[caret-users] Intensity inhomogeneity correction problems...

[Donna Dierker]

Hi Radhika,

I can think of a few former Snyder Lab MSTP students who can recall your 
pain all too well.

Here are tools commonly used to correct non-uniformity:

* AFNI's 3dUniformize (http://afni.nimh.nih.gov/afni)
* FSL's FAST (after preprocessing with BET, also part of FSL -- 
http://www.fmrib.ox.ac.uk/fsl/fast/index.html)
* MNI's nu_correct (what you already have tried)

You can try tweaking nu_correct's parameters; you'll probably need to do 
this with the other tools, as well.

Another tool used by Wash U researchers is Avi Snyder's partitiond_gfc.  
Recently, Avi and Mischa (last name eludes me) developed an algorithm 
that combines the strengths of Avi's old partitiond_gfc program with FSL 
fast's strategy.  Harold Burton raves about the results.  I think they 
were working on publishing a paper about it, but I am unsure what its 
status is.

You have my sympathy.

Donna

On 07/25/2008 10:49 AM, Radhika Palkar wrote:
> Hello,
>  My question is regarding the intensity inhomogeneity in my MRI images. In
> addition to the intensity problems, my images also have a poor signal to noise
> ratio due to the use of a surface coil in our imaging experiments. I am using
> freesurfer for cortical reconstruction and the program that is supposed to
> correct for the intensity inhomogeneity is called "mri_nu_correct.mni"
> (http://www2.bic.mni.mcgill.ca/software/advanced_processing/) which does
> improve the images but only to an extent. We are still having trouble running
> them through the automatic segmentation step. I was looking at the caret
> software to be able to solve the problem but the image that the tutorial says
> won't work because of non-uniform intensity, looks just like our images. Can
> anyone suggest a software or a method to overcome this problem?
>
> Sincerely,
>
> Radhika
>
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