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 formatfrom 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"%vertnumprint "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"%facenumprint "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])
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
2011/10/9 Michael Waskom <mwaskom@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 <fischl@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 <fischl@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.