lGI has a lot of native smoothness in it, often so much that it exceeds the tables that we precompute. I would strongly suggest not using the precomputed tables for this and instead use permutation. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0...
On 5/9/2021 5:13 PM, Georgia Kapizioni wrote:
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Dear FS experts,
I am running a GLM for a group comparison (Healthy versus Patients) for gyrification, using the following command:
mri_glmfit --y lh.HDcvsCons1.pial.10.mgh --fsgd HDcvsCons1.fsgd --C Contrasts/group.mtx --surf fsaverage lh --cortex --glmdir lh.HDcvsCons1_pial.glmdir
which seems to work fine, however when I am running the mri_glmfit-sim command to correct my results, I am getting the following error, which is strange as I use smoothed data of 10 fwhm.
Do you have any ideas why is this happening and how to resolve it?
Thank you in advance, Best, Geo
mri_glmfit-sim --glmdir lh.HDcvsCons1_pial.glmdir --cache 1.3 abs --cwp .05 --2spaces cmdline mri_glmfit.bin --y lh.HDcvsCons1.pial.10.mgh --fsgd HDcvsCons1.fsgd --C Contrasts/group.mtx --surf fsaverage lh --cortex --glmdir lh.HDcvsCons1_pial.glmdir SURFACE: fsaverage lh log file is lh.HDcvsCons1_pial.glmdir/cache.mri_glmfit-sim.log
cd /Users/georgina/Downloads/HDf /Applications/freesurfer/bin/mri_glmfit-sim --glmdir lh.HDcvsCons1_pial.glmdir --cache 1.3 abs --cwp .05 --2spaces
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Mon May 10 00:10:37 EEST 2021 Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64 georgina setenv SUBJECTS_DIR /Users/georgina/Downloads/HDf FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.HDcvsCons1.pial.10.mgh --fsgd HDcvsCons1.fsgd --C Contrasts/group.mtx --surf fsaverage lh --cortex --glmdir lh.HDcvsCons1_pial.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 43.252960 ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm43/abs/th13/mc-z.csd
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