Thanks very much, Doug. I could always hope. > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, March 03, 2016 12:45 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] "wm" boundaries and stats > > 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 > > > > > > > > _______________________________________________ > > 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 > > > 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.
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