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>
> 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>
>
>> 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>
>>> 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
>>>>> ------------------------------**------------------------------**
>>>>> ---------
>>>>> Pedro Paulo de Magalh�es Oliveira Junior
>>>>> Netfilter & SpeedComm Telecom -- www.netfilter.com.br
>>>>> -- For mobile:�http://itunes.apple.**com/br/artist/netfilter/**
>>>>> id365306441 <http://itunes.apple.com/br/artist/netfilter/id365306441>
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