Sections and renderings of an averaged human brain.
The false color composite volume is constructed from MRI data, with each contrast represented in separate color channels. The weighted image values are non-linearly scaled to emphasize various aspects of human brain anatomy.
MRI provides a 3-D map of hydrogen nuclei, mostly within water molecules, weighted by nuclear spin relaxation rates. Different weighting provides slightly different information about the density and molecular environment of hydrogen nuclei.
The averaged data is from the ICBM 152 Nonlinear atlases version 2009, a set of volumetric data constructed from non-linearly coregistered averages from MRI volumes of 152 subjects.
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It seems to me that the use of different colours to show the varying degree of water would make an MRI image easier to read. Just like the satellite electromagnetic radiation images of the earth which more clearly show chemical and land use data.
Yes, generally that is true for an MRI image. So for example, skull, teeth and other bones show up black.
There are other tricks that make this not exactly true. One of the weightings (T1) is designed to make CSF (cerebro-spinal fluid in the central ventricles and surrounding the brain, mostly water) give no signal (black), while water in other tissue does result in signal (gray).
For this color image, I wanted CSF to show up dark or black, so red (T1) is brighter for more water (except CSF which is black), blue and green are darker for more water.
What software do you use to view and process MRIs? I've used aeskulap on Linux. But it's rather limited. Or maybe I just don't know how to use it to good effect. -- Allen Brown [link] Fat people don't listen to advice on diets, drunks don't listen to advice on not drinking, [and W]indows users don't listen to advice on security.... --- anonymous post on [link]
I mostly use Space Software (sorry, Windows only), because I wrote it for what I wanted to do with it.
I recommend MRIcron (Linux, Windows, Mac universal binaries) by Chris Rorden, a very nice stand-alone tool.
I also use FMRIB's FSL tools (Unix, Mac), in particular FSL View. Good (particularly the Mac version), robust for what it is built for.
The ICMB atlas is in NifTi (.nii) format. It is a simple header/flat file format, but I haven't written export tools to write color data types of this format yet.
Just like the satellite electromagnetic radiation images of the earth which more clearly show chemical and land use data.
So does that mean the areas of black have no water molecules?
There are other tricks that make this not exactly true. One of the weightings (T1) is designed to make CSF (cerebro-spinal fluid in the central ventricles and surrounding the brain, mostly water) give no signal (black), while water in other tissue does result in signal (gray).
For this color image, I wanted CSF to show up dark or black, so red (T1) is brighter for more water (except CSF which is black), blue and green are darker for more water.
--
Allen Brown [link]
Fat people don't listen to advice on diets, drunks don't listen to advice on not drinking, [and W]indows users don't listen to advice on security.... --- anonymous post on [link]
I recommend MRIcron (Linux, Windows, Mac universal binaries) by Chris Rorden, a very nice stand-alone tool.
I also use FMRIB's FSL tools (Unix, Mac), in particular FSL View. Good (particularly the Mac version), robust for what it is built for.
The ICMB atlas is in NifTi (.nii) format. It is a simple header/flat file format, but I haven't written export tools to write color data types of this format yet.