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I do not know the answer to this. But I would assume for every registration, you could use a different threshold value, since each mask will be interpolated differently. Perhaps, if I am incorrect, an expert can comment on this. Cheers, Bryson On Thu, Sep 25, 2014 at 12:57 PM, Alshikho, Mohamad J. < [log in to unmask]> wrote: > Thank you very very much. This is helpful > One more question. In a list of subjects (two groups) can I use different > thresholds in fslmaths i.e every subject has it's own threashold?? or it > should be the same value for all the subjects? > > > > ------------------------------ > *From:* FSL - FMRIB's Software Library [[log in to unmask]] on behalf of > Bryson Dietz [[log in to unmask]] > *Sent:* Thursday, September 25, 2014 12:44 PM > > *To:* [log in to unmask] > *Subject:* Re: [FSL] Binarize a mask > > 0.9 and 0.1 should result in * extremely different masks*, so you > should find very different statistics. > > When you visualize the masks in FSLVIEW, which one appears to overlay the > white matter more closely? > > I am saying 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). > > The thresholding is used to re-binarize your mask following the > interpolation and blurring from registration. > > On Thu, Sep 25, 2014 at 12:36 PM, Alshikho, Mohamad J. < > [log in to unmask]> wrote: > >> Hi Bryson, >> The reason why I am not sure about the suitable threshold, because it can >> change the final results dramatically from significant to non significant. >> i.e I have 50 subjects and I want to check if there is any significant >> difference in the mean FA between two groups (23 Patients and 27 controls); >> I created a mask for the left hemispheric white matter and I registered >> (FLIRT) this mask to the FA map for every subject then I used fslmaths >> (after FLIRT) with a threashold 0.9 for all the subjects. I repeated this >> process for the threashold 0.1 in fslmaths. I used fslstats dti_FA -K >> <mask> -M for the subjects with 0.9 and then for the subjects with 0.1. Now >> I have two lists of mean FAs (for the two groups) the first one for >> fslmaths ( 0.9 ) and the second one for fslmaths (0.1). I ran simple two >> tailed t.test for the first list (0.9) and for the second list (0.1) . I >> found that the results are significant in 0.9 and not significant for 0.1!!! >> >> I can't understand this point. The threshold in fslmaths can affect the >> final results >> kindly do you have any interpretation for this difference in the results? >> Thanks >> Mohamad >> >> >> ------------------------------ >> *From:* FSL - FMRIB's Software Library [[log in to unmask]] on behalf of >> Bryson Dietz [[log in to unmask]] >> *Sent:* Thursday, September 25, 2014 12:03 PM >> >> *To:* [log in to unmask] >> *Subject:* Re: [FSL] Binarize a mask >> >> 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 >>>>> >>>> >>>> >>> >>> >>> -- >>> 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. >>> >> >> >