Hi Emanuel,

You can use this command to load customized color table file:

freeview -v brain.mgz:colormap=lut:lut=color_table_file.txt

Best,
Ruopeng

On 4/1/19 10:40 AM, Emanuel Alvaredo wrote:

Thanks Bruce, Do you know what is the command line option?

Thanks!

Emanuel

On Mon, Apr 1, 2019 at 11:34 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

I see. You can give freeview a custom lookup table on the command line

cheers
Bruce


On Mon, 1 Apr 2019, Emanuel Alvaredo wrote:

>
>         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=colorwhe
> el,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=colorwhe
> el,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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