Hi Wei, the argument to -retinotopy should be the period of stimuluation 
(ie, how long it takes the wedge to go around 360 degrees), not the 
duration of your run. Also, it is not set up to handle fixation at the 
beginning or the end, so you might want to cut those frames out.
doug

On 11/29/2012 12:30 PM, Zhou, Wei wrote:
> Dear freesurfers,
>
> I am doing retinotopy analysis using freesurfer 5 with 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis .
> I have four runs, two eccen and two polar.  For each run I have 15 
> seconds fixation, 300 seconds stimuli and 15s fixation at the end 
> (total 330s and 300s for stimuli).
>
> 1) For -retinotopy option in mkanalysis-sess I typed "300". Do you 
> think this setting is fine?
>
> 2) After finishing running, I use tksurfer-sess to display the result. 
> When I typed "tksurfer-sess -s SUBJ01 -analysis rtopy.self.lh  -map 
> angle"  with "-c polar" or "-c eccen'" I got two maps with -4.0 to 4.0 
> color range. I learn from mail list, the two maps do not represent 
> time course of retinotopy, right? So what are these two maps tell us?
>
> 3) I tried rtview cmd and the maps look strange. Color scale is from 
> -1.185 to -0.4 and 0.4 to 1.185 and it does not include all the colors 
> in display.
>
> 4) I tried to use -run-wise in selxavg3-sess, it fails with: 
> "/analysis/retinotopy/SUBJ01/bold/rtopy.self.lh/pr001/Xtmp.mat
> Error using svd
> Input to SVD must not contain NaN or Inf."
>
> Could you please give me some idea? Thank you very much in advance.
>