Hi, I just have a quick question regarding the white matter regional volumes as shown in the wmparc.stats file. How are the white matter regions grown inward from the cortical parcellation? Does each labeled region include only the white matter within the specified gyrus, or does it extend further?
Thanks, Tricia Merkley --- On Tue, 5/27/08, Doug Greve <[EMAIL PROTECTED]> wrote: From: Doug Greve <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] White Matter Regional Volumes To: [EMAIL PROTECTED] Cc: freesurfer@nmr.mgh.harvard.edu Date: Tuesday, May 27, 2008, 9:17 AM Try it on the wmparc.stats file, not the wmparc.mgz file. doug [EMAIL PROTECTED] wrote: > My name is Jennifer as well, and I work in the same lab as Jennifer > Bramen, > who originally wrote to you, below. I am writing while she's out of > town to > follow up on your reply below. Mainly, I am a little confused by your > suggestion to use asegstats2table command, because the resultant text > file when this command is run on the wmparc.mgz file is not openable > in excel - it has too many columns/is too large. Unfortunately, the > --maxsegno flag is not helpful because the white matter volumes are > the second half of the segmentations listed in the wmparc.mgz file. > Thus, the --maxsegno command will only yield an output file that has > none or some of the white matter volumes, rather than only the white > matter volumes. Any suggestions? > > Thanks- > > Jennifer Hranilovich > > > Quoting Jenni Pacheco <[EMAIL PROTECTED]>: > > 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 > > _______________________________________________ > 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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