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/MultipleComparisonsV6.0Perm
On 5/9/2021 5:13 PM, Georgia Kapizioni wrote:
External Email - Use Caution
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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