Hi Konrad

sorry, I never really packaged this up nicely. Currently it is embedded in the mris_thickness binary, and you run it by using:

mris_thickness -variational -w 0 <subject name> <hemi> <thickness file>

this will write out two files:

?h.normals.init.mgz ?h.normals.mgz

the first is the initial vector field along the pial-white direction, and the second is the results of the minimization of the variational functional and should be the ones you want.

It is all pretty experimental and only lightly used so may have problems (but hopefully not).

Let me know how it goes. I'll be curious to hear if it helps

cheers Bruce

On Thu, 16 May 2019, K. Wagstyl wrote:

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Hello FreeSurfer Developers,

I'm interested in regenerating cortical correspondence vectors between pial and white surfaces as described in "Microstructural parcellation of the human brain."

Is this currently the default way that freesurfer extracts the vectors/surfaces? Or is there flag/separate code to generate these vectors?

Thanks!

Konrad

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