The masking is not done as part of the correction for mult comp but when you run mri_glmfit. When you run it on a volume, you have to specify the mask, so the mask depends upon your application. For fsfast, the mask in $FREESURFER_HOME/subjects/fsaverage/mri.2mm is used.

On 11/20/18 4:57 AM, YAN Chao-Gan wrote:

        External Email - Use Caution        

Dear Douglas,

When doing --3spaces, is there a default subcortical mask in MNI space provided by freesurfer? Where is it stored?

Thanks,

Chao-Gan

On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

On 11/16/18 7:34 PM, YAN Chao-Gan wrote:

        External Email - Use Caution        

Dear freesurfer experts,

I have a pretty naive question but would like to confirm.

When we use --3spaces option in multiple comparison correction, does that mean we set the Cluster-wise threshold (cwp, not Cluster Defining Threshold or Cluster Forming Threshold) to 0.5/3=0.0167 for lh. Similar cwp at 0.0167 for rh and subcortical?

Correct.

In addition, if we use "--cortex" to restrict the calculation on cortex only, where can we find the corresponding mask or label file for cortex?

Load the ?h.cortex.label in fsaverage

Thanks,

Chao-Gan

--

Chao-Gan YAN, Ph.D.

Professor, Principal Investigator
Deputy Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China

-

Initiator

DPABI, DPARSF, PRN and The R-fMRI Network (RFMRI.ORG)

http://rfmri.org/yan

http://scholar.google.com/citations?user=lJQ9B58AAAAJ

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Chao-Gan YAN, Ph.D.

Professor, Principal Investigator
Deputy Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China

-

Initiator

DPABI, DPARSF, PRN and The R-fMRI Network (RFMRI.ORG)

http://rfmri.org/yan

http://scholar.google.com/citations?user=lJQ9B58AAAAJ

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer