Michael,
Thanks for the hint.
Here's a program that converts the surface + annotation in a Stanford
PLY Object file
# Create ply
# Stanford Object format
from surfer import io as io_
surface = io_.read_geometry
('/Applications/freesurfer/subjects/bert/surf/lh.pial')
labels = io_.read_annot
('/Applications/freesurfer/subjects/bert/label/lh.aparc.annot')
facenum = len(surface[1])
vertnum = len(surface[0])
print "ply"
print "format ascii 1.0"
print "comment VCGLIB generated"
print "element vertex %d"%vertnum
print "property float x"
print "property float y"
print "property float z"
#print "property int flags"
print "property uchar red"
print "property uchar green"
print "property uchar blue"
print "property uchar alpha"
print "element face %d"%facenum
print "property list uchar int vertex_indices"
print "end_header"
for i in xrange(vertnum):
vert = surface[0][i];
color = labels[1][labels[0][i]]
print "%f %f %f %d %d %d
%d"%(vert[0],vert[1],vert[2],color[0],color[1],color[2],color[3])
for i in xrange(facenum):
face = surface[1][i]
print "3 %d %d %d"%(face[0],face[1],face[2])
2011/10/9 Michael Waskom <mwas...@stanford.edu
<mailto:mwas...@stanford.edu>>
If you know Python, you can likely do this pretty easily with
tools from the PySurfer package: http://pysurfer.github.com/
(Check out surfer.io.read_annotation).
If you're just using the io routines, you won't need the somewhat
heavy Mayavi visualization dependencies. You should be able to
read in and manipulate surfaces/annotations just with numpy.
Best,
Michael
2011/10/8 Bruce Fischl <fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>>
it wouldn't be that hard to put something together if you
want to avoid matlab. Spec out what you need and send me a
sample, maybe on Bert
Bruce
On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior
wrote:
Thanks.
I suppose I can't do this without matlab. Right?
-- iOS 5.0
Em 08/10/2011, às 19:29, Bruce Fischl
<fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>> escreveu:
there is a write_annotation.m file you can use
On Sat, 8 Oct 2011, Anderson Winkler wrote:
ops, it seems the comments inside the dpxwrite.m
no longer reflect what it does. You probably
don't need this, but anyway, the version attached
is more up-to-date.
Anderson
On 08/10/11 17:28, Anderson Winkler wrote:
Hi Pedro,
There is probably a way to do that using FS
tools from the command line, but the attached
script should do the same. The result is a
"data-per-vertex" file, which
is the same as the .asc files from
mris_convert. There is no geometry input, hence
the vertex coordinates are all set to (0,0,0).
Hope it helps!
All the best,
Anderson
On 08/10/11 17:17, Pedro Paulo de Magalh�es
Oliveira Junior wrote:
I need to create a file where I have
the parcellation value (structure name) per vertex.
I've tried�mris_convert --annot
/Applications/freesurfer/subjects/bert/label/lh.aparc.annot
/Applications/freesurfer/subjects/bert/surf/lh.pial
parc.asc
But I get the error:�ERROR: unknown file annot
file type specified for output: saida.asc
Has someone done this before?
Thanks
---------------------------------------------------------------------
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Netfilter & SpeedComm Telecom --
www.netfilter.com.br <http://www.netfilter.com.br>
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