Re: [Freesurfer] "wm" boundaries and stats
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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
[Freesurfer] "wm" boundaries and stats
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 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.
