Re: [Freesurfer] Label creation

Hi Dou,

I have had some issues with running mri_volsynth.

It is not clear how to specify the coordinate for the selected vertex. I tried it by adding the flag --c_ras x y z, but did not work?

Thanks

Cris

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, December 13, 2016 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Label creation

Not that easy. I would do it by selecting a vertex that is close to the coordinate you want, then

1. Create a surface overlay with all vertices = 0 except your chosen vertex

mri_volsynth --template $FREESURFER_HOME/fsaverage/surf/lh.thickness --delta vertexno 0 0 0 --o delta.mgh

2. Smooth the overlay to expand the non-0:

mri_surf2surf --s fsaverage --hemi lh --sval delta.mgh --tval delta.smoothed.mgh --nsmooth-in 10

This will expand out to a radius of 10 vertices

3. Binarize it

mri_binarize --i delta.smoothed.mgh --min .000000001 --o delta.smoothed.bin.mgh

4. Create the label:

mri_cor2label --i delta.smoothed.bin.mgh --l delta.smoothed.bin.label --surf fsaverage lh white

On 12/13/16 12:53 PM, Leyton Moscoso, Cristian Eduardo wrote: Hi Freesurfer's experts

Is there an easy way to create automatically a circular label with a radius centered on a vertex with predifined RAS/Tailarach coordinates on the fsaverage surface?

Thanks

Cris

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