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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 ---------------------------------------------------------------------------