[MINC-users] BEaST - spatial, intensity normalizations

[Gabriel A. Devenyi]

Hi Eve,

I suggest you look into using an alternative method to transform your brain
to MNI space, such as mincANTS

I wrote a fully automated pipeline that does BeAST with some of the stages
improved, see https://github.com/CobraLab/minc-bpipe-library

If you take a look at beast_normalize, its a script that consists of an N3
correction, an affine registration and a intensity normalization, all as
separate commands. If you choose to do one of those steps by yourself, you
can still use the other stages, while skipping some of the stages (see
-help for the "no" options).



-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Mon, Mar 16, 2015 at 1:47 PM, Eve M LoCastro <evl2001 at med.cornell.edu>
wrote:

> Dear BEaST-masters,
>
> I am a newcomer to the MINC toolkit, but I have recently begun testing
> BEaST for skull-stripping in our pipeline and thoroughly enjoying the
> results. Thank you for this great tool.
>
> I have two questions regarding tweaking and modifying the normalization to
> MNI space, and the intensity normalization that is applied to the image.
>
> 1. With some aged and atrophic brains, sometimes the transformation to MNI
> is a little bit off when using beast_normalize. Are there any
> tweaks-to-parameters that I could employ in these subjects to improve the
> matching to the template. (current command usage: beast_normalize head.mnc
> head_mni.mnc anat2mni.xfm -modeldir $MincLibPATH)
>
> 2. If I am still unsatisfied with the spatial normalization results from
> the MINC toolkit,  can I use a transformed MNI image from an alternate
> program (ie FSL, SPM)? If so, what kind of intensity normalization do you
> suggest I apply to best match the smoothed intensity of images in the
> included libraries?
>
>
> Much thanks,
>
> Eve
>
>
> Eve M. LoCastro
> Staff Associate in Radiology
> Imaging Data Evaluation and Analytics Lab (IDEAL)
> Weill Cornell Medical College
> 515 E. 71st St S118
> Tel: 212-746-1289
> Fax: 212-746-4189
> http://ideal-cornell.com/<http://ideal-cornell.com>
>
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>