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 greve@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
- 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
- Run preprocessing
preproc-sess -surface self lhrh -fwhm 5
- 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
- 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 ...
- 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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