Hi Doug, Sorry for the dumb beginner question, but to view the results projected onto their own anatomy, do I have to do anything special to their high res structural scan(like do a recon-all) ?
Thanks. Michelle Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > I don't have a formal manual yet (working on it). Below are a list of > steps that you need to run. The version 5 retinotopy stream is now > integrated with the rest of FSFAST, which is documented here: > http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt > > doug > > 1. Create retinotopy paradigm file in each run directory, eg, > session/bold/001/rtopy.par > session/bold/002/rtopy.par etc > > This text file identifies the data in the directory in terms of the > stimulus type (polar or eccen) and the direction (pos or neg). Its > contents should look somethign like: > > stimtype polar > direction pos > > 2. Run preprocessing > > preproc-sess -surface self lhrh -fwhm 5 > > 3. Create analysis (30 sec period, 'rtopy.par' is the name of the > paradigm file from above): > > mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \ > -retinotopy 30 -paradigm rtopy.par > mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 \ > -retinotopy 30 -paradigm rtopy.par > > 4. Run analysis > > selxavg3-sess -a rtopy.self.lh -sf ... > selxavg3-sess -a rtopy.self.rh -sf ... > fieldsign-sess -a rtopy.self.lh -occip -sf ... > fieldsign-sess -a rtopy.self.rh -occip -sf ... > > 5. View results > a. Significance maps: > tksurfer-sess -a rtopy.self.lh -s sessid > b. Display raw angle > tksurfer-sess -a rtopy.self.lh -s sessid -map angle > c. Display angle masked by by sig > tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked > d. Display field sign > tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign > > > > > > Michelle Umali wrote: >> Dear All, >> I was wondering if anyone knows of a step-by-step guide on how to do >> retinotopic analysis with freesurfer. >> >> Thanks. >> Michelle >> _______________________________________________ >> 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 > > > > 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
