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
<fis...@nmr.mgh.harvard.edu <mailto:fis...@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
<fis...@nmr.mgh.harvard.edu <mailto:fis...@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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>
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