I doubt that renaming is going to do what you want to do. I would follow Dan's suggestion about reading it into matlab. It will probably be slow, but you only need to do it once doug
On 05/20/2014 05:42 PM, dgw wrote: > 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 <chath...@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. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
