Hi Doug,

So the program to be used is mri_vol2surf, correct? Is there any other program that might be related?

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

On 8/6/13 2:55 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu> wrote:


On 08/06/2013 02:49 PM, Yang, Daniel wrote:
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?
You can have it fill the ribbon or sample the maximum. see the --help

(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?
You can do it a bunch of different ways, including max intensity
projection over the ribbon.

(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?
You can give it a negative start to the projection fraction and it will
sample in the WM.
doug


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

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

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

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