[MINC-users] BEaST - spatial, intensity normalizations

[Gabriel A. Devenyi]

Follow-up, I agree with Vlad that if your subjects are significantly
different than the MNI template brain, you will get a far better
registration if you use an appropriate target registration template.

Sidenote: bpipe-library can easily be adapted to target any MINC file as a
target for registration, it works best if head/brainmasks are also
available like MNI atlases.

-- 
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 9:24 PM, Vladimir S. Fonov <vladimir.fonov at gmail.com
> wrote:

> 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?
>>
>
>
> --
>
> Best regards,
>
>  Vladimir S. Fonov
>
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