Hi Doug,
When you say retinotopy 30, where 30 is the 30 second period.
mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 \
-retinotopy 30 -paradigm rtopy.par
Does period mean duration for a cycle or for the whole run?
Thanks.
Michelle
ing 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
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>>
>>
>>
>
> --
> 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
>
>
>
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