Those values are radians. Does that help? doug
On 11/29/2012 06:09 PM, Zhou, Wei wrote:
Hi Doug,
Thank you for your patient. I wanted to see how the polar angle correlates with the map and I expect a wheel bar which distinguish different polar angles. I typed:
rtview --s SUBJ1 --lh --polar --real SUBJ01/bold/rtopy.self.lh/polar/real.nii.gz --imag SUBJ01/bold/rtopy.self.lh/polar/imag.nii.gz --fsig SUBJ01/bold/rtopy.self.lh/polar/fsig.nii.gz
I could see some blue, red and green region in the cortex. Then i click "show the color scale bar" and I get a all-blue and vertical bar ranging from -1.18 to -0.4 and 0.4 to 1.18. I do not know how to interpret the image with this bar.
I am asking if wheel bar is still supported in freesurfer5. If so, how can I get it to interpret the maps?
Thank you.
Hi Wei, I don't think I understand your question. Can you elaborate? doug On 11/29/2012 04:06 PM, Zhou, Wei wrote:
Hi Doug,
Thank you very much. I have thrown all the fixation sessions and run the analysis again. So in rtview how can i get the color scale bar which indicates the corresponding time points of polar or eccen? Is it still supported in free surfer 5?
Best Wei
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.
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