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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
>>
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