[MINC-users] ray_trace colour maps and rendering labels

[EJ Nikelski]

Hi,

  Andrew and Claude -- thanks for the help. Between both suggestions,
I should be able to get the job done.

  Can I add one additional follow-up?  First, for context, I've fit
the AAL labels (manual labeling of the colin-27 brain) to the Civet
model (fit to a 4-mm grid), and am now applying my subject's inverted
non-linear transform to the AAL volume in order to fit the labels onto
my subject's linear fit T1 (out of Civet). The results look good, but
... the "real" values in my label volume appear to be stored as floats
-- or so says register, Display and postf.  How do I convert my label
volume into simply having "real" values = voxel values = label values
= integers?

-Jim



On Thu, Mar 25, 2010 at 4:28 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Jim
>
> On Fri, Mar 26, 2010 at 08:41, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
>> (2) does anyone know the required file format needed to use the
>> ray_trace "-usercc" argument, so that I can cobble my own together?
>
> I can't help on the first bit but I would guess that they would follow
> the same format as minclookup (man minclookup for more). As an example
> here is the spectral colourmap that can be passed to minclookup
>
>
> harold:Downloads$ cat ~rotor/lib/luts/spectral
> 0.00 0.0000 0.0000 0.0000
> 0.05 0.4667 0.0000 0.5333
> 0.10 0.5333 0.0000 0.6000
> 0.15 0.0000 0.0000 0.6667
> 0.20 0.0000 0.0000 0.8667
> 0.25 0.0000 0.4667 0.8667
> 0.30 0.0000 0.6000 0.8667
> 0.35 0.0000 0.6667 0.6667
> 0.40 0.0000 0.6667 0.5333
> 0.45 0.0000 0.6000 0.0000
> 0.50 0.0000 0.7333 0.0000
> 0.55 0.0000 0.8667 0.0000
> 0.60 0.0000 1.0000 0.0000
> 0.65 0.7333 1.0000 0.0000
> 0.70 0.9333 0.9333 0.0000
> 0.75 1.0000 0.8000 0.0000
> 0.80 1.0000 0.6000 0.0000
> 0.85 1.0000 0.0000 0.0000
> 0.90 0.8667 0.0000 0.0000
> 0.95 0.8000 0.0000 0.0000
> 1.00 0.8000 0.8000 0.8000
>
> For a discrete colourmap the first column would be an integer set from 0-255
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University