Re: [Freesurfer] FreeSurfer & Matlab

-- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA 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 colprintf('40;40', 'Reading curvature file', astr_curv); [v_curv, fnum] = read_curv(astr_curv); colprintf('40;40', 'Number of curv elements', sprintf('%d', numel(v_curv))); if b_invCurv colprintf('40;40', 'Invert curvature data sign', sprintf('%d', 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 % ---------------------------------------------------------