For the "spaces" it depends on whether you are going to eventually test cortex. If your hypotheses are only for subcortical regions, then you do not need to include --3spaces. I would also use the permutation as the GRF has eleveated false positives.
On 2/10/2021 9:43 PM, Kim, Gwang-Won wrote:
Hi there,
First, I ran "mri_glmfit" using a mask (subcortical regions) as follows: mri_glmfit --glmdir g1v1.wls --y ces.nii.gz --wis cesvar.nii.gz --fsgd g1v1.fsgd --C age.mtx --mask brain.mni305.2mm.nii.gz --fwhm 5.
Second, I'm going to process "mri_glmfit-sim" to perform a cluster-wise correction for multiple comparisons.
Which I select the comment?
mri_glmfit-sim –glmdir g1v1.wis –3spaces –grf 2 abs
mri_glmfit-sim –glmdir g1v1.wis –perm 1000 2.0 abs –cwp 0.05
–3spaces –bg 16
Especially, I use the mask the subcortical regions, not cortical regions. Should I remove “—3spaces” in the commend or what do I do instead of “—3spaces”?
Thank you,
Gwang-Won
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