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" <gr...@nmr.mgh.harvard.edu<mailto:gr...@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" <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu> <mailto:fis...@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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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