Re: [Freesurfer] retroicor

t is time of pulse or respiration acquisition (eg, .02*[0:1000]). indpeak is the list of indices in t where the peaks were found. doug

On 07/19/2012 09:24 AM, Caspar M. Schwiedrzik wrote:

Hi Doug, I think M is automatically computed, but t needs to be given (in addition to indpeak). What is t? Thanks, Caspar

2012/7/18 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>

M is the number of regressor pairs. Leave out the others and it will
figure them out.

On 07/18/2012 01:43 PM, Caspar M. Schwiedrzik wrote:
> and some more questions: in
fast_retroicor(t,indpeak,M,peakamp,troughamp)
> what is t / M?
> how do I get peakamp and throughamp?
> thanks again, caspar
>
> 2012/7/18 Caspar M. Schwiedrzik <cschwiedrz@rockefeller.edu
<mailto:cschwiedrz@rockefeller.edu>
> <mailto:cschwiedrz@rockefeller.edu
<mailto:cschwiedrz@rockefeller.edu>>>
>
>     great!
>     one more question: how do I choose fmin and fmax?
>     thanks, caspar
>
>     2012/7/18 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>>>
>
>         Try this
>
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_retroicor.m
>
>
>
>         On 07/18/2012 01:25 PM, Caspar M. Schwiedrzik wrote:
>
>             Hi Doug,
>             thanks for your advice. I am using
>             freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full,
>             while I have a copy of peakfinder.m,
fast_retroicor.m does
>             not seem to be part of the package.
>             Could you let me know where to download it?
>             Thanks, Caspar
>
>
>             2012/7/18 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>>>>
>
>
>                 Hi Caspar, I don't have anything that is
plug-and-play
>             for RETROICOR.
>                 You will need a text file to use as an external
>             regressor with one
>                 column for each regressor and one row for each time
>             point. You can
>                 play
>                 with my matlab functions. First, pass the waveform
>             (cardiac or
>                 respiration) to  peakfinder.m, then call
>             fast_retroicor.m passing
>                 it the
>                 peaks and returning the regressors. Then save the
>             regressors you
>                 want in
>                 a text file and specify them using -nuisreg
option to
>             mkanalysis-sess.
>                 doug
>
>                 On 07/18/2012 11:28 AM, Caspar M. Schwiedrzik wrote:
> > Hi!
> > Has someone used retroicor (retroactive correction of
>             physiological
> > noise; Glover at al. 2000) with Freesurfer?
> > I would like to create nuisance regressors for EPI data
>             based on
> > cardiac and respiratory signals.
> > The AFNI version of retroicor produces slice-based
>             regressors, and I
> > am not sure how to use them in Freesurfer.
> > Suggestions for alternative implementations would also be
>                 appreciated.
> > Thanks!
> > Caspar
> >
> >
> >
> >
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>                 --
>                 Douglas N. Greve, Ph.D.
>                 MGH-NMR Center
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>         MGH-NMR Center
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MGH-NMR Center
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Phone Number: 617-724-2358 <tel:617-724-2358>
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