Than you can use mri_binarize with the --match flag.

--match matchval

--Lilla

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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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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.