viewing rgb FA

Questions about Anatomist manipulation

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pron.a
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Joined: Mon Feb 22, 2016 10:09 am

viewing rgb FA

Postby pron.a » Tue Feb 21, 2017 1:43 pm

Hello dear Anatomist team,

I would like to visualize fractional anisotropy colored in RGB according to the first eigen vector coordinates as done in FSLview
From the first eigen vector volume I generated a RGBa volume using the corresponding anatomist fusion method but I do not know how to say to anatomist to interpret them as "color RGB coordinates". Is there an existing functionality to do that ? I found in Brainvisa a RGB eigenvector viewer but it displays colored bars for the coordinates axis and display the rgba volume as it is ( gray scale)
If you have any hint , it would be super cool :)

Have a good day,

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riviere
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Re: viewing rgb FA

Postby riviere » Wed Feb 22, 2017 8:31 pm

Hi,
I do not completely understand what you have done, but probably not what you expect...
RGB[A] volumes are 3D volumes which contain in each voxel 3 or 4 color elements, so they can be displayed directly in anatomist. If you still see them in greyscale, then it means that they do not contain the expected information (either 3 times the same intensity, either they are not RGB volumes).
The problem, I guess, is in the transformation of the eigenvector volume to a RGB volume. How is this eigenvector volume represented ? A volume of scalars with more than 3 dimensions ? Then we don't have (yet) a conversion inside Anatomist - but we could easily do a conversion script using pyaims and numpy.
Denis

pron.a
Posts: 22
Joined: Mon Feb 22, 2016 10:09 am

Re: viewing rgb FA

Postby pron.a » Fri Feb 24, 2017 1:45 pm

Hello Denis,
thank you for you answer. Yes it is exactly what 's happening :P ! My eigen vector volume is a 4D (x,y,z,3) Volume and with the RGBAfusion method I obtain a volume with identical coordinates. Should I convert the eigenvector volume into 3D volume with "vectorial" type ?

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riviere
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Re: viewing rgb FA

Postby riviere » Tue Feb 28, 2017 12:35 pm

Hi,
If I remember, such vector data is stored in a nifti file with more than 4 dimensions. The current 4.5 version of brainvisa/aims only supports 4 dimensions, so you'll need the development version (future 4.6) if you need to deal with it. Moreover we have not made such conversion tools up to now. I can write one when I have a moment.
Denis


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