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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Hi Christopher

that won't work as we assume that the surfaces have the same topology (# of edges, vertices and triangles). You'll need to use a distance transform I expect, which shouldn't be too bad. Check out mris_distance_transform. You'll want to run it with the pial surface, then pick out the samples on the scalp surface (or the other way)

cheers Bruce On Tue, 20 May 2014, Christopher Chatham 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 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?

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?)

Any suggestions or thoughts would be highly appreciated.