Yes, you need to run recon-all in order to run the FSFAST analysis. doug
Michelle Umali wrote: > 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. > > > > -- 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
