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

[John Harwell]

Radhika,

AFNI's 3dUniformize algorithm is available within Caret by selecting  
Volume Menu->Anatomy->Bias Correction in the GUI or by using  
"caret_command -volume-bias-correction" on the command line.

-----------------------------------
John Harwell
john at brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Jul 25, 2008, at 11:12 AM, Donna Dierker wrote:

> 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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>>
>
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