The 10mm is what you applied, but data will have an intrinsic smoothness, and the final smoothness is a combo of the two. LGI data tends to start out extremely smooth. I would re-run it without smoothing and see what fwhm you get

doug

On 01/08/2013 03:24 PM, Gregory Kirk wrote:

run mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos

get

cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf subset_average lh --cortex --glmdir lh.lgi.glmdir SURFACE: subset_average lh log file is lh.lgi.glmdir/cache.mri_glmfit-sim.log

cd /study5/aa-scratch/UTAH/freesurfer_final /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos

$Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Tue Jan 8 14:21:47 CST 2013 Linux tick.keck.waisman.wisc.edu 2.6.32-279.11.1.el6.x86_64 #1 SMP Tue Oct 16 11:16:02 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux gkirk setenv SUBJECTS_DIR /study5/aa-scratch/UTAH/freesurfer_final FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest

Original mri_glmfit command line: cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf subset_average lh --cortex --glmdir lh.lgi.glmdir

DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 38.299834 ERROR: cannot find /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/subset_average/lh/cortex/fwhm38/pos/th20/mc-z.csd

i ran mri_surf2surf with --fwhm 10

whats the problem here ?

thx

greg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer