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])
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.