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.
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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