Hi Nina, I’m very glad to hear that the segmentations look satisfactory :-) The ?h.hippoSfLabel.v10.mgz files already have that information; they are label volumes (FreeView assigns colors to the labels for visualization). The lookup table can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt (you’re interested in the range 200-226). Cheers, /Eugenio
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 7 Apr 2017, at 12:17, Nina Jacobsen <njacob12@student.aau.dkmailto:njacob12@student.aau.dk> wrote:
Hi All,
I have made a hippocampal subfield segmentation using FreeSurfer version 6.0 with multispectral segmentation settings, and have both labels for the right and left hippocampus. The segmentations look very nice when viewed with freeview, so all good.
Now, my problem is the file content. I would like a segmentation file, which labels all subfields with a single value (all voxels in CA1 would for example be with value 1, all voxels in CA2 would be with value 2 and so on). Does anyone know how i can gain this file? Is it in some way possible to convert the label files (lh.hippoSfLabel.v10.mgz) into such a "simple" segmentation file? Currently, the content of the label files (lh.hippoSfLabel.v10.mgz) is values in the range 0-226, which I guess origin from the RGB encoding - I opened the file with matlab.
Hope my question is clear.
Thanks, Nina Jacobsen. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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