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?

1. mri_glmfit-sim –glmdir g1v1.wis –3spaces –grf 2 abs

2. 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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