There is not a difference between mris_fwhm and mri_surf2surf. mris_smooth smoothes the xyz coordinates of the vertices of a surface (the others smooth an overlay).
On 05/05/2016 03:53 PM, Ajay Kurani wrote: > Hi Doug, > Thanks for the quick reply. > > Is there a difference from qcache/mris_fwhm with mris_smooth and > mri_surf2surf -fwhm ? If so, which is recommended for cortical > thickness analysis? > > Thanks, > Ajay > > On Wed, May 4, 2016 at 11:18 PM, Ajay Kurani <dr.ajay.kur...@gmail.com > <mailto:dr.ajay.kur...@gmail.com>> wrote: > > Hi Freesurfer Experts, > Just as a followup through my reading i've come across posts > which use qcache, mris_fwhm, mri_surf2surf or mris_smooth for > smoothing. For my cortical thickness analysis I would like to > smooth all of my rh/lh.thickness.fsaverage.mgh files for each > subject in order to run a group analysis. After finding regions > of difference, I would then like to use the ROI to extract each > individual's mean thickness in the ROI in order to run a > correlation with other measures. Based on this, I assume it would > make sense to use smoothed data to identify the ROI and then use > unsmoothed data for extracting actual thickness measures (does > lh.thickness.fsaverage contain the original thickness or warped > thickness values). > > I am unsure which smoothing is the most accurate or preferred. In > using qcache the smoothness of the images do not seem to reach the > filter level (based on the earlier email) so I am not sure if > there is a freesurfer tool to check the smoothness level or if the > qcache smoothness levels make sense for cortical thickness. > > Thanks, > Ajay > > On Wed, May 4, 2016 at 5:41 PM, Ajay Kurani > <dr.ajay.kur...@gmail.com <mailto:dr.ajay.kur...@gmail.com>> wrote: > > Hi Freesurfer Experts, > I am trying to understand the difference between qcache > option and mris_fwhm and which is appropriate for a cortical > thickness analysis. I processed my files with qcache and > have lh.thickness.fsaverage.fwhm15.gii (converted) files. I > used an afni tool SurfFWHM to estimate the smoothness of a > subject at when looking at the fwhm0 image it iwas 5.5 and for > 10, 15 and 20mm it was approximately 9.3-9.9 smoothness level. > > I also used mris_fwhm --hemi lh --s fsaverage --smooth-only > --i lh.thickness.fsaverage.mgz --fwhm 15 --cortex --o > test_15.gii and when using SurfFWHM on the smae subject the > smoothness was estimated at 11.25. > > > 1) I am not sure if the qcache or the mris_fwhm file is more > appropriate to use for a cortical thickness analysis. > > 2) For qdec if I select the 15mm option does it assume the > smoothness is 15mm when calculating monte carlo corrections? > Would there be a different way to estimate this since my > smoothness at 15mm is closer to 10mm? > > Thanks, > Ajay > > > > > > _______________________________________________ > 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 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 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.
