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
> <cschwiedrz@rockefeller.edu <mailto: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 <mailto: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>
> > <mailto: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>>
> > >>> <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:cschwiedrz@rockefeller.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>>>
> <mailto:cschwiedrz@rockefeller.edu>
> > <mailto:cschwiedrz@rockefeller.edu
> <mailto:cschwiedrz@rockefeller.edu>>
> > >>> <mailto:cschwiedrz@rockefeller.edu
> <mailto:cschwiedrz@rockefeller.edu>
> > <mailto:cschwiedrz@rockefeller.edu
> > <tel:617-724-2358 <tel:617-724-2358>>>>> <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>>>
> > >>> <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
> <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>>>>
> > >>> > <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
> <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>>>
> > >>> > <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
> > >>> > 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>>>
> > >>> <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
> <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>>>
> > >>> <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>
> > >>> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <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>>>>
> > >>> >
> > 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
> > >>> 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
> > >>>
> > >>>
> > >>>
> > >>>
> --> > >>> _______________________________________________
> > >>> 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
> greve@nmr.mgh.harvard.edu <mailto:greve@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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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