Hi Kately,
Katelyn Norton wrote:
> Hi Will, thank you so much for your feedback.
>
> Your point about movement parameters is well taken and something I had
> not thought of. We usually add them to our hadngrip protocols, however I
> am unwarping my data as well and I have heard that you generally only
> need to do one or the other?
>
Yes. With Unwarp you don't need to include the movement regressors.
> I also completely agree with your comments about my protocol timings.
> Unfortunately, I came into this project once it was already designed and
> I did not have the luxury of optimizing my scanning parameters. After
> completing a few fMRI workshops since the beginning of this project, I
> definitely see the flaws in this design and your points are very valid.
>
> As far as the design matrix goes, when I am looking at the results for
> one subject individually, then yes, I see the column for handgrip and
> the movement regressors. However, when I am looking at group results, I
> see nothing. A white box and zero activation/deactivation shows up on my
> brain when I select a contrast. Weird right?
>
I see.
The white box bit is not weird. This is a how a design matrix for a
t-test looks like. It contains only a column of 1's which SPM displays
as the same shade (white).
Perhaps you'll see more activation after changing the first level
designs to remove move pars.
Good luck, Will.
> Katelyn
>
> ----- Original Message -----
> From: Will Penny <[log in to unmask]>
> Date: Wednesday, March 10, 2010 12:37 pm
> Subject: Re: [SPM] Individual Whole Brain Correction
> To: Katelyn Norton <[log in to unmask]>
> Cc: [log in to unmask]
>
> > Dear Kately,
> >
> > Katelyn Norton wrote:
> > >Hi Will.
> > >I am so sorry it took me so long to respond, but I really
> > REALLY appreciated your response to my question (actually both
> > of them were incredibly helpful!!).
> > > The problem I am having with my individual brains is that
> > there is so little signal, I am not able to use an FWE
> > correction, let alone an FDR. I am having to use uncorrected
> > activation clusters (p<0.005) before I see any sort of
> > response (even from the motor cortex which should be active in a
> > subject doing a handgrip protocol!).
> >
> >
> > Yes, this is surprising and suggests there's maybe something
> > more critically wrong with your analysis. I see that you are
> > including movement regressors in the model and am wondering if
> > this is removing your signal. Is it standard to include them in
> > handgrip-fMRI studies ?
> >
> > Also, you don't have a huge number of events. Only 3 epochs per
> > subject (or are there multiple sessions ? - did'nt see
> > this in your script). + there seems an excessive amount of rest
> > (70s) between grip epochs (also grip epochs are quite long). Its
> > maybe not an optimal use of scanner time (but then maybe you
> > have other constraints ?)
> >
> > Other than that I would check each subject in turn. The script
> > you sent me was for a single subject. You should make sure
> > different subjects have the appropriate onsets etc. Sorry, its
> > basic stuff I know.
> >
> > + am not sure what you mean by a blank design matrix - don't you
> > see the column for handgrip, and then the columns for the
> > movement regressors ?
> >
> > BEst,
> >
> > Will.
> >
> >
> >
> > So as much as I
> > >appreciate your support with reporting individual data, you had
> > said at the FWE level and I don't know if it's equally as
> > accepted with uncorrected volumes? Does this make sense?
> > > Also, I had said that I was having a problem with my group
> > analysis which is why I using individuals in the first place. My
> > batches run fine through Matlab, but when I select my contrast
> > results to view, there is a blank design matrix and no
> > activation/deactivation shows up - even at the uncorrected
> > level! So something is obviously wrong... I just don't know what
> > and I don't know how to proceed?
> > > I have included both my individual and group Matlab scripts,
> > so perhaps you can see a problem/better suggestion?
> > > Again, I am truly very appreciative of your help. If you have
> > the time, I would love to hear any suggestions you might have on
> > how to make my analysis more efficient.
> > >Thank you and I look forward to hearing from you soon!
> > >Katelyn
> > >
> > >----- Original Message -----
> > >From: Will Penny <[log in to unmask]>
> > >Date: Monday, March 1, 2010 6:47 am
> > >Subject: Re: [SPM] Individual Whole Brain Correction
> > >To: Katelyn Norton <[log in to unmask]>
> > >Cc: [log in to unmask]
> > >
> > > > Hello again,
> > > >
> > > > I don't see whats wrong with saying 10/12 subjects showed
> > > > activation at
> > > > x,y,z using FWE (p<0.05). Its a precise statement about what
> > > > you've done so readers should be able to interpret accordingly.
> > > > I would'nt use different criteria for different subjects.
> > > >
> > > > Re the group comparison, you could again take the above
> > > > approach. But say 4/12 showed activation in group 1 and 8/12 in
> > > > group 2, all we have is this descriptive statement. And it will
> > > > take you a fair amount of work to collect together these
> > > > statements for a number of different brain regions.
> > > >
> > > > I think it would be better, and it should be easier to use
> > eg. a
> > > > two-sample t-test (or ANOVA) at the second level to test for
> > > > group differences (where in the brain is the group 1 response
> > > > sig diff from group 2). What problem did you run into with the
> > > > ANOVA (where in the brain are there any differences between (>2)
> > > > groups) ?
> > > >
> > > > Best,
> > > >
> > > > Will.
> > > >
> > > > Katelyn Norton wrote:
> > > > >Hi all.
> > > > >I am working with two groups of subjects, each having an n=12.
> > > > After struggling with ANOVA's, I have decided to use whole brain
> > > > anlyses on each subject and simply report "10/12 showed
> > > > activation here" for example.
> > > > >First question, is this an acceptable means of reporting data
> > > > when I will essentially be comparing these results on a group
> > > > vs. group basis?
> > > > >Second question, is it acceptable to use a different level of
> > > > correction (p value) for each subject or should they all be the
> > > > same? My hunch is that they should all be the same, however the
> > > > level of activation among subjects is so variable that for some
> > > > I can use FWE and for others I cannot correct all (p<0.05).
> > > > >I would really appreciate any suggestions?
> > > > >Thanks!
> > > > >
> > > > >
> > > >
> > > > --
> > > > William D. Penny
> > > > Wellcome Trust Centre for Neuroimaging
> > > > University College London
> > > > 12 Queen Square
> > > > London WC1N 3BG
> > > >
> > > > Tel: 020 7833 7475
> > > > FAX: 020 7813 1420
> > > > Email: [log in to unmask]
> > > > URL: http://www.fil.ion.ucl.ac.uk/~wpenny/
> > > >
> >
> > --
> > William D. Penny
> > Wellcome Trust Centre for Neuroimaging
> > University College London
> > 12 Queen Square
> > London WC1N 3BG
> >
> > Tel: 020 7833 7475
> > FAX: 020 7813 1420
> > Email: [log in to unmask]
> > URL: http://www.fil.ion.ucl.ac.uk/~wpenny/
> >
--
William D. Penny
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
Tel: 020 7833 7475
FAX: 020 7813 1420
Email: [log in to unmask]
URL: http://www.fil.ion.ucl.ac.uk/~wpenny/
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