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.edumailto: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 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_
On 3/3/14 2:17 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_
On 3/3/14 1:14 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu 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_mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_ mailto:_yung-jui.yang@yale.edu_
On 3/3/14 12:58 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto: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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/