Hi Bruce and Lilla,
I have a MNC volume that contains area labels, ie voxels belonging to one label all have the same intensity value.
I am trying to get this converted into Freesurfer label files for further analysis in volume space. Following Lilla's advice, I am first using mri_binarize with --match. I figured that I can then use mri_cor2label with --id 1 to get a label file from the binary mask, correct?
There seem to be some individual voxels outside the labeled area that have the same values as the label; they are scattered across the volume. Is there a way to cluster size threshold the binarized mask?
Thanks, Caspar




2014/1/6 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
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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