Hi Jen, In Doug's absence, let me try and give you the best answer I can! The wmparc.mgz uses the cortical parcellation and grows each label down through the white matter - giving a label of the white matter underneath each cortical unit. Because of this there will be both cortical (ctx) and white matter (wm) measures in the wmparc.stats - the ctx regions being taken directly from the cortical parcellation, and the wm regions resulting from growing those inward.
Depending on what version you are using, you can use asegstats2table to tabulate these results, as you would the subcortical segmentation. Check the help on this file, there may be an option to do it directly, or you may have to use a flag to specify a new stats table (i.e., wmparc.stats instead of aseg.stats). Hope this is helpful, Jenni On Wed, Apr 30, 2008 at 8:17 AM, Jenni Pacheco <[EMAIL PROTECTED]> wrote: > Hi Jen, > > In Doug's absence, let me try and give you the best answer I can! The > wmparc.mgz uses the cortical parcellation and grows each label down through > the white matter - giving a label of the white matter underneath each > cortical unit. Because of this there will be both cortical (ctx) and white > matter (wm) measures in the wmparc.stats - the ctx regions being taken > directly from the cortical parcellation, and the wm regions resulting from > growing those inward. > > Depending on what version you are using, you can use asegstats2table to > tabulate these results, as you would the subcortical segmentation. Check > the help on this file, there may be an option to do it directly, or you may > have to use a flag to specify a new stats table (i.e., wmparc.stats instead > of aseg.stats). > > Hope this is helpful, > Jenni > > > On Wed, Apr 30, 2008 at 7:04 AM, Bruce Fischl <[EMAIL PROTECTED]> > wrote: > > > Hi Jen, > > > > Doug is out of town at the fBIRN meeting, and he's the one that will > > answer this so you might have to wait a bit. > > > > cheers, > > Bruce > > > > On Tue, 29 Apr 2008, Jennifer Bramen wrote: > > > > I posted the below question regarding white matter volumes to the list > > > last Friday. I think it fell through the cracks because I sent it out in > > > the > > > late afternoon, and was hoping someone could help me understand 1) the > > > outputs of indicvidual wmparc.stats files and 2) how to tabulate these > > > data > > > like we can with gray matter volumes. Thanks again. > > > > > > Jen > > > > > > Hi Freesurfer Users, > > > > > > > > This may be a newbie question. I am trying to evaluate regional > > > > volumes. I have been able to tabulate the gray matter volumes, but > > > > cannot > > > > figure out how to tabulate all the white matter volumes. I see that in > > > > individual folders, there is a file called wmparc.stats. Do any of the > > > > tools > > > > query this file, or will I need to pull the data manually? Inside this > > > > file, > > > > I see some of the regions listed as wm-?h-<regionname>. Next to these > > > > are > > > > sometimes a lot of zeros and sometimes a bunch of values. I am > > > > wondering why > > > > so many of these do not have values associated with them. I am also > > > > wondering why only some of the regions listed in this file are labeled > > > > wm, > > > > when the file suggests it contains white matter stats... > > > > > > > > If there is somewhere on the site that explains white matter > > > > volumetric analyses, could someone please send me the link? > > > > > > > > Thank you > > > > > > > > Jennifer Bramen > > > > > > > > ---------------------------------------------------------- > > > > IMPORTANT WARNING: This email (and any attachments) is only > > > > intended for the use of the person or entity to which it is addressed, > > > > and > > > > may contain information that is privileged and confidential. You, the > > > > recipient, are obligated to maintain it in a safe, secure and > > > > confidential > > > > manner. Unauthorized redisclosure or failure to maintain > > > > confidentiality may > > > > subject you to federal and state penalties. If you are not the intended > > > > recipient, please immediately notify us by return email, and delete this > > > > message from your computer. > > > > ---------------------------------------------------------- > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > ---------------------------------------------------------- > > > IMPORTANT WARNING: This email (and any attachments) is only intended > > > for the use of the person or entity to which it is addressed, and may > > > contain information that is privileged and confidential. You, the > > > recipient, are obligated to maintain it in a safe, secure and confidential > > > manner. Unauthorized redisclosure or failure to maintain confidentiality > > > may > > > subject you to federal and state penalties. If you are not the intended > > > recipient, please immediately notify us by return email, and delete this > > > message from your computer. > > > ---------------------------------------------------------- > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Jenni Pacheco, MA > Learning and Memory Lab > The University of Texas at Austin > Department of Psychology > 1 University Station A8000 > Austin, TX 78712 > phone: (512) 471-2727 > fax: (512) 471-5935 > email: [EMAIL PROTECTED] -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED]
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