Hi Karen
you need to grab a new version then:
mri_label2label --help|grep close
--close N close the label N times before writing
--paint dmax surfname : map to closest vertex on source surfname if d
< dmax
the closest surface vertices:
what hardware/software environment are you running in?
Bruce
On Mon, 24 Mar
2014, Karen Marie Sandø
Ambrosen wrote:
Hi Bruce,
Thanks for your answer. I will like to do it automatically as I have a lot of
labels. However, I can't find an option called
close in mri_label2label. Can you give me another hint?
Best,
Karen
On 03/24/2014 03:24 PM, Bruce Fischl wrote:
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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