matlab lme toolbox on github

Qdec/Qdec2num.m

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+function M = Qdec2num(Qdec)
+% M = Qdec2num(Qdec)
+%
+% Attempts to convert the two dimensional cell string array Qdec to numeric
+% matrix M.
+%
+% Input
+% Qdec: Two dimensional cell string array of Qdec data (eg. read with 
+% fReadQdec).
+%
+% Output
+% M: Numeric matrix (without the name of the variables).
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+Qdec = Qdec(2:end,:);
+M = str2double(Qdec);

Qdec/fReadQdec.m

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+function Qdec = fReadQdec(fname)
+% Qdec = fReadQdec(fname) 
+%
+% Reads a Freesurfer's Qdec table file into cell string array Qdec.
+%
+% Input
+% fname: The name of a Qdec table data file. 
+%
+% Output
+% Qdec: Two dimensional cell string array with the data.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+fid = fopen(fname);
+tline = fgetl(fid);
+Qdec = [];
+i = 1;
+while ischar(tline)
+    j = 1;
+    [str,remain] = strtok(tline, ' ');   
+    while ~isempty(str)
+        Qdec{i,j} = str;
+        j = j + 1;
+        [str,remain] = strtok(remain, ' ');
+    end
+    i = i + 1;
+    tline = fgetl(fid);
+end
+fclose(fid); 

Qdec/fWriteQdec.m

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+function fWriteQdec(fname,Qdec)
+% fWriteQdec(fname,Qdec)
+%
+% Writes cell string array Qdec to a Freesurfer's Qdec table data file.
+%
+% Input
+% fname: The name of a Qdec table data file. 
+% Qdec: Two dimensional cell string array with the data.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+if nargin < 2
+    error('Too few inputs');
+end;
+szQ = size(Qdec);
+fid = fopen (fname,'w');
+if fid < 0
+    error('Do you have write permissions for %s?', pwd);
+end
+if ~strcmp(Qdec{1,1},'fsid')
+      warning('Dat{1,1} is not ''fsid'' will change it ');
+      Qdec{1,1} = 'fsid';
+end;
+for i=1:szQ(1)
+    j = 1;
+    while j < szQ(2)
+        fprintf(fid, [char(Qdec{i,j}) ' ']);
+        j = j + 1;
+    end;
+    fprintf(fid, [char(Qdec{i,j}) '\n']);
+end;
+fclose (fid);

Qdec/findQdecVar.m

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+function col = findQdecVar(Qdec,name)
+% col = findQdecVar(Qdec,name)
+%
+% Gives the column of a variable in a Freesurfer's Qdec table that was read 
+% into the two dimensional cell string array Qdec. Returns empty if the 
+% variable is not in the Qdec table.
+%
+% Input
+% Qdec: Two dimensional cell string array of Qdec data (eg. read with 
+% fReadQdec).
+% name: A string with the name of the variable. 
+%
+% Output
+% col: Column of the variable in the cell string array Qdec.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+if nargin < 2
+    error('Too few inputs');
+end;
+col = find(strcmp(getQdecVars(Qdec),name));

Qdec/getQdecVarData.m

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+function Qdec2 = getQdecVarData(Qdec1,Vars)
+% Qdec2 = getQdecVarData(Qdec1,Vars)
+%
+% Returns the data for the variables in Qdec table Qdec1 that are named in 
+% Vars.
+%
+% Input
+% Qdec1: Two dimensional cell string array of Qdec data (eg. read with 
+% fReadQdec).
+% Vars: One dimensional cell string array.
+%
+% Output
+% Qdec2: Two dimensional cell string array of Qdec data.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+if nargin < 2
+    error('Too few inputs');
+end;
+Qdec2 = {};
+for i=1:length(Vars)
+    col = findQdecVar(Qdec1,Vars{i});
+    if ~isempty(col)
+        Qdec2 = [Qdec2 Qdec1(:,col)];
+    else
+        error(['The variable ''' Vars{i} ''' is not in the Qdec table']);
+    end;
+end;

Qdec/getQdecVars.m

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+function Vars = getQdecVars(Qdec)
+% Vars = getQdecVars(Qdec)
+%
+% Returns a one dimensional cell string array with the name of the variables
+% in Qdec.
+%
+% Input
+% Qdec: Two dimensional cell string array of Qdec data.
+%
+% Output
+% Vars: One dimensional cell string array.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+Vars = Qdec(1,:)';

Qdec/num2Qdec.m

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+function Qdec = num2Qdec(M,Vars)
+% Qdec = num2Qdec(M,Vars)
+%
+% Converts numeric matrix M to two dimensional cell string array Qdec.
+%
+% Input
+% M: Numeric matrix.
+% Vars: One dimensional cell string array with the name of the Qdec 
+% variables corresponding to the columns of M.
+%
+% Output
+% Qdec: Two dimensional cell string array of Qdec data .
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+if nargin < 2
+    error('Too few inputs');
+end;
+szM = size(M);
+Qdec = cell(szM(1)+1,szM(2));
+Qdec(1,1:end) = Vars;
+for i=2:szM(1)+1
+    for j=1:szM(2)
+        Qdec{i,j} = num2str(M(i-1,j));
+    end;
+end;

