Hi Don, there is not an easy way to get this information. You can use mri_binarize to create a surface of each ROI, something like
mri_binarize --i wmparc.mgz --match 3013 --surf lh.wm.lingual
Use this version of mri_binarize ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
but doing the other things you want is a real programming job
doug
On 03/01/2016 09:29 AM, Krieger, Donald N. wrote:
Freesurfer provides 34 ctx label volumes on each side of the brain with adjacent wm labels.
The boundary between each ctx volume and the co-named adjacent wm volume is a third “white” label.
I would like to extract a few pieces of information from the analogous boundary between each wm volume and those adjacent volumes to it which are not the co-named ctx volume.
For instance many wm volumes share a boundary with the unsegmented white matter.
Some share a boundary with sub-cortical structures.
Here are some of the information I would like to extract.
What do you think?
What are the xyz coordinates of the complete boundary surrounding each wm volume and what is the name of the adjacent volume for each point on the boundary?
I understand that for the boundary between the ctx volume and the adjacent wm volume, the white label provides this information.
What is the percentage and area of the complete boundary surrounding a wm volume which is adjacent to the co-named ctx volume.?
What are the names of the other volumes with which each wm volume shares a boundary and what is the percentage and area of the boundary shared with each?
For each point within a wm volume, are the nearest points on the wm boundary adjacent to the co-named ctx volume or are some adjacent to unsegmented white matter or sub-cortical structures?
More generally, is a particular few mm voxel surrounded by gray matter and so is likely primarily composed primarily of relatively short range fibers or is it adjacent to the deep white matter (unsegmented) and likely composed of a mix of relatively short range fibers and long range “en passage” fibers.
It is this last question which most closely gets at the ideas I wish to explore.
We are able to measure electric current in the white matter with mm resolution from the MEG.
The mix of local and “en passage” fibers should effect the direction of the electric currents in the white matter and I can measure that.
The distance scale is at the edge of that provided by DTI-derived tractography so we may be able to meld these measurements with those.
Your thoughts would be welcome on what is already there in freesurfer that will help with this and what you think might be a good direction to proceed to develop what we need from what is there.
Thanks – Don
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