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> 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> > 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 >> > >
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