Hi Doug, Thanks for the clarification. So in the case of cortical thickness, qcache, mris_fwhm or mri_surf2surf would all do the same thing and so I should be getting similar results if everything is entered in the same fashion. This would be the approriate choice compared to mri_smooth.
For mri_surf2surf I used the following command for smoothing LGI and cortical thickness and converting to .gii files. mris_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.mgz --cortex mris_convert -c rh.thickness.fwhm15.mgz $FREESURFER_HOME/subjects/fsaverage/surf/rh.white rh.thickness.fwhm15.gii 1) For cortical thickness does it make sense to use the --cortex option or should I specify a mask of some type (if so which) in mris_surf2surf? 2) For converting files to .gii should I be using rh.white as the option or should it be rh.pial? Best, Ajay On Thu, May 5, 2016 at 2:53 PM, Ajay Kurani <dr.ajay.kur...@gmail.com> 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> > 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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