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 <jenni.pacheco@gmail.com> 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 <fischl@nmr.mgh.harvard.edu> 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

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--
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: jpacheco@mail.utexas.edu



--
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: jpacheco@mail.utexas.edu