Re: [Freesurfer] MNC label to Freesurfer

Hi Caspar

can you describe in more detail what you are trying to do. Do you mean to sample each unique label into a surface label format? Do you have surfaces for this subject?

cheers Bruce On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote:

Hi Lilla, unfortunately, there is no correspondence between the Freesurfer labels and the labels in the MNC volume at this point. I would simply like to convert each label in the MNC file to a new Freesurfer label file. Caspar

2014/1/6 Lilla Zollei lzollei@nmr.mgh.harvard.edu

  Hi Caspar,

  One thing you can do, if you have the label correspondences
  between your lables and the FS ones, is to use mri_binarize with
  the --replace option in your volumes.

  --replace V1 V2 : replace voxels=V1 with V2

  For label descriptions you can loook up
  $FREESURFER_HOME/FreeSurferColorLUT.txt.

  --Lilla

  On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote:

        Hi!
        I have a volume in MNC format that contains labels,
        and I was wondering whether there is a way to
        quickly convert them into Freesurfer labels?
        Within the MNC file, voxels belonging to one label
        all have the same intensity value, which is,
        however, not in RGB space but just a single number,
        ranging from 1 to the number of labels.
        Thanks, Caspar

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