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 <cschwie...@rockefeller.edu > <mailto:cschwie...@rockefeller.edu>> > > great! > one more question: how do I choose fmin and fmax? > thanks, caspar > > 2012/7/18 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > > > > > > > > > > _______________________________________________ > > 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 > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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: > 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> > > _______________________________________________ > 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 > > > 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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
