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FSL  March 2009

FSL March 2009

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Subject:

Re: Discrepancies between feat output and fslview

From:

Lin Nga <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 5 Mar 2009 18:44:28 +0000

Content-Type:

text/plain

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text/plain (213 lines)

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
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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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