there is some code around to display each parcel with a different value,
but I'm not sure exactly what it is. YOu could certainly do it in matlab
if you wanted to (use read_annotation.m to read in the .annot file)
Cheers
Bruce
On Wed, 11 Jul 2018, Ben Smith wrote:
External Email - Use Caution
Hi Bruce,
Some background:
----
I have already extracted ROI timeseries using the following method:
* use mri_vol2vol to transform the functional images to structural space (yes
these were very
large images; I did it one at a time)
* use mri_segstats to segment the image into cortical parcellations and
subcortical segmentations
That gave me raw timecourses for each segment and parcellation. I used my own
code to mean-center
and high-pass filter (specificaly, linear, quadratic, and cubic regressors);
then applied an HRF
function. I was then able to extract a single activity value for each ROI and
each event in my
design.
So for each subject I now have an N*M matrix where N is the number of events
and M is the number of
ROIs, representing mean activity in each ROI during each event.
I'm then estimating the covariance of activity in these ROIs with reward
prediction error according
to an RL model.
---
So back to freesurfer - I have a single covariance value for each ROI and I
want to show that
covariance in an illustration, where each ROI is color-coded according to its
covariance value.
It's good to know the annotations (e.g., label/rh.aparc.a2009s.annot, right?)
are what I need for
this, but they're not plain text, so I don't know how to use them to create a
colormap like Ruopeng
suggested.
_______________________
Ben Smith, MSc.
Ph.D. Candidate
University of Southern California
https://bjsmith.github.io/
p | +1 323-385 9349
skype | ben.smith.nz
On Tue, Jul 10, 2018 at 5:54 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Ben
can you explain a bit more explicitly what you are trying to do? The
annotations are exactly what you suggest (a parcellation ID for every
vertex)
cheers
Bruce
On Tue, 10 Jul 2018, Ben Smith wrote:
>
> External Email - Use Caution
>
> Got it, thanks!
> Could you tell me how I can map a particular ROI (for instance the
Destrieux cortical
surface ROIs)
> to a set of vertices that make up the ROI? Is there a lookup table I
can use?
> _______________________
> Ben Smith, MSc.
> Ph.D. Candidate
> University of Southern California
> https://bjsmith.github.io/
> p | +1 323-385 9349
> skype | ben.smith.nz
>
>
>
> On Tue, Jul 10, 2018 at 2:08 PM Ruopeng Wang
<rpw...@nmr.mgh.harvard.edu> wrote:
>
> Hi Ben,
>
> My last email was referring to how to load custom color map for
volume viewing.
If you
> want to load custom color for surface, you need to create and
load an RGB map
file. The
> file can be a text file contains N lines of RGB color like this:
>
> R1, G1, B1
> R2, G2, B2
>
> ...
>
> or a volume file with dimension of N x 3 x1. N must match the
number of
vertices of the
> surface.
>
> Best,
> Ruopeng
>
>
> On 07/10/2018 04:57 PM, Ben Smith wrote:
>
> External Email - Use Caution
>
> I've been trying to do this as well, but I can't see the right
place to specify
in
> freesurfer to specify an alternative lookup table.
> For instance, if I am coloring a pial surface, then the first
possibility is to set a
> Color (where I can "load RGB map"). But I get an error "Cannot load
RGB" file if I try
> to use that to load an LUT format file. The other option is where it says
"heatmap" i
> can change the option to select a custom label, but if I try to enter
an LUT file into
> there, freeview crashes (which is fine, I guess that was the wrong
place).
>
> So can anyone tell me what I'm missing for the place to load the LUT
file or an
> alternative colormap?
>
> Thanks for your help!
>
> Regards
>
> Ben
>
> On Tue, Mar 27, 2018 at 1:10 PM Ruopeng Wang
<rpw...@nmr.mgh.harvard.edu> wrote:
>
> It looks like a customized look up table will work for your case.
You can
> simply select "Lookup table" as the colormap and load your own
lookup table.
> To create your own look up table, you can refer to the content of
> FreeSurferColorLUT.txt file in your freesurfer installation
directory.
>
> Best,
> Ruopeng
>
> On 03/27/2018 03:59 PM, Anna Mynick wrote:
> Hi all,
> I’m wondering whether there’s a way to create a custom color map in
Freeview
> that would operate as a alternative to the preset Greyscale, Heatmap,
NIH,
> PET, Jet and GE Color options.
>
> Ideally, I could assign each number value a given color, e.g. every “0”
> value in an .nii file is black, every “1” value is red, every “2” value
is
> blue, every “3" is green and so on. I already have the RGB values
worked out
> for each number value; I just need to know how to format this
information
> and where to put it so that I can my custom colormap as an option in
> Freeview.
>
> For my purposes, there would be no need to adjust the assigned colors
based
> on the overall range of values. For instance, there would be no need to
> assign a different color value to a “1” value depending on whether the
> highest value in the overall .nii file is 1 or 100.
>
> I did try reading the related conversation here but I can’t seem to
find the
> file it references, annotval2surfoverlay.m, in the Freesurfer
directory.
>
> Thanks very much for your help!
> Anna
>
>
>
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