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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 >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >