Luke,
attached is a modified read_surf.m which reads the stuff written after
the vertex and face data normally found in the surface binary-formatted
file. this was reverse-engineered from the source files
'mrisurf.c' (function MRISwriteTriangularSurface) and
'transform.c' (function writeVolGeom). so the new call is:
[v,f,flags,tags]=read_surf('rh.pial');
you can ignore 'flags', and 'tags' is char array, which can be printed,
like this:
sprintf('%s',tags)
giving output like:
ans =
valid = 1 # volume info valid
filename = ../mri/filled-pretess127.mgz
volume = 256 256 256
voxelsize = 1.000000000000000e+00 1.000000000000000e+00
1.000000000000000e+00
xras = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e
+00
yras = 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e
+00
zras = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e
+00
cras = 5.399719238281250e+00 1.800000000000000e+01 0.000000000000000e
+00
mris_remove_intersection ../surf/rh.orig ......
the volume geometry will always be the first eight lines of text.
unfortunately, being text, you will need to do further parsing to
extract what you need. after the volume geometry info are provenance
strings.
Nick
On Thu, 2012-11-08 at 08:21 -0500, Luke Bloy wrote:
> Thanks for the reply Nick,
>
>
> Yes mris_info does return information I would need.
>
>
> volume geometry:
> extent : (256, 256, 256)
> voxel : ( 1.0000, 1.0000, 1.0000)
> x_(ras) : (-1.0000, 0.0000, 0.0000)
> y_(ras) : ( 0.0000, 0.0000, -1.0000)
> z_(ras) : ( 0.0000, 1.0000, 0.0000)
> c_(ras) : ( 5.8612, -8.9756, -36.8004)
> file : ../mri/filled-pretess255.mgz
>
>
> interestingly even if I move the surface file out of the subject's
> surf directory it still returns this info, making me think that it is
> in the file somewhere.
>
>
> I was looking at read_surf.m last night and it doesnt seem to do
> anything with this info,
> and http://wideman-one.com/gw/brain/fs/surfacefileformats.htm doesn't
> mention any of this info being in the file. is there an updated spec
> file on the file formats?
>
>
> Thanks.
> -Luke
>
>
>
>
>
> On Wed, Nov 7, 2012 at 3:26 PM, Nick Schmansky
> <ni...@nmr.mgh.harvard.edu> wrote:
> Luke,
>
> A quick answer (w/o looking into it too much): does:
>
> mris_info rh.pial
>
> give you the info you need? what i'm not sure of is whether
> everything
> you see in that output is available in the structure that the
> matlab
> surface reader loads.
>
> Nick
>
>
> On Wed, 2012-11-07 at 09:17 -0500, Luke Bloy wrote:
> > Hi all,
> >
> >
> >
> > I’m not sure where the best place to make this request is…
> so I
> > thought I’ll put this here.
> >
> >
> >
> > I often use freesurfer generated surfaces and images in
> other software
> > packages (Slicer, Matlab etc) for various things. The MGZ
> files
> > include the origin in the file headers, meaning that
> software can
> > correctly interpret the world spaces of these images,
> allowing correct
> > overlays with other results computed from the same scans.
> The problem
> > is that the surface files treat the 128,128,128 voxel ( of
> the T1.mgz
> > and other images) as the origin. But the world coordinates
> of this
> > origin are, to my knowledge not in the surface files.
> >
> >
> >
> > This creates the situation that to correctly interpret these
> surfaces
> > in relation to other coordinates systems, basically I either
> need to
> > ignore the world coordinates and do some registration, or I
> need to
> > load both an mgz file (to get the origin) and surface files
> to learn
> > correct world coordinates of the surfaces. Ideally it seems
> like this
> > information should be included in the surface files
> themselves.
> >
> >
> >
> > Hopefully my description of the problem makes some sense.
> >
> >
> >
> > Thanks.
> >
> > Luke
> >
> >
> >
> >
>
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
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function [vertex_coords, faces, flags, tags] = read_surf(fname)
%
% [vertex_coords, faces] = read_surf(fname)
% reads a the vertex coordinates and face lists from a surface file
% note that reading the faces from a quad file can take a very long
% time due to the goofy format that they are stored in. If the faces
% output variable is not specified, they will not be read so it
% should execute pretty quickly.
%
%
% read_surf.m
%
% Original Author: Bruce Fischl
% CVS Revision Info:
% $Author: fischl $
% $Date: 2011/09/29 14:20:17 $
% $Revision: 1.5 $
%
% Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
%
% Terms and conditions for use, reproduction, distribution and contribution
% are found in the 'FreeSurfer Software License Agreement' contained
% in the file 'LICENSE' found in the FreeSurfer distribution, and here:
%
% https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
%
% Reporting: freesurfer@nmr.mgh.harvard.edu
%
%fid = fopen(fname, 'r') ;
%nvertices = fscanf(fid, '%d', 1);
%all = fscanf(fid, '%d %f %f %f %f\n', [5, nvertices]) ;
%curv = all(5, :)' ;
% open it as a big-endian file
%QUAD_FILE_MAGIC_NUMBER = (-1 & 0x00ffffff) ;
%NEW_QUAD_FILE_MAGIC_NUMBER = (-3 & 0x00ffffff) ;
TRIANGLE_FILE_MAGIC_NUMBER = 16777214 ;
QUAD_FILE_MAGIC_NUMBER = 16777215 ;
fid = fopen(fname, 'rb', 'b') ;
if (fid < 0)
str = sprintf('could not open curvature file %s.', fname) ;
error(str) ;
end
magic = fread3(fid) ;
if(magic == QUAD_FILE_MAGIC_NUMBER)
vnum = fread3(fid) ;
fnum = fread3(fid) ;
vertex_coords = fread(fid, vnum*3, 'int16') ./ 100 ;
if (nargout > 1)
for i=1:fnum
for n=1:4
faces(i,n) = fread3(fid) ;
end
end
end
elseif (magic == TRIANGLE_FILE_MAGIC_NUMBER)
fgets(fid) ;
fgets(fid) ;
vnum = fread(fid, 1, 'int32') ;
fnum = fread(fid, 1, 'int32') ;
vertex_coords = fread(fid, vnum*3, 'float32') ;
if (nargout > 1)
faces = fread(fid, fnum*3, 'int32') ;
faces = reshape(faces, 3, fnum)' ;
end
flags=fread(fid, 3, 'int32');
tags=fread(fid, 100000, 'char');
end
vertex_coords = reshape(vertex_coords, 3, vnum)' ;
fclose(fid) ;
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