External Email - Use Caution        

Thanks for the answer Bruce.

Is For segmentations. I have run freesurfer for 100 nomal patients. I have calculated standard desviation and mean, then I am comparing the results against a patological patient. So, I would like to open freeview, for example with this command

freeview -v mri/orig.mgz -f  surf/lh.white:edgecolor=blue surf/lh.pial:edgecolor=red  surf/rh.white:edgecolor=blue  
surf/rh.pial:edgecolor=red 
surf/rh.inflated:overlay=surf/rh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwheel,inverse:overlay=surf/rh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse:overlay=surf/rh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse 
surf/lh.inflated:overlay=surf/lh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwheel,inverse:overlay=surf/lh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse:overlay=surf/lh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse

and show in my custom colores in segments.




Emanuel


On Mon, Apr 1, 2019 at 11:17 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Emanuel

can you tell us more. For parellations or segmentations? Are you just
changing the color of existing parcels/segments? If so you can just
import it in freeview
cheers
Bruce

On Mon, 1 Apr 2019, Emanuel Alvaredo wrote:

>
>         External Email - Use Caution        
>
> Hello!
> I would like to ask you  about customs colormaps. I have created my
> own FreeSurferColorLUT.txt and I  would like configure the color map using command line. 
> Is it possible?
>
> Thanks in advance.
>
> Emanuel
>
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