Mark,
thank you. Two (final) questions:
1) how is zstat different from tstat then (given they both are defined
as cope/sqrt(varcope))?
2) am I correct in interpreting your mail that comparing various zstats
obtained with a 'standard' FEAT high level (with the option of grand
mean scaling) session means comparing EVs' regression coefficients
(scaled such that m=0 and sd=1) [hence allowing me to compare across
runs/sessions]?
thank you for the clarification,
martin
Mark Woolrich wrote:
> Martin,
>
> zstat is COPE/sqrt(VARCOPE)
>
> To allow for higher-level analyses which compare EVs from different
> sessions (or runs), we strongly recommend that you do grand mean
> scaling, in which the whole 4D data set is normalised by a single
> scaling factor (each volume is scaled by the same amount), so that
> datasets from different sessions have the same grand mean. This
> controls for between session variability in the scaling of intensities
> the scanner spits out. The COPEs themselves should then be comparable
> between sessions.
>
> Grand mean scaling is the default in Feat.
>
> Cheers, Mark.
>
> ----
> Dr Mark Woolrich
> EPSRC Advanced Research Fellow University Research Lecturer
>
> Oxford University Centre for Functional MRI of the Brain (FMRIB),
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
>
> Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich
> <http://www.fmrib.ox.ac.uk/%7Ewoolrich>
>
>
>
>
> On 1 Nov 2006, at 16:14, Martin M. Monti wrote:
>
>> Steve,
>>
>> I just now realized that when saying PE vs COPE I in fact meant
>> (CO)PE vs ZSTAT.
>>
>> Just to make sure I understand, zstat is COPE-mean(COPE)/sqrt(VARCOPE)?
>>
>> my point is that I compare patterns of activations across different
>> EVs, and some are collected in separate runs (with a run being
>> machine ON to machine OFF), hence comparing measures that do not
>> account for differences in signal mean and variability across runs I
>> may be getting non-interpretable results.
>>
>> cheers
>> martin
>>
>> Steve Smith wrote:
>>> Hi Martin,
>>>
>>> On 31 Oct 2006, at 20:35, Martin M. Monti wrote:
>>>
>>>> Dear Lords of FSL,
>>>>
>>>> I have a simple question re the contents of the PE and COPE images.
>>>>
>>>> At a first level (single sub - single run) PE1 is a matrix
>>>> containing the GLM parameter estimate (b) for each voxel for EV1.
>>>> If I created a contrast with (say) a 1 in EV1 and zeros in all
>>>> other EVs I would then get COPE1 to be in fact the same thing as
>>>> PE1 except it's a beta as opposed to a non standardized estimate
>>>> (i.e. b). [the betas are what I need..]
>>>>
>>>> So far so good (right? ..I think we previously discussed this
>>>> already..)
>>>
>>> Not quite - in this case (contrast [1 0 0...]) then COPE1 is
>>> _exactly_ PE1 - neither is standardised in any way at this point.
>>> PE1 is the beta, and for this contrast COPE1=PE1.
>>>
>>> I'm not sure what distinction you're making between b and beta. In
>>> the GLM:
>>> Y=Xb+e
>>> Then b (ie beta) is the parameter estimates.
>>>
>>>> Now, say that I have multiple runs and multiple subjects, and all I
>>>> do is average (i.e. no subtractions) EV1 across multiple sessions
>>>> (for each given subject) and across multiple subjects.
>>>> This group analysis will yield again a PE1 and a COPE1 (obtained
>>>> again just by creating a contrast with 1 in all EV1s and 0 for all
>>>> other EVs).
>>>>
>>>> Are the EP1 and COPE1 matrices just (group) average bs and (group)
>>>> average betas, respectively?
>>>
>>> Apart from the fact that the "bs" _are_ the betas, then yes, the
>>> rest is correct.
>>>
>>> Cheers, Steve.
>>>
>>>
>>>>
>>>> cheers
>>>> Martin
>>>>
>>>>
>>>> --
>>>>
>>>>
>>>>
>>>> --------------------------------------------
>>>> "Upward, not Northward!" [Edwin Abbott - FlatLand]
>>>> I became insane, with long intervals of horrible sanity. [E.A. Poe]
>>>> Would you tell me, please, which way I ought to go from here?
>>>> ''That depends a good deal on where you want to get to.'' Said the
>>>> Cat. I don't much care where -- Said Alice. Then it doesn't matter
>>>> which way you go, said the Cat. [Lewis Carroll]
>>>> Che si trattasse di una gara? ..Un colpo il mondo e un colpo tu, a
>>>> chi stupiva un po' di piu'.. [Per Un Vecchio Bambino - Roberto
>>>> Vecchioni]
>>>> --------------------------------------------
>>>> Martin M. Monti
>>>> Princeton University
>>>> Department of Psychology
>>>> Green Hall 3-S-8
>>>> (609) 258-5679
>>>> --------------------------------------------
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> 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] <mailto:[log in to unmask]>
>>> http://www.fmrib.ox.ac.uk/~steve
>>> ---------------------------------------------------------------------------
>>>
>>
>> --
>>
>>
>>
>>
>> --------------------------------------------
>> "Upward, not Northward!" [Edwin Abbott - FlatLand]
>> I became insane, with long intervals of horrible sanity. [E.A. Poe]
>> Would you tell me, please, which way I ought to go from here? ''That
>> depends a good deal on where you want to get to.'' Said the Cat. I
>> don't much care where -- Said Alice. Then it doesn't matter which way
>> you go, said the Cat. [Lewis Carroll]
>> Che si trattasse di una gara? ..Un colpo il mondo e un colpo tu, a
>> chi stupiva un po' di piu'.. [Per Un Vecchio Bambino - Roberto Vecchioni]
>> --------------------------------------------
>> Martin M. Monti
>> Princeton University
>> Department of Psychology
>> Green Hall 3-S-8
>> (609) 258-5679
>> www.webmartin.net
>> --------------------------------------------
>
--
--------------------------------------------
"Upward, not Northward!" [Edwin Abbott - FlatLand]
I became insane, with long intervals of horrible sanity. [E.A. Poe]
Would you tell me, please, which way I ought to go from here? ''That depends a good deal on where you want to get to.'' Said the Cat. I don't much care where -- Said Alice. Then it doesn't matter which way you go, said the Cat. [Lewis Carroll]
Che si trattasse di una gara? ..Un colpo il mondo e un colpo tu, a chi stupiva un po' di piu'.. [Per Un Vecchio Bambino - Roberto Vecchioni]
--------------------------------------------
Martin M. Monti
Princeton University
Department of Psychology
Green Hall 3-S-8
(609) 258-5679
www.webmartin.net
--------------------------------------------
|