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> 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 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.
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