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Hi Steve, That really clarified it, thank you! I have a couple more questions: 1. Is there a way to perform cluster-based thresholding in FSLView? 2. Which method does the cluster function use? Thank you, Lin On Thu, 5 Mar 2009 05:30:20 +0000, Steve Smith <[log in to unmask]> wrote: >Hi, the reason that just thresholding voxelwise the zstat image >doesn't look like thresh_zstat is probably because you chose a >different method than voxelwise thresholding in FEAT ;-) > >If you chose cluster-based thresholding then only clusters large >enough to be significant will have been included in thresh_zstat - so >that's not the same as just thresholding voxelwise in FSLView. > >Cheers. > > >On 5 Mar 2009, at 00:57, Lin Nga wrote: > >> Liam >> >> Typing 2.3 into the min box works just fine. My question is just, >> why is it >> that for the same given range, my zstat does not look like my >> thresh_zstat >> image? From my understanding, thresh_zstat is the thresholded z >> statistics >> image and zstat is the raw z statistics image; is this wrong? If I >> play >> around with the threshold with the zstat image, does this not tell me >> anything significant? >> >> Thanks again, >> Lin >> >> On Wed, 4 Mar 2009 16:40:34 -0800, Nestor, Liam (Contractor) >> <[log in to unmask]> wrote: >> >>> Lin >>> >>> Overlay the thresh_zstat. When you do this, your underlay image >>> should be >> entirely covered by (but you should able to see signs of clusters >> underneath). Now type 2.3 into the min box. Does typing 2.3 (your z >> stat >> threshold as used in FEAT) still leave the brain very covered in >> activity? >> If so, playing around with the min value (e.g., try typing 2.81 >> which is >> p=0.005) might give you a better idea of thresholding for an >> additiona/futurel FEAT analysis. >>> >>> Your axial (horizontal) image map in fslview should look like that >>> in the >> report. I have just checked some of my files to confirm this. >>> >>> Liam. >>> >>> >>> >>> >>> ******************************************* >>> Liam Nestor, Ph.D >>> Office C8-523 >>> Laboratory for Molecular Neuroimaging >>> Semel Institute for Neuroscience and Human Behavior >>> 760 Westwood Plaza >>> Los Angeles 90024 >>> Tel: 310-206-0655 >>> E-mail: [log in to unmask] >>> ******************************************* >>> ________________________________________ >>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf >>> Of Lin >> Nga [[log in to unmask]] >>> Sent: Wednesday, March 04, 2009 4:13 PM >>> To: [log in to unmask] >>> Subject: Re: [FSL] Discrepancies between feat output and fslview >>> >>> Hi Liam, >>> >>> Thank you for your response. Typing 2.3 into the min box does >>> indeed make >>> the image look like the feat output but that wasn't really my main >>> confusion. What I'd like to know is that if I overlay the raw zstat >>> file and >>> change the min and max threshold to reflect those given in the feat >>> report ( >>> 2.3 and 3.4 respectively ), this does not look anything like the feat >>> report. If I want to play around with the threshold to see if this >>> affects >>> my results, should I not be doing so with the zstatX.nii.gz and use >>> thresh_zstatX.nii.gz instead? But isn't the thresh_zstatX.nii.gz >>> image a >>> result of thresholding at 2.3? >>> >>> Thanks, >>> Lin >>> >>> On Wed, 4 Mar 2009 14:49:12 -0800, Nestor, Liam (Contractor) >>> <[log in to unmask]> wrote: >>> >>>> Lin >>>> >>>> I think what is happening here is you are thresholding at 2.3 in >>>> your FEAT >>> analyses; the end product of which is a FEAT report telling you >>> that the >>> range is from 2.3 (min) to 3.4 (max). >>>> >>>> When you overlay your thresholded zstat file on top of your >>>> 152MNI, you >>> need to type 2.3 into the min box provided. >>>> >>>> Try doing this and see what happens. >>>> >>>> Liam. >>>> >>>> ******************************************* >>>> Liam Nestor, Ph.D >>>> Office C8-523 >>>> Laboratory for Molecular Neuroimaging >>>> Semel Institute for Neuroscience and Human Behavior >>>> 760 Westwood Plaza >>>> Los Angeles 90024 >>>> Tel: 310-206-0655 >>>> E-mail: [log in to unmask] >>>> ******************************************* >>>> ________________________________________ >>>> From: FSL - FMRIB's Software Library [[log in to unmask]] On >>>> Behalf Of Lin >>> Nga [[log in to unmask]] >>>> Sent: Wednesday, March 04, 2009 2:47 PM >>>> To: [log in to unmask] >>>> Subject: Re: [FSL] Discrepancies between feat output and fslview >>>> >>>> I also want to add a couple more thing I noted. I opened up the >>>> thresh_zstat >>>> in fslview, which should look like what is displayed on the feat >>>> report (and >>>> it does as expected), and the threshold ranges from 0 to 2.9. Why >>>> does the >>>> range on the feat report say 2.3 to 3.4 when the thresholded image >>>> goes from >>>> 0 to 2.9? Could someone please explain what is going on here? >>>> >>>> Thanks for the help, >>>> Lin >>>> >>>> On Wed, 4 Mar 2009 21:38:13 +0000, Lin Nga <[log in to unmask]> wrote: >>>> >>>>> Hi everyone, >>>>> >>>>> I am looking at one zstat image for one cope of a group analysis. >>>>> I have the >>>>> zstat overlay the bg_image in fslview and I adjusted the >>>>> threshold to match >>>>> that of the feat output (in my case 2.3 to 3.4). What I see in >>>>> fslview does >>>>> not look like what I see in the feat output. What is wrong here? >>>>> Shouldn' >>>>> the two look the same? Am I looking at the wrong statistical image? >>>>> >>>>> Thank you so much, >>>>> Lin >>>> >>>> IMPORTANT WARNING: This email (and any attachments) is only >>>> intended for >>> the use of the person or entity to which it is addressed, and may >>> contain >>> information that is privileged and confidential. You, the >>> recipient, are >>> obligated to maintain it in a safe, secure and confidential manner. >>> Unauthorized redisclosure or failure to maintain confidentiality >>> may subject >>> you to federal and state penalties. If you are not the intended >>> recipient, >>> please immediately notify us by return email, and delete this >>> message from >>> your computer. >>> >>> IMPORTANT WARNING: This email (and any attachments) is only >>> intended for >> the use of the person or entity to which it is addressed, and may >> contain >> information that is privileged and confidential. You, the >> recipient, are >> obligated to maintain it in a safe, secure and confidential manner. >> Unauthorized redisclosure or failure to maintain confidentiality may >> subject >> you to federal and state penalties. If you are not the intended >> recipient, >> please immediately notify us by return email, and delete this >> message from >> your computer. >> > > >--------------------------------------------------------------------------- >Stephen M. Smith, Professor of Biomedical Engineering >Associate Director, Oxford University FMRIB Centre > >FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >+44 (0) 1865 222726 (fax 222717) >[log in to unmask] http://www.fmrib.ox.ac.uk/~steve >---------------------------------------------------------------------------