Hi Pedro,
There is probably a way to do that using FS tools from the command line,
but the attached script should do the same. The result is a
"data-per-vertex" file, which is the same as the .asc files from
mris_convert. There is no geometry input, hence the vertex coordinates
are all set to (0,0,0).
Hope it helps!
All the best,
Anderson
On 08/10/11 17:17, Pedro Paulo de Magalhães Oliveira Junior wrote:
I need to create a file where I have the parcellation value (structure
name) per vertex.
I've tried mris_convert --annot
/Applications/freesurfer/subjects/bert/label/lh.aparc.annot
/Applications/freesurfer/subjects/bert/surf/lh.pial parc.asc
But I get the error: ERROR: unknown file annot file type specified for
output: saida.asc
Has someone done this before?
Thanks
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Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
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function annot2dpv(annotfile,dpvfile)
% Convert an annotation file to a DPV file.
%
% Usage:
% annot2dpv(annotfile,dpvfile)
%
% Inputs:
% annotfile : Annotation file.
% dpvfile : Output DPV file.
%
% Before running, be sure that ${FREESURFER_HOME}/matlab is in your
% OCTAVE/MATLAB path.
%
% _____________________________________
% Anderson M. Winkler
% Yale University / Institute of Living
% Aug/2011
% Read the annotation file
[vtx,lab,ctab] = read_annotation(annotfile);
% For each structure, replace its coded colour by its index
for s = 1:ctab.numEntries,
lab(lab==ctab.table(s,5)) = s;
end
% Save the result
dpxwrite(dpvfile,lab)
function crvwrite(varargin)
% Write a curvature file (DPV or DPF), in ASCII format.
% This function is much faster than 'dlmread' for large files,
% and works only in Linux and Mac.
%
% crvwrite(filename,crv)
% crvwrite(filename,crv,crd,idx)
%
% - fname is the file name to be created
% - crv contains the values for each vertex or face
% - crd contains the vertex coordinates or face indices
% - idx contains vertex or face sequential index
%
% _____________________________________
% Anderson M. Winkler
% Yale University / Institute of Living
% Aug/2011
% File name
fname = varargin{1};
% Get the actual data
crv = varargin{2}(:);
nX = numel(crv);
% Check if all are integers and use appropriate formating
if all(mod(crv,1)==0),
fstr = '%d';
else
fstr = '%f';
end
if nargin == 2,
% Organise the data, fill the coords with zeros amd prep to save
crv = [(0:nX-1) ; zeros(3,nX) ; crv'];
elseif nargin == 4,
% Organise the coords
crd = varargin{3};
if size(crd,1) > size(crd,2),
crd = crd';
end
% Take the indices
idx = varargin{4}(:);
% Prepare to save
crv = [idx' ; crd ; crv'];
else
error('Incorrect number of arguments');
end
% Save
fid = fopen(fname,'w');
fprintf(fid,['%d %g %g %g ' fstr ' \n'],crv);
fclose(fid);
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
