Hi Bruce,
The freesurfer version is:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and I am running on a
Linux Mint 16 machine.
Best,
Karen
On 03/24/2014 05:06 PM, Bruce Fischl wrote:
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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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.
