[Homer-users] Homer support: changing colors in images

[thuppert]

This is in response to a question that I was asked about displaying images
in Homer (the NIRS data analysis GUI).


Someone asked the question:

"is there anyway to set the color
scales in the imaging window between the two frequencies and when the time
scale is moved?  we are having difficulties comparing two conditions,
wavelengths, and time windows due to changing scales.  any help would
really be appreciated."

%%%%%%%%%%%%
Answer:

   If you click on the "Advanced Options" button on the imaging tab (or
select "Image Options"  from the pulldown menu on top), there is an option
to "autoscale intensities".
If this option is set then the color bar scale of the image will be set to
+/- max(intensity) {so green is set at zero}.  This will scale both
wavelengths (or concentrations) to the same range and they will be directly
comparable.

Currently this scales to the max/min of that subject so comparing one
subject to anouther or condition to anouther still has a scaling issue.  I
will (have already) made this change for the next release.  But for now,
image scales can be manually edited from the Matlab "colorbar" editor which
is on the figure pulldown (edit >> colormap).  You can set the max/min
values from there (after the image was created).






P.S.  - In the future, we are encouraging people to submit questions
regarding Homer directly through the homer-users at nmr.mgh.harvard.edu email
list server.

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Ted Huppert, MS

PhD student-Harvard Univ.
Dept of Biophysics
Photo Migration Imaging lab
Mass General Hospital/CNY

Tele: (617)726-1223
Cell: (617) 869-1205

thuppert at nmr.mgh.harvard.edu