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.
Best Wei Zhou Medical Physics Ph.D. Student
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).
- For -retinotopy option in mkanalysis-sess I typed "300". Do you
think this setting is fine?
- 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?
- 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.
- 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.
Best Wei Zhou Medical Physics Ph.D. Student
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Zhou, Wei