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). > > > > 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
