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Subject:

RE: Significance levels for random effects analysis

From:

Jon Brooks <[log in to unmask]>

Reply-To:

Jon Brooks <[log in to unmask]>

Date:

Sun, 4 Jun 2000 12:37:19 +0100 (BST)

Content-Type:

TEXT/PLAIN

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TEXT/PLAIN (107 lines)

Thanks Karl, Jack,

Thanks for getting back to me.

Masking using the segmented cortex as a template does sound
like an interesting proposition - and perhaps more valid than a
post-hoc ROI analysis. Though I do have some ideas
about which areas might show a BOLD response, I was just
having an initial "look see" at the data using random effects.

Prior to performing the random effects (RE) analysis, I had a
look with fixed effect (FE) analysis - which gave several significant
areas of activation (corrected-p). The finding that
these areas vanished with the RE analysis wasn't unexpected,
but when I dropped the significance level I didn't obtain
the same pattern of activation (as in the FE analysis). Is this
to be expected? I guess it may have been a consequence of the
FE results being biased by a single subject (?) - or am I
missing the point?

Is there a good reference for RE/FE analysis?

Thanks again,

Jon.
_____________________________________________________
Jonathan Brooks Ph.D. (Research Fellow)
Magnetic Resonance and Image Analysis Research Centre
University of Liverpool, Pembroke Place, L69 3BX, UK
tel: +44 151 794 5629 fax: +44 151 794 5635


On Sat, 3 Jun 2000, Foucher Jack wrote:

>Dear Jon, Karl and others
>
>>
>> Dear Jon,
>>
>> > I have recently been experimenting with a random effects analysis of
>> > several trials in an fMRI study. I have 18 subjects, so I guess this is
>> > the right analysis to use. Basically, I was wondering whether I should
>> > use a corrected height threshold in the generation of the SPMs? If I do
>> > I get no supra-threshold clusters.
>> >
>> > Is it appropriate to use an uncorrected p, given that the random
>> > effects analysis is quite stringent? Is there any general consensus on
>> > the best approach to choosing p-levels in this situation?
>>
>> I am afraid exactly the same inference criteria apply to first and
>> second level analyses. I would think about any anatomical priors that
>> could be used to provede small volume correction to the p values. One
>> point you might want to take forward is that inter-subject differences
>> may include anatomical variations in the response profile. Increasing
>> the smoothing (of the con??? or beta???.img) prior to the 2nd level
>> analysis might improve your sensitivity (e.g. 8mm FWHM).
>>
>> I hope this helps - Karl
>
>I hope that the following proposition won't seems to odd !
>
>Let say that you have no clear idea of which cortical region should activate
>except that you are looking for cortical activation only.
>Why not using a mask constructed on the basis of gray matter segmentation for
>corrected p ?
>You will just have to choose a threshold from your gray matter segmentation map
>in order to put the above values to 1 and the others to 0. Than you could
>eliminate the basal ganglia by a logical routine setting to 0 every voxel
>between a certain coordinate.
>I tried this approach once just for testing the feasibility, and it allowed me
>to use less conservative threshold (although the gain was not proportional to
>the volume loss - see Matthew's pages on SVC for reasons to that).
>
>Does this sounds reasonable ? Did anyone else tried this, and what difficulty
>did they have to cope with ? The most critical point I faced was the threshold
>do use (as far as I remember, 200 seems to be resonable). Any advice on that
>point ?
>
>Since I did try this at the time of SPM99 beta and using Matthew's SVC routines
>(that gave the uncorrected p to use for equivalent corrected p), I faced a
>problem of representation : how to display the only activation falling within
>the mask (except by removing them 'by hand' from the T.img using the same mask
>- I haven't tried that) ?
>
>Thanks for any input
>Sincerely
>
>
>
>Jack
>
>_________________________________________________________________
>| Jack Foucher Universite Louis Pasteur |
>| Institut de Physique Biologique UPRES-A 7004 du CNRS |
>| 4 rue Kirschleger Tel: 33 (0)3 88 77 89 90 |
>| 67085 STRASBOURG Fax: 33 (0)3 88 37 14 97 |
>| France |
>| Faster E-mail: [log in to unmask] |
>| Other [log in to unmask] |
>|_______________________________________________________________ |
>
>



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