Hi Molly, you can use the y.mgh file that is created by qdec. This is a stack of all of your subjects in the standard surface space. You can convert to nifti if that is more convenient. BTW, the stats table just gives you the stats for each ROI. If this is something you want, then use aparcstats2table and/or asegstats2table. doug

On 08/15/2012 04:55 PM, Molly DuBray wrote:

thanks for the prompt reply-

i'd like to export raw thickness values for each vertex for a number of subjects. (i.e. as if the parcellation were 200,000 rois)

in order to concatenate this for all subjects, i envisioned using qdec's 'generate stats table' function.

my understanding is that freesurfer does not store an image file of thickness values, but instead computes these on the fly within qdec...

the main reason we are trying to do this is because i am trying to run longitudinal study with multiple timepoints, and am having all kinds of trouble. i decided to run the stats models in another package (outside of qdec) with the hope of reimporting the analyzed data.

thanks again. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, August 15, 2012 2:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Whole brain vertex values?

Hi Molly, I don't understand what you are asking. Can you elaborate? doug

On 08/15/2012 04:10 PM, Molly DuBray wrote:

...

Hello,

Is there a way to export cortical thickness values for each vertex across the entire cortex? Can this be done using Qdec to generate a larger stats table for a group of participants?

Thank you, Molly

---

Molly DuBray Prigge, PhD Research Associate Department of Psychiatry University of Utah

---

Freesurfer mailing list 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.edu 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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.