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