date:20111009

Re: [Freesurfer] mris_convert exporting parcellation per vertex

2011-10-09 Thread Michael Waskom

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 Magalhï¿½es Oliveira Junior wrote:
I need to create a file where I have the parcellation value
(structure name) per vertex.
I've triedï¿½mris_convert --annot /Applications/freesurfer/**
subjects/bert/label/lh.aparc.**annot
/Applications/freesurfer/**subjects/bert/surf/lh.pial
parc.asc
But I get the error:ï¿½ERROR: unknown file annot file type specified for
output: saida.asc
Has someone done this before?
Thanks
--**--**
-
Pedro Paulo de Magalhï¿½es Oliveira Junior
Netfilter SpeedComm Telecom -- www.netfilter.com.br
-- For mobile:ï¿½http://itunes.apple.**com/br/artist/netfilter/**
id365306441 http://itunes.apple.com/br/artist/netfilter/id365306441
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Re: [Freesurfer] mris_convert exporting parcellation per vertex

2011-10-09 Thread Pedro Paulo de Magalhães Oliveira Junior

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 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 Magalhï¿½es Oliveira Junior
 wrote:
   I need to create a file where I have the parcellation value
 (structure name) per vertex.
 I've triedï¿½mris_convert --annot /Applications/freesurfer/**
 subjects/bert/label/lh.aparc.**annot 
 /Applications/freesurfer/**subjects/bert/surf/lh.pial
 parc.asc
 But I get the error:ï¿½ERROR: unknown file annot file type specified
 for output: saida.asc
 Has someone done this before?
 Thanks
 --**--**
 -
 Pedro Paulo de Magalhï¿½es Oliveira Junior
 Netfilter  SpeedComm Telecom -- www.netfilter.com.br
 -- For mobile:ï¿½http://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.

 __**_
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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/**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
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Re: [Freesurfer] mris_convert exporting parcellation per vertex

Re: [Freesurfer] mris_convert exporting parcellation per vertex

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