Thanks, Doug, for the procedure. I'm just wondering how the ROI sampling is performed.

May I ask three questions?

(a) when you say sample the ROIs from the fMRI space to the "surface", are you referring to white or pial surface? 

(b) Let's say, the functional activation is halfway inside a certain region and closer down to the white surface (that is, the gray matter near the pial surface is not significantly activated, while the gray matter near the white surface is activated). When the program samples this ROI to a "surface", does it basically do a maximum intensity projection to the pial surface? that is, underneath certain pial/cortical surface, there exists a functional activation?

(c) if the activation is partially inside the white matter, how would the sampling program deal with it? would it just ignore the part within the white matter?

Thanks,
Daniel

-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 8/6/13 2:28 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu> wrote:

Register your fMRI to the anatomical, sample the ROIs from the fMRI
space to the surface, display in tksurfer, create and save the labels
you want, then run mri_segstats using the label and thickness as input.

doug

On 08/06/2013 10:00 AM, Yang, Daniel wrote:
Hi Bruce,

Thanks for your reply. Those functional ROIs are volume-based (that
is, generated by spm/fsl/BrainVoyager).

So it seems that I need to generate a label for them in order to
use mris_anatomical_stats -l.

Do you know what I can generate label files based on volumetric
functional ROIs? I'm also a little bit puzzled because a given
functional ROI may not capture the whole gray matter within a certain
region, how can we determine its volume/area/thickness?

Many thanks!
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 8/6/13 9:33 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu

     yes, if they are surface-based then it is really trivial (just
     give them to
     mris_anatomical_stats with the -l <label name> flag)

     cheers
     Bruce


     On Tue, 6 Aug 2013, Yang, Daniel wrote:

         Dear FreeSurfer Experts,
         Theoretically, if you have a set of functional ROIs, is it
         possible to
         derive the cortical thickness, white surface area, and gray
         matter volume of
         those functional ROIs in FreeSurfer?
         Many thanks!!
         Daniel
         --
         Yung-Jui "Daniel" Yang, PhD
         Postdoctoral Researcher
         Yale Child Study Center
         New Haven, CT
         (203) 737-5454



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