Bruce Fischl wrote:
(2) Import that surface onto Matlab and visualize it there.
There is such a visualizer in the 'dev' tree of FreeSurfer -- called
'mris_display'. I've appended the relevant m files -- just save to a dir
on your MatLAB path.
-=R
--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
function [] = colprintf(aC, astr_LC, varargin)
%
% NAME
%
% function [] = colprintf(aC, astr_LC, format, ...)
% $Id: colprintf.m,v 1.2 2010/02/01 20:52:10 rudolph Exp $
%
% ARGUMENTS
% INPUT
% aC class/col width if class - queried for col
% widths, else parsed for
% width spec
% astr_LC string Left-column 'intro' text
% format, ... string C-style format string to print
% in right column.
%
% OPTIONAL
%
% DESCRIPTION
%
% Prints two-tuple text inputs in two-columns, with column widths
% defined in the hosting class <aC> or alternatively if aC is a
% string of form "<LC>;<RC>"
%
% A carriage-return is appended to the end of the right string
% col.
%
% NOTE:
%
% HISTORY
% 18 September 2009
% o Initial design and coding.
%
LC = 40;
RC = 40;
verbosity = 1;
if isobject(aC)
LC = aC.m_LC;
RC = aC.m_RC;
verbosity = aC.m_verbosity;
else
[str_LC, str_RC] = strtok(aC, ';');
LC = str2num(str_LC);
RC = str2num(str_RC);
end
sfrmt = sprintf(varargin{:});
if length(astr_LC) & verbosity
fprintf(1, '%s', sprintf('%*s', LC, astr_LC));
end
if length(sfrmt) & verbosity
fprintf(1, '%s', sprintf('%*s\n', RC, sfrmt));
end
end
function [hf, hp, av_filtered] = mris_display(astr_mris, astr_curv, varargin)
%
% NAME
% [hf, hp, av_filtered] = ...
% mris_display( astr_mris, ...
% astr_curv ...
% <, a_az, ...
% a_el, ...
% af_bandFilter, ...
% ab_invMap>
% )
% $Id: mris_display.m,v 1.2 2010/02/01 20:52:10 rudolph Exp $
%
%
% ARGUMENTS
%
% INPUT
% astr_mris string filename of surface file to load
% astr_curv string filename of curvature file to load
%
% OPTIONAL
% a_az float azimuth of viewpoint
% a_el float elevation of viewpoint
% af_bandFilter float apply a symmetrical band pass filt
% between +- <af_bandFilter>
% ab_invMap bool if true, invert the sign of the
% curvature data -- useful if 'neg'
% values are on gyri and 'pos' values
% in sulci.
%
% OUTPUT
% hf handle handle to generated figure
% hp handle handle to patch
% av_filtered vector number of vertices in original curv
% that have been filtered out by the
% <af_bandFilter>.
%
% DESCRIPTION
%
% 'mris_display' reads a FreeSurfer surface structure and
% displays it as seen from an optional <a_az, a_el>.
%
% The <av_curv> can be further band pass filtered by passing
% an <af_bandFilter> parameter, in which case the curvature
% vector is hardlimited to [-<af_bandFilter>, ... <af_bandFilter>].
%
% PRECONDITIONS
% o <astr_mris> and <astr_curv> should be valid filenamesi.
% o FreeSurfer environment.
%
% POSTCONDITIONS
% o Figure is generated.
% o handle to figure is returned.
%
% HISTORY
% 26 August 2009
% o Initial design and coding.
