Hi Joost, you can load the label into matlab with read_label.m and then convert it into the vector you want. Alternatively, there is a new version of mri_annotation2label (x64 below) which you can use to create a "segmentation" surface in nifti or mgz from an annotation. Then find "voxels" that have a value equal to that of the structure you are looking for.

doug

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_annotation2label

j janssen wrote:

Hi,

using version 4.0.5.

i want to convert the lh.Medial_wall.label found in the fsaverage label subdir into a mask which consists of 1 x v vector, with value 1 inside the mask, 0 outside the mask and v=#vertices. should i follow mri_label2vol and thereafter mri_vol2surf? i guess i am looking for a way to put binary masks on surface data.

thanks,
-joost
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