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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.