Re: [Freesurfer] Convert volume label to surface label

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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