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
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
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 CautionHello! 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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 CautionThanks 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 youjust
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 createdmy
> own FreeSurferColorLUT.txt and I would like configure the colormap using
command line. > Is it possible? > > Thanks in advance. > > Emanuel > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 mailto: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 <mailto: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 > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks! Emanuel
On Mon, Apr 1, 2019 at 12:13 PM Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
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 CautionThanks 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 youjust
changing the color of existing parcels/segments? If so you canjust
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 havecreated my
> own FreeSurferColorLUT.txt and I would like configure thecolor map using
command line. > Is it possible? > > Thanks in advance. > > Emanuel > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Emanuel Alvaredo -
Ruopeng Wang