Hi Sergey,
here's read_annotation.m. It should also return the embedded colormap
that's in the .annot file, including structure names. Not sure why it's not
in your distribution.
cheers,
Bruce
On Sat, 8 Dec 2007, Sergey Plis wrote:
Thank you! Although I did not find the exact function you're describing,
there is a function with the same name that has the following help:
>> help read_annotation
[annots] = read_annotation(fname)
reads a binary annotation file into a vector
or this one
>> help freesurfer_read_annotation
freesurfer_read_annotation - reads a binary annotation file into a vector
[annots] = freesurfer_read_annotation(fname)
See also freesurfer_read_surf, freesurfer_read_curv,
freesurfer_read_wfile
The vector returned has 7-8 digit numbers in it, and they do look like if
they can be ROI labels.
e.g:
>> label(1:1000:10000)
ans =
9182740
9182740
9182740
9182740
6558940
9182740
9221140
9182740
3957880
14433500
Now how do I tell which ROI these indices correspond to?
Thank you!
--
Sergey
On Dec 7, 2007, at 8:43 PM, Bruce Fischl wrote:
Hi Sergey,
In matlab you you can use read_annotation.m:
function [vertices, label, colortable] = read_annotation(filename)
% [vertices, label, colortable] = read_annotation(annotfilename.annot)
%
% vertices expected to be simply from 0 to number of vertices - 1;
% label is the vector of annotation
%
% colortable is empty struct if not embedded in .annot. Else, it will be
% a struct.
% colortable.numEntries = number of Entries
% colortable.orig_tab = name of original colortable
% colortable.struct_names = list of structure names (e.g. central sulcus and so
on)
% colortable.table = n x 5 matrix. 1st column is r, 2nd column is g, 3rd column
% is b, 4th column is flag, 5th column is resultant integer values
% calculated from r + g*2^8 + b*2^16 + flag*2^24. flag expected to be all 0.
%
% read_annotation.m
%
% Original Author: Bruce Fischl
% CVS Revision Info:
% $Author: nicks $
% $Date: 2007/01/10 22:55:09 $
% $Revision: 1.4 $
%
% Copyright (C) 2002-2007,
% The General Hospital Corporation (Boston, MA).
% All rights reserved.
%
% Distribution, usage and copying of this software is covered under the
% terms found in the License Agreement file named 'COPYING' found in the
% FreeSurfer source code root directory, and duplicated here:
% https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
%
% General inquiries: [email protected]
% Bug reports: [EMAIL PROTECTED]
%
fp = fopen(filename, 'r', 'b');
if(fp < 0)
disp('Annotation file cannot be opened');
return;
end
A = fread(fp, 1, 'int');
tmp = fread(fp, 2*A, 'int');
vertices = tmp(1:2:end);
label = tmp(2:2:end);
bool = fread(fp, 1, 'int');
if(isempty(bool)) %means no colortable
disp('No Colortable found.');
colortable = struct([]);
fclose(fp);
return;
end
if(bool)
%Read colortable
numEntries = fread(fp, 1, 'int');
if(numEntries > 0)
disp(['Reading from Original Version']);
colortable.numEntries = numEntries;
len = fread(fp, 1, 'int');
colortable.orig_tab = fread(fp, len, '*char')';
colortable.orig_tab = colortable.orig_tab(1:end-1);
colortable.struct_names = cell(numEntries,1);
colortable.table = zeros(numEntries,5);
for i = 1:numEntries
len = fread(fp, 1, 'int');
colortable.struct_names{i} = fread(fp, len, '*char')';
colortable.struct_names{i} = colortable.struct_names{i}(1:end-1);
colortable.table(i,1) = fread(fp, 1, 'int');
colortable.table(i,2) = fread(fp, 1, 'int');
colortable.table(i,3) = fread(fp, 1, 'int');
colortable.table(i,4) = fread(fp, 1, 'int');
colortable.table(i,5) = colortable.table(i,1) +
colortable.table(i,2)*2^8 + colortable.table(i,3)*2^16 +
colortable.table(i,4)*2^24;
end
disp(['colortable with ' num2str(colortable.numEntries) ' entries read
(originally ' colortable.orig_tab ')']);
else
version = -numEntries;
if(version~=2)
disp(['Error! Does not handle version ' num2str(version)]);
else
disp(['Reading from version ' num2str(version)]);
end
numEntries = fread(fp, 1, 'int');
colortable.numEntries = numEntries;
len = fread(fp, 1, 'int');
colortable.orig_tab = fread(fp, len, '*char')';
colortable.orig_tab = colortable.orig_tab(1:end-1);
colortable.struct_names = cell(numEntries,1);
colortable.table = zeros(numEntries,5);
numEntriesToRead = fread(fp, 1, 'int');
for i = 1:numEntriesToRead
structure = fread(fp, 1, 'int')+1;
if (structure < 0)
disp(['Error! Read entry, index ' num2str(structure)]);
end
if(~isempty(colortable.struct_names{structure}))
disp(['Error! Duplicate Structure ' num2str(structure)]);
end
len = fread(fp, 1, 'int');
colortable.struct_names{structure} = fread(fp, len, '*char')';
colortable.struct_names{structure} =
colortable.struct_names{structure}(1:end-1);
colortable.table(structure,1) = fread(fp, 1, 'int');
colortable.table(structure,2) = fread(fp, 1, 'int');
colortable.table(structure,3) = fread(fp, 1, 'int');
colortable.table(structure,4) = fread(fp, 1, 'int');
colortable.table(structure,5) = colortable.table(structure,1) +
colortable.table(structure,2)*2^8 + colortable.table(structure,3)*2^16 +
colortable.table(structure,4)*2^24;
end
disp(['colortable with ' num2str(colortable.numEntries) ' entries read
(originally ' colortable.orig_tab ')']);
end
else
disp('Error! Should not be expecting bool = 0');
end
fclose(fp);
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
