Hi Doug, coming back to this once more. I am thinking that I can bypass mkcontrast-sess entirely if I provide a contrast matrix that has ContrastMtx_0 and WCond set to the contrast that I am interested in. For example [1 -0.2 -0.2 -0.2 -0.2 -0.2] to contrast my first continuous predictor and against the remaining five continuous predictors. For that, I would just place a corresponding mat file in a subdirectory in mystudy. Is there anything that speaks that and anything else that I need to consider? Thanks! Caspar
2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik <cschwie...@rockefeller.edu >: > Hi Doug, > I am a little bit confused about the variance. Shouldn't the relevant > variance be the variance over the differences, not the mean variance over > all? > Of course at the level of ces and cesvar, I do not have access to the > timepoint by timepoint differences anymore. > Is there another way to do this? > Thanks, Caspar > > > 2014-11-11 13:54 GMT-05:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > yes >> On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote: >> > 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 >> > <mailto: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> >> > >>> <mailto: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>> >> > >>> <mailto: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>> >> > >>> <mailto: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>>> >> > >>> > <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 >> > <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>> >> > >>> > <mailto: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 >> >> >> > >>> <mailto: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>> >> > >>> <tel: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>> <tel: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> >> > >>> > >> > <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> >> > >>> > >> > >>> >> > <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>> >> > >>> > <mailto: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> >> > >>> <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 >> > >>> >> > >>> >> > >>> >> > >>> >> > >>> _______________________________________________ >> > >>> 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 >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > _______________________________________________ >> > 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 >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> 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 >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >
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