Dear freesurfers
Have you ever tried to get an average retinotopic map across all subjects on freesurfer's standard surface (fsaverage)?
I obtained an individual map for each subject using the fsfast stream (mkanalysis-sess, selxavg3-sess) and plotted the results using rtview: e.g.
rtview.sh --s subj1 --lh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz
Now for the group map, my initial idea was to sample each subject's real and imaginary component to the fsaverage surface and average them separately across subjects. However, I am not sure how I would threshold such an average map on fsaverage using rtview (i.e. what would I use as fsig.nii) given that averaging log p-values is probably not a good idea.
Within each subject's rtopy.self.?/polar(or /eccen) folder the following files (and few more but probably not important here) exist:
fsig.nii -> I understand this contains the unsigned log p values probably obtained via an F-test (frequency of interest) / (noise frequencies) sig.nii -> this might then be the signed counterpart of fsig.nii imag.nii -> this must contain the imaginary component of the polar angle or eccen map real.nii -> this must contain the real component of the polar angle or eccen map mag.nii -> I suppose this might contain the amplitude of the signal at the frequency of interest (i.e. the frequency the wedge / ring is traveling)
However, I don't quite know what the remaining files are good for
iminsig.nii minsig.nii cwmap-imag.nii cwmap-real.nii
ces.nii cesmag.nii cesmagpct.nii cespct.nii cesvar.pct cesvarpct.nii
For the ces* files I understand that they generally contain effect sizes / variances and are used for group analyses. However, I am not quite sure what effects they correspond to in the case of retinotopy.
When browsing the web for similar problems I found the following post:
> Hi Michelle, try this: > > isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o retgroup > > cd retgroup/rtopy.fsaverage.lh > > mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real --surface > fsaverage lh > mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag --surface > fsaverage lh > mri_glmfit --y polar/ces.000.nii.gz --osgm --o polar/glm.real --surface > fsaverage lh > mri_glmfit --y polar/ces.001.nii.gz --osgm --o polar/glm.imag --surface > fsaverage lh > > mri_fieldsign --fs lh.fieldsign.mgh \ > --eccen eccen/glm.real/osgm/gamma.mgh eccen/glm.imag/osgm/gamma.mgh \ > --polar polar/glm.real/osgm/gamma.mgh polar/glm.imag/osgm/gamma.mgh \ > --s fsaverage --hemi lh --sphere --old > > tksurfer fsaverage lh inflated -aparc -ov lh.fieldsign.mgh -fthresh .5
However, as mentioned above I wonder what effect sizes are used here and why (different to rtview) there is no significance map needed to plot the data.
Is there a way to use rtview for the result of a group analysis? And if yes how would I get a fsig.nii file for that?
I really appreciate your help!
many thanks & best wishes
Andreas