This may not be the correct answer (I have never done this myself), but it will be trial and error. Try several values and find the one that has the best fit. Applying fslmaths only takes a few seconds so I would just try a bunch of values.

Citing the website again: "For example, if the mask is being used to quantify values within an ROI and it is important to not include contamination from surrounding areas, then a high threshold should be used".

The threshold value will differ depending on the interpolation and blurring from registration.

Hope this helps,

Bryson

On Thu, Sep 25, 2014 at 11:56 AM, Alshikho, Mohamad J. <[log in to unmask]> wrote:
Hi Micheal and Bryson,
Thank you very much for your quick response.
In FSLWiki they mentioned the following "The threshold used (with fslmaths) should be set depending on the intended use of the output mask. " Let's say that I want to binarize a mask for the left hemispheric white matter and another mask for the cerebellum and I want to calculate the mean FA using fslstats with the flag K. What is the suitable threshold for my masks here is it 0.9, 0.5 or 0.1? 

Looking forward to learn from you guys

thanks,
Mohamad  
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Michael Dwyer [[log in to unmask]]
Sent: Thursday, September 25, 2014 10:42 AM
To: [log in to unmask]
Subject: Re: [FSL] Binarize a mask

Hi Mohamad,

Take a look at the following entry in the FLIRT FAQ:

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ#How_do_I_transform_a_mask_with_FLIRT_from_one_space_to_another.3F

On Thu, Sep 25, 2014 at 8:30 AM, Bryson Dietz <[log in to unmask]> wrote:
-thr <value> does not have to be between 0-1. You specify the cut off value i.e. 750 => every pixel below this intensity = 0.

On Wed, Sep 24, 2014 at 10:58 PM, M. alshikho <[log in to unmask]> wrote:
Hi FSL experts,
After FLIRT I am using fslmaths to binarize my mask using the following command line :
fslmaths mask -thr <value> -bin mask
my question is about the threshold value? I know that this value should be between 0-1 but I am wondering how can I choose this threshold correctly? what can control this value up or down between 0-1 ??

Thanks in advance
Mohamad




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Michael G. Dwyer, Ph.D.
Assistant Professor of Neurology and Biomedical Informatics
Director of Technical Imaging Development
Buffalo Neuroimaging Analysis Center
University at Buffalo
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