Destrieux atlas mni coordinates

[Sabin Khadka]

Hi Chris, 

I am trying to display destrieux parcellation nodes using BrainNet. For that I was using x.mni, y.mni, z.mni coordinates (I believe these are in mni305 space). I overlayed these nodes on BrainMesh_ICBM152 surface template provided with BrainNet. However, when I look at the overlayed nodes the nodes seem to be inside brain and not on the surface of the brain (see attached). I was wondering if these   x.mni, y.mni, z.mni coordinates are mni coordinates of parcellated regions in surface? If not what are these values and how can I get mni coordinates of surface of parcellation regions.

Thanks,

Sabin

[Chris Watson]

Hi Sabin, it's been awhile so I don't remember exactly where I got the coordinates from (either from a colleague, or I calculated them myself.

Here are some commands that may be useful to you:

1) First, in Bash (or tcsh, i.e. the command line)

mri_annotation2label --subject fsaverage --hemi lh --outdir aparc.a2009s/ --annotation aparc.a2009s --surf pial

cd aparc.a2009s

2) Open R, and:

lhlabels <- dir()[-75]    # Exclude the "unknown" label

dt.labels <- vector('list', length=length(lhlabels))

for (i in seq_along(lhlabels)) {

  dt.labels[[i]] <- fread(lhlabels[i])

  dt.labels[[i]][, name := gsub('.label', '', gsub('lh\\.', 'l', gsub('-', '.', lhlabels[i])))]    % To match the names in brainGraph

}

dt.labels <- rbindlist(dt.labels)

dt.labels[, .(x.mni=mean(V2), y.mni=mean(V3), z.mni=mean(V4)), by=name]

The results I get from this are very close to the coordinates in brainGraph, so I assume this is what I did in the past (however, they are not exact so I am not 100% sure). The reason your attached picture looks "off" is probably because I just took a simple mean; this obviously won't give the most appropriate answer in a region which has a lot of curvature.

Figuring out  a solution to this isn't a priority for me right now; perhaps there are a set of standard coordinates that are available already? If there is the same issue with the other atlases, I will look into it sooner.

Chris

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[Chris Watson]

Hello again,

I saw Doug Greve's reply to your post on the Freesurfer list. I followed his recommended command, and once again came up with similar coordinates. However, not the same. I can try the coordinates that Doug's command returns, and see how that looks, but won't get around to doing any of that for a few days. Still, I am not sure if it will make much of a difference. It might be necessary to do a transform from MNI305 to MNI152.

Chris

[Sabin Khadka]

Great. Thanks. I am going to try the same. Keep us posted. 

Cheers,

Sabin Khadka

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