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
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<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.eduFreesurfer@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
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<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<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
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<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 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html