Hi Doug, just to clarify: If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6)) and cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
Is that correct? Thanks, Caspar 2014-11-11 13:19 GMT-05:00 Bill Taylor <b...@cs.wisc.edu>: > Sorry, Though we do have freesurfer pipelines we run in Madison, I > responded to wrong email. > > Bill Taylor > Center for High Throughput Computing > Computer Sciences > University of Wisconsin, Madison > > On 11/11/2014 12:09 PM, Bill Taylor wrote: > > I'll start the process thursday. > > On 11/11/2014 12:04 PM, Douglas N Greve wrote: > >> It will be the same as the DOF of the individual contrasts (don't sum > them). > >> > >> On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote: > >>> ok, I will try that. How do I get the degrees of freedom? Thanks! > Caspar > >>> > >>> 2014-11-11 12:04 GMT-05:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu > >>> <mailto:gr...@nmr.mgh.harvard.edu>>: > >>> > >>> > >>> Actually, you can still do each contrast individually. Each will > >>> produce > >>> ces and cesvar files. Take the difference between the ces files > >>> and the > >>> average of the cesvar files, then feed the result into > mri_glmfit FFX > >>> > >>> doug > >>> > >>> > >>> On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote: > >>> > Hi Doug, > >>> > I wanted to follow up on this. Would you be able to provide a > >>> > workaround for contrasting multiple taskregs against each > other? Is > >>> > there something I can try in the meantime? Thanks, Caspar > >>> > > >>> > > >>> > 2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik > >>> > <cschwie...@rockefeller.edu <mailto:cschwie...@rockefeller.edu > > > >>> <mailto:cschwie...@rockefeller.edu > >>> <mailto:cschwie...@rockefeller.edu>>>: > >>> > > >>> > Hi Doug, > >>> > thanks for your reply. I would like to feed the differences > >>> into a > >>> > FFX group analysis, so I think I will need to resort to > your > >>> > workaround. It would be great if you could provide that. > Thanks! > >>> > Caspar > >>> > > >>> > 2014-11-10 13:45 GMT-05:00 Douglas N Greve > >>> > <gr...@nmr.mgh.harvard.edu > >>> <mailto:gr...@nmr.mgh.harvard.edu> > >>> <mailto:gr...@nmr.mgh.harvard.edu > >>> <mailto:gr...@nmr.mgh.harvard.edu>>>: > >>> > > >>> > > >>> > To get sig maps for an individual, this is problematic > >>> but I > >>> > could > >>> > probably come up with a work-around. For a group > >>> analysis, you can > >>> > simply compute each taskreg separately, then subtract > >>> the two > >>> > prior to > >>> > running mri_glmfit. > >>> > doug > >>> > > >>> > On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote: > >>> > > Hi! > >>> > > A quick follow-up: > >>> > > I have a taskreg file with 6 continuous predictors. I > >>> would > >>> > like to > >>> > > run specific contrasts, e.g., predictor 1 vs. > >>> mean(predictor > >>> > 2:6). > >>> > > From what I gather, selxavg3-sess will run automatic > >>> > contrasts on > >>> > > taskregs, but the automatic contrasts are against > >>> baseline. > >>> > This is > >>> > > not what I need at this point. > >>> > > mk-contrast-sess does not like what I am putting in > >>> because > >>> > I do not > >>> > > have a paradigm file in which condition numbers are > >>> specified. > >>> > > Is there a way to compute specific contrasts between > >>> multiple > >>> > > taskregs, and if not, is there a workaround? > >>> > > Thank you very much, Caspar > >>> > > > >>> > > > >>> > > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik > >>> > > <cschwie...@rockefeller.edu > >>> <mailto:cschwie...@rockefeller.edu> > >>> > <mailto:cschwie...@rockefeller.edu > >>> <mailto:cschwie...@rockefeller.edu>> > >>> > <mailto:cschwie...@rockefeller.edu > >>> <mailto:cschwie...@rockefeller.edu> > >>> > <mailto:cschwie...@rockefeller.edu <mailto: > cschwie...@rockefeller.edu>>>>: > >>> > > > >>> > > Hi! > >>> > > I have several external regressors in my analysis > >>> that I > >>> > configure > >>> > > with -taskreg in mkanalysis-sess (something like > >>> -notask > >>> > -taskreg > >>> > > nameoffile 6). > >>> > > I was wondering how to set up mkcontrast-sess to > >>> > contrast these > >>> > > regerssors given that I do not have a paradigm > >>> file for > >>> > them. > >>> > > Can I just do something like -a 1 -c 2 -c 3 -c 4 > -c 5? > >>> > > > >>> > > Thanks, Caspar > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > _______________________________________________ > >>> > > Freesurfer mailing list > >>> > > Freesurfer@nmr.mgh.harvard.edu > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > > >>> > -- > >>> > Douglas N. Greve, Ph.D. > >>> > MGH-NMR Center > >>> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto: > gr...@nmr.mgh.harvard.edu>> > >>> > Phone Number: 617-724-2358 <tel:617-724-2358> > >>> <tel:617-724-2358 <tel:617-724-2358>> > >>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > >>> <tel:617-726-7422>> > >>> > > >>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > >>> > FileDrop: 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> > >>> > > >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > Outgoing: > >>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >>> > > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer@nmr.mgh.harvard.edu > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >>> > 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 . 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 > >>> > Freesurfer@nmr.mgh.harvard.edu > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> -- > >>> Douglas N. Greve, Ph.D. > >>> MGH-NMR Center > >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > >>> Phone Number: 617-724-2358 <tel:617-724-2358> > >>> Fax: 617-726-7422 <tel: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 > >>> 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/ > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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