The underlying trm file is somewhere
in the distribution.

To be honest, I am not sure that our Talairach transformation is such a good choice
for group analysis, except if you design a method that do not depend strongly on
normalization, which is our usual strategy. If you have a look at the recent paper
of Perrot in Medical Image Analysis, you will see what I mean. By the way
Perrot's sulcus recognition method performs a better affine normalization
based on the sulci that must be output somewhere, I do not know exactly where,
as another trm file. This one is in my opinion much more interesting for normalization.
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