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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. >