Hi,
Please see responses in text (also FS experts please fill in on the things I am unsure of).
On Tue, May 20, 2014 at 5:09 PM, Christopher Chatham chathach@gmail.com wrote:
Dear Freesurfer experts,
I would like to get a map of scalp-cortex distance for every vertex on the pial surface (for use in predicting the effects of TMS). I believe there is no existing automated method for doing this.
Are there any suggestions for how to calculate a scalp-cortex distance map?
My suggestion would be to just read in the two surfaces in python/matlab/octave/etc. and then calculate it point by point for each.
My current plan is simply rename my files so that the outer_skin takes the place of the pial surface, and the pial surface takes the place of the white matter boundary. Would this allow me to run mri_thickness as normal and get a scalp-cortex distance map?
Someone please help with this (read: I don't know much about this)
Alternatively, I might create a new version of mris_thickness.c in which all references to the "white" surface are replaced with references to the outer_skin surface constructed by mri_watershed, though I am new to c and thus hesitant to take this approach. (Also, I have only a MEMPRAGE and no FLASH 5/30 sequences, so I cannot use mri_make_bem_surfaces; is the latter is still considered preferable?)
This is only preferable if you want to measure the inner skull and outer skull surfaces.
HTH D
Any suggestions or thoughts would be highly appreciated.
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