[Brains-users] Problems with tissue class models and linux paths

[Ronald Pierson]

The T1 image appears to be quite dark, which is why you have no csf
getting picked.  Also, the third image should be the PD if you have it.
Do you have a PD to work with, too?

If adding the T1 image to itself didn't work to brighten things up, then
you need to threshold away some of the bright stuff outside of the
brain.  The attached script is built to do this, but I don't know how
you might run it through cygwin.  Anyone know the best way to do this
with cygwin?

The first part of the script loads the image and talairach parameters
and talairach boxes for brain, occiputal and parietal lobes.  Masks are
created for the boxes.  The occiputal and parietal lobe masks are OR'ed
together (combined into a large region) and intersected with the brain
box mask, just to be sure we are only sampling a region of the scan that
is truly brain, and is far away from potential bright flares of the
arterial flow in the middle cerebral arteries, etc.  Next, the maximum
intensity of the T1 image in this area is found.  To this number, 20 (or
some other offset you desire) is added to create a new maximum
intensity.  All voxels above this are then "clipped" from the image. 
Next the new image is added to itself several times, then the clipped
areas are filled with intensity of 255, and it is saved.

This seems like a lot of work to brighten the image, but BRAINS was
built to work by default with 8 bit images, and if something in the scan
is quite bright, alot of the useful range of intensities is wasted on
parts of the scan that aren't brain.  This clips off the highest part of
the histogram so the image can be brightened and stay in the 8-bit
range.  A script could also be developed to do this on the raw image
first, and I think that process would be better, but I haven't developed
it yet.

Ronald Pierson

On Mon, 2005-09-26 at 05:45, Kevin Berne wrote:
> Hello,
> I have just put the recommendations you gave me some days ago to use and located the lines you asked for in the bash shell. Since I could not figure out how to cut-and-past them directly, I am just sending you the Image 0: Centers.... lines. In my output, they read as follows:
> 
> Image 0: Centers: 30.916 12.944 0.000
> Image 0: Permutation: 2 1 3
> Image 1: Centers: 47.856 109.182 0.000
> Image 1: Permutation: 3 1 2
> Diagnostic: class 0 labeling according to image 1 differs from first image
> Diagnostic: class 2 labeling according to image 1 differs from first image
> 
> Later on, it reads:
> 
> Image 0: Centers: 30.521 15.264 0.000
> Image 0: Permutations: 2 1 3
> Image 1: Centers: 48.987 101.076 0.000
> Image 1: Permutations: 3 1 2
> Diagnostic: class 0 labeling according to image 1 differs from first image
> Diagnostic: class 2 labeling according to image 1 differs from first image
> 
> Strangely, there is no mention of the Image 2: .... line anywhere, and I also have to pick the T2 image manually in the dialog box.
> I hope someone can make some sense of this and give me a tip what the problem might be.
> 
> Again, thank you very much in advance!
> 
> Kevin Berne
> ZI Mannheim
> 
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