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 > > > ---------------------------------------------- > > 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 email in > error, please delete it and any attachments. > > Please think of our environment and only print this e-mail if necessary. > > > On Thu, Aug 17, 2017 at 8:24 AM, Douglas N Greve > <[email protected] <mailto:[email protected]>> 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* [email protected] > <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>>, > [email protected] <mailto:[email protected]> > > <mailto:[email protected] > <mailto:[email protected]>> | *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 > email in > > error, please delete it and any attachments. > > > > Please think of our environment and only print this e-mail if > necessary. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > <mailto:[email protected]> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] <mailto:[email protected]> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > [email protected] <mailto:[email protected]> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
