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.