2014-11-11 13:19 GMT-05:00 Bill Taylor <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>>:
>>>
>>>
>>> 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>>>:
>>> >
>>> > 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>>>:
>>> >
>>> >
>>> > 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>>>>:
>>> > >
>>> > > 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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>>> > <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/
>>> >
>>> > _______________________________________________
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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>
>>> Phone Number: 617-724-2358 <tel:617-724-2358>
>>> Fax: 617-726-7422 <tel: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/
>>>
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>>> Freesurfer mailing list
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>>>
>>>
>>>
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