Re: [Freesurfer] extracting cortical parcellation

Hi Atena

the vertex indices are stored in the first column. You should be able to use them to look up into any overlay you want

cheers Bruce

On Wed, 6 Mar 2019, Atena Rezaei wrote:

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Hi Bruce, I am going to extract the cortical parcellation file with its color table from freesurfer then import that in the other interface to detect and visualize the somatosensory (3b broadmann ) area. Therefore, I need the fifth column with some values for vertices.

BR, Atena

On Wed, Mar 6, 2019 at 5:47 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Atena

  what were you hoping would be in the fifth column? What are you hoping to
  create your own annotation files from? Can you give us a bigger picture of
  what you are trying to achieve?

  cheers
  Bruce


  On Wed, 6 Mar 2019, Atena Rezaei
  wrote:

  >
  >         External Email - Use Caution        
  >
  > Hi Bruce,
  >
  > Thanks for your comment!
  > I used mri_annotation2label to existed lh.aparc.annot file in label folder
  > and got the labels. but the labels' text file contain 0 in fifth column.
  > I need to create atlas from my own data  including surface parcellation. how
  > can I do that? I found commands;
  > mris_ca_train and mris_ca_label,
  > how can I make the annotation files from my own data?
  >
  > BR,
  > Atena
  >
  > On Wed, Mar 6, 2019 at 1:10 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
  > wrote:
  >       Hi Atena
  >
  >       yes, mri_annotation2label should work, although it really
  >       depends on what
  >       you want to do next
  >
  >       cheers
  >       Bruce
  >       On Wed, 6 Mar 2019, Atena Rezaei wrote:
  >
  >       >
  >       >         External Email - Use Caution        
  >       >
  >       > Hello,
  >       >
  >       > I am trying to extract the cortical parcellation(atlas) file
  >       from freesurfer with all the labels. I found
  >       > the lh.aparc.annot file in label folder. Should I use
  >       mri_annotation2label to create labels? or how can I
  >       > extract the whole file?
  >       > Thanks for ur help!
  >       >
  >       > BR,
  >       > Atena
  >       >
  >       >
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