Underneath, they both use the same code, so they should give the same results. Are you saying they are different? I don't know what SurfFWHM is doing so I can't comment on what those results mean. Measuring the FWHM on the surface is quite tricky. doug
On 5/4/16 6:41 PM, Ajay Kurani 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.
- I am not sure if the qcache or the mris_fwhm file is more
appropriate to use for a cortical thickness analysis.
- 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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