See if this tutorial will help

On 2/14/2020 3:28 PM, Kim, Gwang-Won wrote:

Dear Douglas N. Greve,

Thank you very much for your email.

I ran mri_glmfit without --wis. Then I tried to ran mri_glmfit-sim as following: mri_glmfit-sim –glmdir g2v3.wls –2spaces –perm 1000 1.3 abs.

But there is an error message “ERROR: design matrix is not orthogonal, cannot be use with permutation. If this something you really want to do, run with –perm-force”.

How can I do if I want to solve this problems?




Message: 6

Date: Fri, 14 Feb 2020 09:42:28 -0500

From: "Douglas N. Greve" <>

Subject: Re: [Freesurfer] Cluster-wise correction for multiple


To: <>

Message-ID: <>

Content-Type: text/plain; charset="utf-8"

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


Freesurfer mailing list

Freesurfer mailing list

Reply via email to