Hi Doug,

Thank you for your help! Yes, I have followed the points using vertex indices but there were some that didn't match up. It could be because of the 1-based indexing. Where would I change this? I am using freesurfer_read_surface.m to read in the vertices and faces :

function [vertices, faces] = freesurfer_read_surf(fname)

% freesurfer_read_surf - FreeSurfer I/O function to read a surface file

%

% [vertices, faces] = freesurfer_read_surf(fname)

%

% Reads the vertex coordinates (mm) and face lists from a surface file.

% Copyright (C) 2000  Darren L. Weber

% History:  08/2000, Darren.Weber_at_radiology.ucsf.edu

%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% There used to be a line here where ver was set to the version of

% the file. Without it, "ver" reverts to a matlab defined structure

% and generates an error.

%fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

if(nargin < 1)

    help freesurfer_read_surf;

    return;

end

%QUAD_FILE_MAGIC_NUMBER =  (-1 & 0x00ffffff) ;

%NEW_QUAD_FILE_MAGIC_NUMBER =  (-3 & 0x00ffffff) ;

TRIANGLE_FILE_MAGIC_NUMBER  =  16777214;

QUAD_FILE_MAGIC_NUMBER      =  16777215;

% open it as a big-endian file

fid = fopen(fname, 'rb', 'b');

if (fid < 0),

    str = sprintf('could not open surface file %s.', fname);

    error(str);

end

fprintf('...reading surface file: %s\n', fname);

tic;

magic = freesurfer_fread3(fid);

if (magic == QUAD_FILE_MAGIC_NUMBER),

    Nvertices = freesurfer_fread3(fid);

    Nfaces = freesurfer_fread3(fid);

    fprintf('...reading %d quad file vertices\n',Nvertices);

    vertices = fread(fid, Nvertices*3, 'int16') ./ 100 ; 

    if (nargout > 1),

        fprintf('...reading %d quad file faces (please wait)\n',Nfaces);

        faces = zeros(Nfaces,4);

        for iface = 1:Nfaces,

            for n=1:4,

                faces(iface,n) = freesurfer_fread3(fid) ;

end

            if(~rem(iface, 10000)), fprintf(' %7.0f',iface); end

            if(~rem(iface,100000)), fprintf('\n'); end

end

end

elseif (magic == TRIANGLE_FILE_MAGIC_NUMBER),

    fprintf('...reading triangle file\n');

    tline = fgets(fid); % read creation date text line

    tline = fgets(fid); % read info text line

    Nvertices = fread(fid, 1, 'int32'); % number of vertices

    Nfaces = fread(fid, 1, 'int32'); % number of faces

    % vertices are read in column format and reshaped below

    vertices = fread(fid, Nvertices*3, 'float32');

    % faces are read in column format and reshaped

    faces = fread(fid, Nfaces*3, 'int32');

    faces = reshape(faces, 3, Nfaces)';

else

    str = sprintf('unknown magic number in surface file %s.', fname);

    error(str);

end

vertices = reshape(vertices, 3, Nvertices)';

fclose(fid);

fprintf('...adding 1 to face indices for matlab compatibility.\n');

faces = faces + 1;

t=toc; fprintf('...done (%6.2f sec)\n\n',t);

return

ii) Also, I want to transform a section
            of the inflated surface into a 2D flatmap, and
            import it into MATLAB while maintaining the same
              VertexIDs so I know which vertex on the flatmap
            corresponds to a vertex on a pial surface. Do you know how I
            can do this? I have created multiple flatmaps in Freeview by
            :

Creating a patch on lh.inflated in Freeview and saving
                it

              
Flattening the patch using mris_flatten() in terminal 
Loading lh.inflated in Freeview and then loading the
                flattened patch which then creates a 2D flatmap
However, I cannot figure out how to load this 2D
              flatmap into MATLAB. I've tried saving the result in (3)
              as a surface and then loading it into matlab with
              freesurfer_read_surf.m. This takes a long time and the
              result looks a bit distorted. It also does not conserve
              the VertexIDs. Do you have any recommendations?

Many thanks again for your help,

Sarah