[MINC-users] BEaST - spatial, intensity normalizations

[Vladimir S. Fonov]

Hello,


1. in our experiments we found that it's more reliable to use a template 
based on aged population instead of MNI ICBM 2009c, for example we have 
got ADNI average template. In case of beast_normalize , you can specify 
-modeldir <location of ADNI template> -modelname model_t1w.mnc

2. you can run beast_normalize with -noreg and use file that was already 
registered in stereotaxic space.


On 15-03-16 01:47 PM, Eve M LoCastro 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?


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Best regards,

  Vladimir S. Fonov