Re: [Freesurfer] adding additional manually-defined labels to atlas-derived .annot file

Hi James

yes, I guess that is the right workflow. YOu will also need to modify the color lut to include your new parcel. As for overlap you could just remove it in matlab I guess. Or maybe mris_label2annot handles it, I'm not sure (Doug may know)

cheers Bruce On Mon, 23 Jul 2018, James Hobart wrote:

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Good Morning All, Just wondering if anyone had any advice regarding this problem? I am still struggling to get things running as intended!

Any help would be greatly appreciated.

BW James

On Tue, Jun 26, 2018 at 1:20 PM, James Hobart jameshobart2@gmail.com wrote:

  Hi Freesurfer community,

   

  I have an issue in adding a surface label to an annot file.

  I had a manually drawn  .nii mask in native space for each subject  which I have used
  mri_vol2surf to create a surface overlay and then mri_vol2label (with the surf argument)
  to create a surface label for the mask.

   

  I also have a custom parcellation of fsaverage which I have mapped to individual native
  space using mri_surf2surf.

   

  My issue is I want to combine the outputted binarymask.label file with the custom
  parcellation. My understanding is that I would need to combine the binarymask.label with
  the custom.parc.annot file. In order to do this wopuld I break down the annot file with
  mri_annot2label and then rebuild including the new binarymask.label?

   

  Could I also just add another row to the LUT from the custom.parc.annot file to allow
  this?

   

  And finally, how do I deal with the fact that the binarymask.label will overlap with
  other labels? Ideally I need to force the overwrite of vertex labels so that the
  binarymask.label is prioritised?

   

  BW

  James