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 Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
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 Magalhães 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 Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br http://www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
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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 Magalhães 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 Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br http://www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
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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 Magalhães 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 Magalhães 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
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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.
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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.
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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 commandline, 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 ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks.
It works as I wished.
from surfer import io as sIo a = sIo.read_annot('label/lh.aparc.annot') b = sIo.read_geometry('surf/lh.pial')
And now I can have each vertex labeled --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
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 commandline, 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 Juniorwrote: 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 ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Have you tried using mri_annotation2label with the --seg output option? doug
Michael Waskom wrote:
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 mailto: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 <mailto: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 <http://www.netfilter.com.br> -- For mobile:�http://itunes.apple. com/br/artist/netfilter/ id365306441 <http://itunes.apple.com/br/artist/netfilter/id365306441> ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <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 <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 <mailto: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.
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Yes, but --seg in mri_annotation2label --subject bert --hemi lh --seg saida.mgz produces a volume and not a surface. --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
On Tue, Oct 11, 2011 at 13:12, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Have you tried using mri_annotation2label with the --seg output option? doug
Michael Waskom wrote:
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 <mailto: fischl@nmr.mgh.**harvard.edu 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 <mailto:fischl@nmr.mgh.**harvard.edu <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 <http://www.netfilter.com.br> -- For mobile:�http://itunes.apple. com/br/artist/netfilter/ id365306441 <http://itunes.apple.com/br/**artist/netfilter/id365306441<http://itunes.apple.com/br/artist/netfilter/id365306441>______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------**------------------------------**
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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 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 commandline, 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 Juniorwrote: 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 ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://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/**compliancelinehttp://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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 <mwaskom@stanford.edu mailto: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 <mailto: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 <mailto: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 <http://www.netfilter.com.br> -- For mobile:�http://itunes.apple.com/br/artist/netfilter/id365306441 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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.
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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.
oops, sorry list, this was supposed to go to Pedro...
On 15/10/11 17:39, Anderson Winkler wrote:
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 <mwaskom@stanford.edu mailto: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 <mailto: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 <mailto: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 <http://www.netfilter.com.br> -- For mobile:�http://itunes.apple.com/br/artist/netfilter/id365306441 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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.
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freesurfer@nmr.mgh.harvard.edu