Ritobrato Datta wrote: > Hello All, > > Many thanks for all the help that you provide to freesurfer users. > > I have a few questions - > > 1. Where do I find ch2better brain ? I want to pipe it through freesurfer all > the way to register to the spherical atlas and plot functional data across > subjects to it. > What is the ch2better brain? > 2. I have retinotopy data (expanding rings and wedges) for 6 subjects and I > want to generate average functional eccentricity and polar angle data for > these subjects in surface or sphere space. Can you tell me how do I average > the functional data across subjects in the surface domain ? That will be gr8 > help. > What are you trying to do, exactly? Eg, average the phase maps across subjects? > 3. I was trying to plot the retinotopy data for 1 subject onto the inflated > surface using tksurfer (following the instructions > http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferWorkingWithData/TkSurferOverlay) > and am able to plot it but I am not able to fit a proper color scale and > threshold to show color gradation reflecting the different phases. Can anyone > please suggest what am I doing wrong ? I have attached a figure here. This is > how it plots before any fiddling. > I've created a new retinotopy-related script that you can get from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/sfa2fieldsign It makes running the retinotopy analysis a little easier. See the --help for how to run it and, more to the point, there are example tksurfer commands for visualization, including how to set the color scale. > 4. Also is there a way to calculate gray matter thickness of V1 in subjects > after it has been registered to the spherical atlas. I have already generated > V1 labels using Dr. Fischl and Dr. Hind's method. > It is easier to do in the individual space with mris_anatomical_stats. You'll have to use mri_segstats passing it the label and using the thickness map in fsaverage space as the input. > Thanks a lot for your help > > Ri > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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