%
% ---------------------------------------------------------
%%%%%%%%%%%%%%
%%% Nested functions :START
%%%%%%%%%%%%%%
function error_exit( str_action, str_msg, str_ret)
fprintf(1, '\tFATAL:\n');
fprintf(1, '\tSorry, some error has occurred.\n');
fprintf(1, '\tWhile %s,\n', str_action);
fprintf(1, '\t%s\n', str_msg);
error(str_ret);
end
function vprintf(level, str_msg)
if verbosity >= level
fprintf(1, str_msg);
end
end
%%%%%%%%%%%%%%
%%% Nested functions :END
%%%%%%%%%%%%%%
sys_printf('mris_display: START\n');
az = 270;
el = 0;
b_bandFilter = 0;
af_bandFilter = 1;
b_invCurv = 0;
% Parse optional arguments
if length(varargin) >= 1, az = varargin{1}; end
if length(varargin) >= 2, el = varargin{2}; end
if length(varargin) >= 3
b_bandFilter = 1;
af_bandFilter = varargin{3};
end
if length(varargin) >= 4, b_invCurv = varargin{4}; end
% Read curvature file
cprintsn('Reading curvature file', astr_curv);
[v_curv, fnum] = read_curv(astr_curv);
cprintdn('Number of curv elements', numel(v_curv));
if b_invCurv
cprintdn('Invert curvature data sign', b_invCurv);
v_curv = v_curv * -1;
end
% Read surface
colprintf('40;40', 'Reading mris file', astr_mris);
[v_vertices, v_faces] = read_surf(astr_mris);
v_vertSize = size(v_vertices);
v_faceSize = size(v_faces);
str_vertSize = sprintf('%d x %d', v_vertSize(1), v_vertSize(2));
str_faceSize = sprintf('%d x %d', v_faceSize(1), v_faceSize(2));
colprintf('40;40', 'Size of vert struct', str_vertSize);
colprintf('40;40', 'Size of face struct', str_faceSize);
if numel(v_curv) ~= v_vertSize(1)
error_exit( 'reading inputs', ...
'mismatch between curvature size and surf vertices', ...
'1');
end
v_vertices = single(v_vertices);
v_faces = int32(v_faces+1); % for matlab compliance
av_filtered = [0 0];
if b_bandFilter
lowerCount = numel(find(v_curv<-af_bandFilter));
upperCount = numel(find(v_curv>af_bandFilter));
av_filtered = [lowerCount upperCount];
v_curv = filter_bandPass(v_curv, ...
-af_bandFilter, af_bandFilter, 1);
end
% Display:
hf = figure;
hp = patch('vertices', v_vertices, ...
'faces', v_faces(:,[1 3 2]), ...
'facevertexcdata', v_curv, ...
'edgecolor', 'none', ...
'facecolor', 'interp');
axis equal;
grid;
%colormap('winter');
demcmap(v_curv);
title(sprintf('%s: %s', astr_mris, astr_curv));
colorbar;
view(az, el);
sys_printf('mris_display: END\n');
end
% ---------------------------------------------------------
function [s] = sys_printf(varargin)
%
% NAME
%
% function [s] = sys_printf(format, ...)
% $Id: sys_printf.m,v 1.2 2010/02/01 20:52:10 rudolph Exp $
%
% ARGUMENTS
% INPUT
% format, ... string C-style format string to print
% OPTIONAL
%
% OUTPUT
% s string syslog-style prefixed string
%
% DESCRIPTION
%
% This function prepends <format> with syslog_prefix().
%
% PRECONDITIONS
%
% POSTCONDITIONS
% o string is returned and printed.
%
% NOTE:
%
% HISTORY
% 12 December 2008
% o Initial design and coding.
%
sfrmt = sprintf(varargin{:});
s = sprintf('%s %s', syslog_prefix(), sfrmt);
fprintf(1, '%s', s);
function [s] = syslog_prefix(varargin)
%
% NAME
%
% function [s] = syslog_prefix()
% $Id: syslog_prefix.m,v 1.2 2010/02/01 20:52:10 rudolph Exp $
%
% ARGUMENTS
% INPUT
%
% OPTIONAL
%
% OUTPUT
% s string syslog-style prefix string
%
% DESCRIPTION
%
% This function generates a syslog-style prefix string,
% suitable for time stamping log-type messages
%
% PRECONDITIONS
%
% o un*x runtime that understands the 'host' command
%
% POSTCONDITIONS
%
% o s = "YYYY mmm dd hh:mm:ss <host>"
%
% NOTE:
%
% HISTORY
% 02 August 2007
% o Initial design and coding.
%
[str_ret str_hostname] = system('hostname');
[str_host str_rem] = strtok(str_hostname, char(10));
clk = fix(clock);
year = clk(1);
month = clk(2);
day = clk(3);
hour = clk(4);
minute = clk(5);
seconds = clk(6);
switch(month)
case 1
str_month = 'Jan';
case 2
str_month = 'Feb';
case 3
str_month = 'Mar';
case 4
str_month = 'Apr';
case 5
str_month = 'May';
case 6
str_month = 'Jun';
case 7
str_month = 'Jul';
case 8
str_month = 'Aug';
case 9
str_month = 'Sep';
case 10
str_month = 'Oct';
case 11
str_month = 'Nov';
case 12
str_month = 'Dec';
end
s = sprintf('%d %s %02d %02d:%02d:%02d %s', year, str_month, ...
day, hour, minute, seconds, str_host);_______________________________________________
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