You can set the min, mid, and slope from the command-line with -fmin, -fmid, and -fslope (it computes the max based on those 3).

The min and the max you can set with env variables, like:

setenv FS_TKFTHRESH 2 setenv FS_TKFMAX 3

this will apply to both tksurfer and tkmedit. Note that when the MAX is set, it will automatically compute the slope for linearity.

I don't know a way to have it set to piecewise automatically (probably a way with a tcl script, but I don't know -- Krish might know).

doug

Adam Nitenson wrote:

Hi Freesurfers,

I was wondering if there was a way to save any configurations you make to functional overlays (sig.mgh / sig.nii) in Tksurfer so you don't need to change them again. When I go to View --> Configure --> Overlay, it seems that the default is "Linear Opaque" with Min = 2.0 and Max = 5.0. For our purposes, I normally switch to "Piecewise" with Min = 1.3, Mid = 2.3, and Max = 3.3. It's an easy change to make normally, but I am having trouble loading these functional overlays into Slicer since it only loads the default settings with no way (as far as I know) to configure the overlay to display my preferences.

Is there anyway I can permanently save these changes to a specific overlay so that it would load automatically that way, which will allow me to import it into other programs? I tried File --> Save Overlay As... after applying the changes, but it only saved the default config.

Thanks,

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer