Hi Karen
This is typically caused because the surface just misses the voxels that have your label in some points. You can either thicken the label in the volume, or use morphological operations like close (in mri_label2label or manually in tksurfer) to fill the holes
cheers Bruce
On Mon, 24 Mar 2014, Karen Marie Sandø Ambrosen wrote:
Hi Freesurfer experts,
I have a volume label only which is only different from zero in the white matter-gray matter boundary. I am trying to convert this volume label to a surface label in order to visualize it in tksurfer. I am using mri_vol2surf:
mri_vol2surf --mov volume_label.nii --out volume_label2surf.mgh --out_type mgh --hemi lh --regheader H01 --surf white --ref volume_label.nii
However, when I load this surface as an overlay in tksurfer, to check the correctness, the original surface is not fully covered by the surface created by mri_vol2surf. Is there any way to make the surface fully cover the original surface so it doesn't look speckled?
After creating the surface I want to convert the surface to labels by mri_cor2label and finally to an annotation file by mris_label2annot.
Best, Karen
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