Hi Doug,

There are several posts in which you mention the mri_surfcluster --centroid option as a method for obtaining MNI coordinates of the centroid of each parcellation label. When I type the below command, I get and error saying "ERROR: Option --centroid unknown". What am I doing wrong?

mri_surfcluster --in lh.thickness --clabel lh.G_and_S_cingul-Ant.label --sum sum.lh.G_and_S_cingul-Ant --centroid --thmin 0 --hemi lh --subject ###

I am using Freesurfer version 5.1 and the Destrieux parcellation.

Thank you,

Simon

On 24 July 2013 13:59, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

We don't have those number available, but you can generate them with something like:

#1 Convert the annotation to a set of labels. This is for the Desikan atlas, but you can spec the destrieux instead
mri_annotation2label --subject fsaverage --hemi lh --outdir ~/tmp/aparc

# For each label, run mri_surfcluster to get the centroid
mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel lh.pericalcarine.label --sum sum.lh.pericalcarine --centroid --thmin 0 --hemi lh --subject fsaverage

This will actually be weighted by the thickness, but that should not matter much

The centroid coordinates will be in MNI305 space

doug

On 7/23/13 11:57 AM, LAOUCHEDI MAKHLOUF wrote:

Hi

    i am using corticals parcels (destrieux) as nodes in a connectivity study using the NBS (Network Based Statistics) tool; i want to assign MNI coordinates for these nodes. is there any MNI coordinates in freesurfer for each component of this parcellation (not for every vertex in those components) or any other strategy to assign coordinates for these components ?

otherwise, i intend to non-linearily register the freesurfer's labels for a healthy subject in MNI and for each label i will use coordinates of one of its points to represent that label

thanks for help

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