[Mristudio-users] Noise level setting for AIR in DTI Studio

[Patrick Rizzuto]

My colleague and I are also experiencing a problem that I suspect may be related to this.  While preparing a B0 file for distortion correction LDDMM, I attempt to normalize the intensities of the B0 file as well as a related T2 file.  In another step, I also strip the skull from the T2 image.

I have found, however, that while intensity normalization appears to work normally BEFORE stripping the T2-skull, attempting to do so AFTER skull-stripping results in a halo appearing on the updated image, radiating out a little ways from the brain.  My colleague and I also experienced this last week, while attempting to prepare a separate set of images for nonlinear LDDMM.

The reason why I ask this as a reply to this particular thread, however, is because I am now concerned that this halo-generation may be in part due to the noise threshold I set previously being too low - the value I have been working with is 20.  While the problem appears to be solved simply by reordering the relevant steps, I want to make sure this is not symptomatic of a noise threshold problem.  Are the two at all related?

Thank you,
Pat Rizzuto - JHU Center for Imaging Science

----- Original Message -----
From: susumu mori <susumu at mri.jhu.edu>
Date: Wednesday, September 9, 2009 3:22 pm
Subject: Re: [Mristudio-users] Noise level setting for AIR in DTI Studio
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>


> If you have two repeated sets of DTI, yu can easily see the degree of
>  motion by showing substraction images. When AIR is working, you can
>  see that the subtraction images become just noises. The subtraction
>  images can be created by the "mean, STD" button.
>  
>  The threshold for AIR is empirical. When it's too low, AIR trys to
>  match noises and motion may not be corrected. When it's too high, the
>  brains are not well defined and the results deteriorates. In between
>  these is a range of values AIR works. You have to figure it out
>  although once you find it you can keep using the same value for other
>  data from the same scanner.
>  
>  On 9/9/09, [Seongjin] <choisj70 at gmail.com> wrote:
>  > Dear all,
>  >
>  > I heard of that empirical noise level is 40 for AIR in DTI Studio 
> and AIR
>  > is
>  > sensitive to the noise level.What kind of differences we should 
> know about
>  > AIR between using higher noise level and lower noise level?
>  >
>  > -SC
>  >
>  
>  -- 
>  Sent from my mobile device
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