Copy the attached matlab file into $FREESURFER/matlab/freesurfer_read_surf.m
On 11/24/2023 12:53 PM, 笹林大樹 wrote:
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Dear Freesurfer experts,
I’m sorry, I would like to add some missing information about the
following question.
OS: CentOS Linux 7
FS ver: fs7.1.0
Matlab ver: R2017a or R2022a
I would be grateful for your answer when you have time.
Best,
Daiki Sasabayashi
転送されたメッセージ:
*差出人: *笹林大樹 <ds...@med.u-toyama.ac.jp>
*件名: **[Freesurfer] Errors in LGI command*
*日付: *2023年11月22日 15:19:36 GMT-5
*宛先: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*返信先: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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Dear Freesurfer experts,
I have run the following command:
*recon-all -s sub-1001 -localGI -no-isrunning*
However, I got the error message as below.
>> Warning: Input argument must be a character vector.
> In ver (line 41) In freesurfer_read_surf (line 70) In
find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>>
ERROR: find_corresponding_center_FSformat did not complete
successfully! Linux dn003 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar
7 15:41:52 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-1001 exited with ERRORS at Wed Nov 22 14:59:33 EST 2023
How can I resolve the problem?
Thank you for your consideration.
Best,
Daiki Sasabayashi
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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.
%
% Surface files are stored as either triangulations or quadrangulations.
% That is, for a triangulation, each face is defined by 3 vertices. For a
% quadrangulation, each face is defined by 4 vertices. The rows of 'faces'
% contain indices into the rows of 'vertices', the latter holds the XYZ
% coordinates of each vertex.
%
% The freesurfer faces index the vertices in counter-clockwise order (when
% viewed from the outside of the surface). This is consistent with a
% right-hand rule. If we have vertices
%
% C B
%
%
% A
%
% Then we can calculate an edge vector from A to B (ie, AB = B - A) and
% another edge vector from A to C (ie, AC = C - A). If you form a "gun"
% with your thumb and forefinger of the right hand, then align your thumb
% with the AB vector and your forefinger with the AC vector, your palm is
% facing out of the screen and extending your middle finger in the
% orthogonal direction to the plane of the screen will give the outward
% surface normal of the triangle ABC. (If you lookup "triangle" on
% Wolfram's mathworld, you can see that AB is referred to as c and AC is
% referred to as b.)
%
% However, if this surface is read into matlab, it will give INWARD surface
% normals in the matlab patch command. For some reason, matlab is not
% following the right hand rule. To get OUTWARD normals with the matlab
% patch command, use faces(:,[1 3 2]) (see below).
%
% The vertex coordinates are in mm. The FreeSurfer coordinate
% system for surfaces is quite simple, but relating to their MRI
% cor-??? files is too confusing to explain here; see the FreeSurfer
% homepage or google the documentation by Graham Wideman. For the
% surfaces, at least, the origin is somewhere in the center of the
% head, and the vertex XYZ coordinates are oriented such that +X is
% right, +Y is anterior and +Z is superior (this is the
% FreeSurfer RAS coordinate system).
%
% Note that reading the faces of a quad file can take a long
% time due to their compact storage format. In this case, the return of
% vertices can be faster if the face output variable is not specified; in
% this case, the faces are not read.
%
% Try this to visualize the surface:
% Hp = patch('vertices',vertices,'faces',faces(:,[1 3 2]),...
% 'facecolor',[.5 .5 .5],'edgecolor','none')
% camlight('headlight','infinite')
% vertnormals = get(Hp,'vertexnormals');
%
% See also freesurfer_write_surf, freesurfer_read_curv,
% freesurfer_read_wfile
%
% 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
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