Qdec/rmQdecCol.m

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+function Qdec2 = rmQdecCol(Qdec1,col)
+% Qdec2 = rmQdecCol(Qdec1,col)
+%
+% Removes the specify column from cell string array Qdec1. 
+%
+% Input
+% Qdec1: Two dimensional cell string array of Qdec data (eg. read with 
+% fReadQdec).
+% col: Column to be removed.
+%
+% Output
+% Qdec2: Two dimensional cell string array of Qdec data.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+if nargin < 2
+    error('Too few inputs');
+end;
+Qdec2 = [Qdec1(:,1:col-1) Qdec1(:,col+1:end)]; 
+
+

fs_read_Y.m

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+function [Y,mri] = fs_read_Y(Y_fname)
+% [Y,mri] = fs_read_Y(Y_fname)
+% 
+% Reads Freesurfer's .mgh or .mgz data files (eg. cortical thickness data 
+% files generated with mris_preproc).
+%
+% Input
+% Y_fname: A Freesurfer's cortical data file.
+%
+% Output
+% Y: Data matrix (nmxnv, nm total # of maps, nv #vertices). 
+% mri: Mri structure.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+
+if nargin < 1
+    error('Too few inputs');
+end;
+mri = struct('M',[],'mr_parms',[],'volsz',[]);
+[Y,M,mr_parms,volsz] = load_mgh(Y_fname);
+if (isempty(M))
+    error(['Can not load ' Y_fname ' as an mgh or mgz file']);
+end;
+mri.M = M;
+mri.mr_parms = mr_parms;
+mri.volsz = volsz;
+nv = volsz(1)*volsz(2)*volsz(3);
+Y = reshape(Y,[nv volsz(4)])';

fs_read_label.m

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+function [vtxs,nvtxs] = fs_read_label(labelf)
+% [vtxs,nvtxs] = fs_read_label(labelf)
+% 
+% Reads the indices of the vertices of a Freesurfer's label. 
+%
+% Input
+% labelf: A Freesurfer's label file.
+%
+% Output
+% vtxs: Indices of the vertices (1-based). 
+% nvtxs: The number of vertices in the label.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+fid = fopen(labelf);
+tline = fgetl(fid);
+nvtxs = fscanf(fid,'%d',1);
+vtxs = uint32(fscanf(fid,'%d %*g %*g %*g %*g',[1 nvtxs])); 
+vtxs = vtxs + 1;
+fclose(fid); 
+

fs_read_surf.m

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+function Surf = fs_read_surf(fname)
+% Surf = fs_read_surf(fname)
+% 
+% Reads coordinates and triangles of a Freesurfer's surf (Depends on 
+% Freesurfer's read_surf function).
+%
+% Input
+% fname: A Freesurfer's surface file.
+%
+% Output
+% Surf: Surface which represent a coordinate system where the analysis is 
+% to be done. It is a structure with Surf.tri = t x 3 matrix of triangle 
+% indices, 1-based, t=#triangles and Surf.coord = 3 x nv matrix of 
+% coordinates, nv=#vertices.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/02/02 11:25:52 $
+%    $Revision: 1.1 $
+%
+[coord,faces] = read_surf(fname);
+Surf.tri = uint32(faces + 1);
+Surf.coord = coord';

fs_write_Y.m

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+function fs_write_Y(Y,mri,fname)
+% fs_write_Y(Y,mri,fname)
+% 
+% Writes volume Y to a Freesurfer's .mgh or .mgz data file.  
+%
+% Input
+% Y: Data matrix or vector.
+% mri: Mri structure (read with fs_read_Y).
+% fname: Output file name.
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/07/19 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/07/19 11:25:52 $
+%    $Revision: 1.1 $
+%
+if nargin < 3
+    error('Too few inputs');
+end;
+save_mgh(reshape(Y',mri.volsz),fname,mri.M,mri.mr_parms);

fs_write_fstats.m

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+function fs_write_fstats(fstats,mri,fname,data_type)
+% fs_write_fstats(fstats,mri,fname,data_type)
+% 
+% Writes F-statistic or p-value or Freesurfer significance maps to Freesurfer's 
+% .mgh or .mgz data file. This can be useful for visualization and post-processing 
+% in Freesurfer. 
+%
+% Input
+% fstats: Structure obtained from lme_mass_F.
+% mri: Mri structure (read with fs_read_Y).
+% fname: Output file name.
+% data_type: Determines what is going to be written. This input can be one 
+% of three strings: 'fval' (signed F-statistic map), 'pval' (signed p-value map) 
+% or 'sig' (Freesurfer significance map -log10(pval).*sgn).
+%
+% $Revision: 1.1.1.1 $  $Date: 2012/07/19 11:25:52 $
+% Original Author: Jorge Luis Bernal Rusiel 
+% CVS Revision Info:
+%    $Author: jbernal$
+%    $Date: 2012/07/19 11:25:52 $
+%    $Revision: 1.1 $
+%
+if nargin < 4
+    error('Too few inputs');
+end;
+mri.volsz(4) = 1;
+if strcmpi(data_type,'fval')
+    fs_write_Y(fstats.F.*fstats.sgn,mri,fname);
+elseif strcmpi(data_type,'pval')
+    pval = fstats.pval.*fstats.sgn;
+    pval(pval==1) = 1;
+    fs_write_Y(pval,mri,fname);
+elseif strcmpi(data_type,'sig')
+    fs_write_Y(-log10(fstats.pval).*fstats.sgn,mri,fname);
+else
+    error('Valid strings for data_type are ''fval'' or ''pval'' or ''sig''');
+end;
+
+