2014-11-11 16:37 GMT-05:00 Caspar M. Schwiedrzik <cschwiedrz@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 <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
> >>> > >
> >>> > >
> >>> > >
> >>> > >
> >>> > > _______________________________________________
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> >>> >
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> >>> >
> >>> > --
> >>> > 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>>
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> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
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> >>> --
> >>> 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>>
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> >>>
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--
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