External Email - Use Caution 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. < dgr...@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. < > 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 >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > <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 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 <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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