Hi,
On 5 Mar 2009, at 18:44, Lin Nga wrote:
> 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?
No, the "cluster" program must be run outside of FSLView
> 2. Which method does the cluster function use?
Please see the FEAT manual:
http://fsl.fmrib.ox.ac.uk/fsl/feat5/detail.html#poststats
Cheers, Steve.
>
> 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
>>>>>
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>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>
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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
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