Thanks Chris, can you point us to the offending wiki page?
doug
On 9/28/18 12:44 PM, Christopher Markiewicz wrote:
External Email - Use Caution
Hi all,
I believe I've gotten to the bottom of this, and the problem is incorrect
documentation, both in the read/write_annotation.m files and in the wiki.
Taking the FreeSurfer C source as the de facto specification, we can refer to
the colortab.c file. Here, the labels are not constructed or decoded using the
transparency (255 - alpha) information at all, but are simply (R + G << 8 + B
<< 16).
For more complete discussion, see:
https://github.com/nipy/nibabel/issues/649#issuecomment-424755969
I think the most parsimonious resolution of this confusion is simply to update
the documentation on the wiki page (I cannot; someone with permissions will
need to), and to patch the MATLAB code to build its labels from RGB values
alone. I will submit a patch to the GitHub branch.
Please let me know if I've gotten something wrong.
Best,
Chris Markiewicz
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of paul mccarthy
<pauldmccar...@gmail.com><mailto:pauldmccar...@gmail.com>
Sent: Thursday, September 20, 2018 11:39:53 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Clarification about .annot file format
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Howdy,
There is a discussion regarding the .annot file format over at the nibabel
github repository, regarding the interpretation of the flag/alpha value:
https://github.com/nipy/nibabel/issues/649
If one wishes to create an .annot file with colours that have a transparency
value, how should it be stored in the file? By piecing together the information
from the freesurfer code [1,2], and Graham Wideman's helpful notes [3], I came
to the conclusion that alpha values should be stored as 1-the actual value. But
it would be great to get some clarification on this from somebody who knows
more than me
Thanks very much,
Paul McCarthy
[1] https://github.com/freesurfer/freesurfer/blob/dev/matlab/read_annotation.m
[2] https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_annotation.m
[3]
https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annotation
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