Dear all,
I notice that there is a file called wmparc_stats.txt
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#Tableofwhitematterparcellationvolumes
Is it possible to get corresponding WM info for a given label?
Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral
That is the jacobian of the white matter surface when it is registered
to fsaverage (not related to the actual white matter).
On 03/02/2014 08:40 PM, Yang, Daniel wrote:
Hi FreeSurfers,
A related question (I can't find the answers on the FS website):
what's jacobian_white (as a measure)?
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
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.y...@yale.edu
On 3/3/14
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).
--
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
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
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:
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
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
Right. How do you define the complete WM vol underneath the label?
On 03/03/2014 03:01 PM, Yang, Daniel wrote:
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
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
Hi FreeSurfers,
A related question (I can't find the answers on the FS website): what's
jacobian_white (as a measure)?
Thanks!
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
On 3/2/14
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