Re: [Freesurfer] Custom Colormap

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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

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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:

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overlay=surf/rh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse

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surf/lh.inflated:overlay=surf/lh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwhe

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el,inverse:overlay=surf/lh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse:

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overlay=surf/lh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse

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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:

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  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

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  command line.
  > Is it possible?
  >
  > Thanks in advance.
  >
  > Emanuel
  >
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