Right. How do you define the "complete WM vol underneath the label"?
Sounds like a lot of work, but thanks for your reply.
By the way, the wm vol generated this way is 5mm from white surface
into the center of the brain, correct? Thus, it is not necessarily the
complete WM vol underneath the label?
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
yes, but not easily. You will have to create an annotation with
your new
label in it (and any other label for the other parts of cortex)
(probably using mris_label2annot), then run mri_aparc2aseg to
generate a
new wmparc-style volume, then run mri_segstats. You can look in the
recon-all.log file for example command lines for mri_aparc2aseg
(used to
generate the wmparc.mgz)
doug
On 03/03/2014 02:31 PM, Yang, Daniel wrote:
Sorry, I wasn't clear. It's a cortical label that I manually
created,
based on the pial surface.
Is it possible to generate the corresponding WM vol based on a
new
label (not pre-defined)?
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
On 3/3/14 2:17 PM, "Douglas N Greve"
I don't understand. What label do you have? Do you mean a
WM label
or a
cortical label that you want to find the WM under?
On 03/03/2014 02:12 PM, Yang, Daniel wrote:
Hi Doug,
I am able to find wmparc.stats in stats. It shows WM
vol based on
pre-defined ROIs.
However, do you know how can we generate
corresponding WM vol
for a
given label (not the D-K ROIs)?
I'd like to use WM vol as DV but are limited to
pre-defined ROIs.
Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
On 3/3/14 1:14 PM, "Douglas N Greve"
It should be there if the recon did not fail.
The file is
called
wmparc.stats (not wmparc_stats.txt)
On 03/03/2014 01:07 PM, Yang, Daniel wrote:
Thanks, Doug! But that is about using
wmparc.stats as
IV or
continuous/covariate variables. I would like
to use
WM vol as
the DV
(measure).
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
On 3/3/14 12:58 PM, "Douglas N Greve"
you can just add them into your qdec
file (from
wmparc.stats)
doug
On 03/02/2014 07:18 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
FS provides thickness as the DV in
qdec and
mri-glmfit. Do you
know how I can have WM vol as the DV in
these tools
with the
same GLM model? For example, I want
to test
the WM
regions
that is most strongly positively
correlated
with a
given factor.
Thanks!
Daniel
_______________________________________________
Freesurfer mailing list
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
_______________________________________________
Freesurfer mailing list
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
you in error
but does not contain patient
information, please
contact the
sender and properly
dispose of the e-mail.
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
Douglas N. Greve, Ph.D.