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Hi Rosalia,

As I mentioned before "for your white matter mask, perhaps try 0.7, 0.75, 0.8, 0.85, 0.9, 0.95 and see which one appears more accurate (i.e. do not rerun your analysis for every mask)".

Again be sure to read the link posted by Michael: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ#How_do_I_transform_a_mask_with_FLIRT_from_one_space_to_another.3F

Also be aware of Matthew's comment on introducing bias.

Hope this helps,

Bryson
 

On Fri, Sep 26, 2014 at 12:45 PM, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:

Dear Michael and Bryson, sorry for introducing myself in the conversation. I have a WM mask, a ROI mask in the contralesional hemisphere of a group of stroke subjects. The problem is that I have found significant fmri and metabolite differences and I know that there are wm differences and I think that the problem is in the threshold I am using with fslmaths (0.5).  Any suggestion about what can I do? Prove different thresholds and choose which gives me significant results is tricky....

Kind regards,
Rosalia.

El 25/09/2014 17:57, "Alshikho, Mohamad J." <[log in to unmask]> escribió:

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




--
Michael G. Dwyer, Ph.D.
Assistant Professor of Neurology and Biomedical Informatics
Director of Technical Imaging Development
Buffalo Neuroimaging Analysis Center
University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]
(716) 859-7065

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