Re: [Freesurfer] extracting cortical parcellation

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:

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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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