11 Nov
2014
11 Nov
'14
4:37 p.m.
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 greve@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 <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-mailwas
>>> > 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
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 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer