Hi Maria
I think we didn't realize there was any standard. As I remember, we do:
r << 16 + g << 8 + b
and stuff them into a 32 bit quantity
cheers
Bruce
On
Wed, 21 May 2014, Maria Jalbrzikowski wrote:
Dear Freesurfer experts,
Last week I asked a question about altering annotation and color tables so
that I could plot groups of vertices that covaried together. I have figured
out the solution to this, if anyone else is trying to do this too. You can
read in an annotation file with the read_annotation.m function in Matlab.
You can then edit the color table (a structure in Matlab) and then save the
newly edited annotation file using write_annotation.m. I came across a
couple of interesting issues when I was editing the colors and I was
wondering if anyone knew the answers to them.
1. It looks like Freesurfer ultimately uses the decimal value for the
specified color that is in the “label” variable. For example, if you wanted
an all white brain, you would put in “16777215” in 163843 rows in 1 column
in the variable “labels.” If you edit colortable.table, though this does
not seem to affect anything. What is the purpose of corlortable.table if
the label file overrides anything you put in the colortable.table?
2. I also noticed that the R G B values for colortable.table are backwards.
To specify the correct color you have to enter it B G R. Does anyone know
why this is the case?
3. Along those same lines, you need to enter the decimal color that is in
the B G R order, not in R G B order. For example, if you enter 255,
Freesurfer displays this as red, not blue. From what I researched, the
correct decimal value for blue is 255. To get Freesurfer to display blue,
you actually need to enter in 16711680, which is traditionally red. Why is
this? I find it to be quite confusing.
Perhaps these issues have already been discussed on the listserve, and if
they have, could someone direct me to the discussion. I’ve looking through
the archives extensively.
Thank you so much for any suggestions you may have.
Maria
On Fri, May 16, 2014 at 4:02 PM, Maria Jalbrzikowski
<mjalbrzikow...@gmail.com> wrote:
Dear Freesurfer experts,
I would like to get your help. I extracted cortical thickness
values from each vertex from each of my individual subjects (example:
path/subject_id/surf/lh.thickness.fsaverage.mgh). I then ran a
covariance analysis over the whole group and identified "modules" or
groups of vertices that covary together. The modules are given the
names of colors. I end up with a module (color) assigned to each
vertex. I now want to visualize this data (so I can if these module
reflect specific neuroanatomical structures), but I'm not sure about
how to do this. Does anyone know how to do this? I tried to make a
new color table, with my different module colors as the structures. I
don't know how to then incorporate this information so that I can view
it. I've read the tutorials on the label and annotation files, but I
have only become more confused. If anyone can help me with this
problem, I'd be very greatful!
Thank you,
Maria
--
Maria Jalbrzikowski, Ph.D.
Department of Psychiatry & Biobehavioral Sciences
University of California, Los Angeles
--
Maria Jalbrzikowski, Ph.D.
Department of Psychiatry & Biobehavioral Sciences
University of California, Los Angeles
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