I don't know whether that will work or not. If it runs, you can compare the result to computing the contrast manually to see if there is a difference. If there is no difference, then it works.
On 11/13/2014 10:18 AM, Caspar M. Schwiedrzik wrote: > 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 <mailto: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 <mailto: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> > > <mailto: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>> > > >>> <mailto: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>>> > > >>> <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 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>>> > > >>> <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 > <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>>>> > > >>> > <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 > <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>>> > > >>> > <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 > <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>>> > > >>> <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 > <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>>> > > >>> <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 <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>>> <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 <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> > > >>> > > > <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> > > >>> > > > >>> > > > <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>>> > > >>> > <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 > <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>> > > >>> <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 > > >>> > > >>> > > >>> > > >>> > > >>> _______________________________________________ > > >>> 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> > > <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> > <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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > 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 > 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 -- 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
