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:
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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.
<dgr...@mgh.harvard.edu<mailto:dgr...@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/DPARSF>DPABI<http://rfmri.org/DPABI><http://rfmri.org/DPARSF>,
<http://dpabi.org> DPARSF<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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--
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/DPARSF>DPABI<http://rfmri.org/DPABI><http://rfmri.org/DPARSF>,
<http://dpabi.org> DPARSF<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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