Ah Pedro,
Se era isso que você precisava, poderia ter falado. Eu tenho isso
pronto, que pode ser chamado via linha de comandos. Foi usado no paper
que vc deve ter visto...
Abração,
Anderson
On 15/10/11 13:09, Pedro Paulo de Magalhães Oliveira Junior wrote:
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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