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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 http://rfmri.org/DPARSFDPABI http://rfmri.org/DPABI http://rfmri.org/DPARSF, http://dpabi.orgDPARSF http://rfmri.org/DPARSF, PRN http://rfmri.org/PRN and The R-fMRI Network http://rfmri.org (RFMRI.ORG http://rfmri.org/) http://rfmri.org/yan http://scholar.google.com/citations?user=lJQ9B58AAAAJ

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Thanks, Douglas!

I found subcort.mask.mgz there, that should work (subcortical mask in MNI space)!

Best,

Chao-Gan

On Wed, Nov 21, 2018 at 12:45 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

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 http://rfmri.org/DPARSFDPABI http://rfmri.org/DPABI http://rfmri.org/DPARSF, http://dpabi.orgDPARSF http://rfmri.org/DPARSF, PRN http://rfmri.org/PRN and The R-fMRI Network http://rfmri.org (RFMRI.ORG http://rfmri.org/) http://rfmri.org/yan http://scholar.google.com/citations?user=lJQ9B58AAAAJ

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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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 http://rfmri.org/DPARSFDPABI http://rfmri.org/DPABI http://rfmri.org/DPARSF, http://dpabi.orgDPARSF http://rfmri.org/DPARSF, PRN http://rfmri.org/PRN and The R-fMRI Network http://rfmri.org (RFMRI.ORG http://rfmri.org/) http://rfmri.org/yan http://scholar.google.com/citations?user=lJQ9B58AAAAJ

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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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