You don't need to specify a mask when you run mri-glmfigt-sim. When you ran mri_glmfit, you already specified the mask and that gets stored in the glmdir and then read by mri_glmfit-sim. Your mri_glmfit-sim command line look right (but you don't need the --bg 1 unless you really want to background the process, but using only one process will not speed it up).

the other thing I want to point out is that (pseudo) weighted-least squares will not be taken into account by the permutation. I would rerun mri_glmfit without --wls and then run mri_glmfit-sim

On 2/7/2020 3:01 PM, Kim, Gwang-Won wrote:

Hi there,

First, I ran "mri_glmfit" using mask including 4 ROIs(file name: 4_ROI.label) as follows: mri_glmfit --glmdir g2v3.wls --y ces.nii.gz --wis cesvar.nii.gz --fsgd 2group.fsgd --C group.diff.mtx --lable 4_ROI.label  --surface fsaverage lh - --fwhm 5 –eres-save.

Second, I'm going to process "mri_glmfit-sim" to perform a cluster-wise correction for multiple comparisons.

Please let me know how to process "mri_glmfit-sim" using masks (file name: 4_ROI.label) .

Is it right? “mri_glmfit-sim --glmdir g2v3.wls --perm 1000 3 abs --2spaces --bg 1”

Thank you,

Gwang-Won

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