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
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MGH-NMR Center
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