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
E-mail: yung-jui.yang@yale.edu

On 3/3/14 2:48 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu> wrote:

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" <greve@nmr.mgh.harvard.edu


     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"
         <mailto:greve@nmr.mgh.harvard.edu%3E>> wrote:

              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
                  E-mail: _yung-jui.yang@yale.edu_

                  On 3/3/14 12:58 PM, "Douglas N Greve"
                  <greve@nmr.mgh.harvard.edu
                  <mailto:greve@nmr.mgh.harvard.edu>
                  <mailto:greve@nmr.mgh.harvard.edu%3E>
         <mailto:greve@nmr.mgh.harvard.edu%3E%3E>> wrote:

                       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
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                       --
                       Douglas N. Greve, Ph.D.
                       MGH-NMR Center
                  <mailto:greve@nmr.mgh.harvard.edu>
                       Phone Number: 617-724-2358
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              --
              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
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              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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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