11 Nov
2014
11 Nov
'14
1:54 p.m.
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 <bt@cs.wisc.edu mailto:bt@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >>> > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@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 >>> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >>> > > <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> >>> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>> >>> > <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@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 >>> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/