selxavg uses scenario #1, which corresponds to the 2nd image below, ie,
all the task regressors are in a single column and not pulled out on a
run-by-run basis. The nuisance regressors are specific to each run.


>

On 08/16/2017 08:24 PM, Kevin Aquino wrote:
> Thanks for that Doug,
>
> [I was hoping i could do the parametric modulation in the contrast
> weights -- SPM style of doing this after the betas were fit].
>
> Regarding the X.mat question, sorry I wasn't clear. I can see it has
> the nuisance regressors and constant terms, but is that x.mat used to
> estimate the betas?
Yes
>
> In the beta estimation which scenario is happening?
>
> 1. concatenate all the model regressors onto one column, add the
> nuisance regressors and constant terms into one big matrix (X.mat) to
> estimate the beta values
> 2. create a matrix for each run separately and estimate the betas.
> Save regression coefficients, compute contrasts and significances of
> contrasts. The end (default) result is the average (i guess average of
> all the estimated quantities).
>
> From the help message it looks like it is #2, and if thats the case
> then X.mat looks like its a summary. I ask this because I would like
> to use a X that looks something like below:
> Inline image 1,
>
> which is essentially the scenario in #2, but the output of X.mat looks
> like this:
>
> Inline image 2
> (the image hasn't been normalized so that is why there are blank
> spaces for 3 of the 6 nuisance regressors)
>
> There are slight differences between the two (so it doesn't matter in
> the long run) but I just want to know which one is being used. On a
> quick look of selxag3-sess, the matlab files look like compiled mex
> files, so I can't access them.

>
> Thanks!
>
>
> *Dr Kevin Aquino*
> Research fellow,
> Sir Peter Mansfield Magnetic Resonance Center, The University of
> Nottingham.
>
> Honorary Research Fellow
> School of Physics, Faculty of Science, University of Sydney
>
>
> ----------------------------------------------
>
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> up and does not stop until you get into the office.
> -
> Robert Frost
>
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> On Thu, Aug 17, 2017 at 8:24 AM, Douglas N Greve

> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     It has the design matrix plus a lot of other stuff in it. For
>     parametric
>     modulation, have you seen this page
>
>     https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation
>     <https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation>
>
>     On 08/15/2017 09:52 PM, Kevin Aquino wrote:
>     > Dear all,
>     >
>     > I have a question regarding the output from selxavg3-sess. I noticed
>     > that within an analysis there  is a X.mat that looks like a design
>     > matrix -- however is this used at any stage of the analysis?
>     The help
>     > message in selxavg3-sess reads:
>     >
>     > "This program will construct the design matrix for each run, fit
>     > the GLM, save regression coefficients, compute contrasts and
>     > significances of contrasts. The runs are combined together so the
>     > output is the average across runs (some would call this a
>     > "second-level" analysis)."
>     >
>     > so this looks like that x.mat is constructed and used for each run
>     > (and not saved by default). This then looks like X.mat is not
>     used in
>     > the analysis -- it is just there for illustrative purposes? or
>     have I
>     > misinterpreted the help message.
>     >
>     >
>     > If this is correct (i.e. X.mat in the output is not used) when
>     making
>     > contrasts using mkcontrast-sess, is there a way to parametrically
>     > modulate each run? e.g. to model behavioural changes per run etc.
>     >
>     > Cheers,
>     >
>     >
>     > *Dr Kevin Aquino*
>     > Research fellow,
>     > Sir Peter Mansfield Magnetic Resonance Center, The University of
>     > Nottingham.
>     >
>     > Honorary Research Fellow
>     > School of Physics, Faculty of Science, University of Sydney
>     >
>     > *E* Kevin.aquino@nottingham.ac.uk
>     <mailto:Kevin.aquino@nottingham.ac.uk>

>     > <mailto:Kevin.aquino@nottingham.ac.uk
>     <mailto:Kevin.aquino@nottingham.ac.uk>>,
>     aquino@physics.usyd.edu.au <mailto:aquino@physics.usyd.edu.au>
>     > <mailto:aquino@physics.usyd.edu.au
>     <mailto:aquino@physics.usyd.edu.au>> | *W* *MailScanner has detected a
>     > possible fraud attempt from "www.physics.usyd.edu.au
>     <http://www.physics.usyd.edu.au>" claiming to be*
>     > https://kevinaquino.github.io
>     <http://www.physics.usyd.edu.au/%7Eaquino/
>     <http://www.physics.usyd.edu.au/%7Eaquino/>>
>     >
>     > ----------------------------------------------
>     >
>     > The brain is a wonderful organ. It starts working the moment you get
>     > up and does not stop until you get into the office.
>     > -
>     > Robert Frost
>     >
>     > CRICOS 00026A
>     > This email plus any attachments to it are confidential. Any
>     > unauthorised use is strictly prohibited. If you receive this
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>     >
>     >
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MGH-NMR Center
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