1. Surface-based Interhemispheric Registration

Those using this procedure should site the following paper: Greve, Douglas N., Lise Van der Haegen, Qing Cai, Steven Stufflebeam, Mert R. Sabuncu, Bruce Fischl, and Marc Bysbaert. "A surface-based analysis of language lateralization and cortical asymmetry." (2013). Journal of Cognitive Neuroscience. In press.

1.1. Installation

Note: you only need to do this installation if you have version 5.1 or lower

Download these files

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/surfreg
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_preproc
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/fsaverage_sym.tar.gz
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mult-comp-cor.tar.gz
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mri_convert.{linux,mac}
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mri_vol2vol.{linux,mac}

Copy surfreg, xhemireg, mris_preproc into $FREESURFER_HOME/bin Copy mri_convert.{linux,mac} into $FREESURFER_HOME/bin/mri_convert Copy mri_vol2vol.{linux,mac} into $FREESURFER_HOME/bin/mri_vol2vol

# Untar fsaverage_sym.tar.gz into your $SUBJECTS_DIR cd $SUBJECTS_DIR tar xvfz fsaverage_sym.tar.gz

# Untar mult-comp-cor.tar.gz into $FREESURFER_HOME/average cd $FREESURFER_HOME/average tar xvfz mult-comp-cor.tar.gz

# Copy mris_preproc into $FREESURFER_HOME/bin after making a backup To apply an existing atlas (eg, fsaverage_sym) to an anatomical analysis

1.2. Apply an existing atlas (fsaverage_sym)

# Reg to atlas (1-2 hours per subject) # Creates $subject/xhemi # Creates lh.fsaverage_sym.sphere.reg in $subject and $subject/xhemi

foreach subject (subjectlist)
  surfreg --s $subject --t fsaverage_sym --lh
  surfreg --s $subject --t fsaverage_sym --lh --xhemi
end

# Create a stack of subjects

mris_preproc --target fsaverage_sym --hemi lh 
  --xhemi --paired-diff \
  --srcsurfreg fsaverage_sym.sphere.reg \
  --meas thickness \
  --out lh.lh-rh.thickness.sm00.mgh \
  --s subj1 --s subj2 ...

# Smooth

mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 5\
 --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm05.mgh

# Analyze

mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 \
 --osgm --surf fsaverage_sym lh 

# View

tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh

# Correct for multiple comparisons

mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 \
   --cwpvalthresh .5 --cache 2 abs

1.3. Build Your Own Atlas

# Create xhemi subject (don't reg, a few minutes to finish)

foreach subject (subjectlist)
  xhemireg --s $subject
end

# Reg to existing sym atlas # Note: if you want test how symmetrical the atlas is use --lhrh # (but it takes twice as long)

foreach subject (subjectlist)
  surfreg --s $subject --t fsaverage_sym --lh
  surfreg --s $subject --t fsaverage_sym --xhemi --lh
end

# Make first iteration (<5min)

make_average_subject --out myatlas.i1 \
  --surf-reg fsaverage_sym.sphere.reg \
  --subjects subjectlist \
  --xhemi \
  --no-vol --template-only 

# Reg to first iteration # Note: if you want test the symmetry, use --lhrh

foreach subject (subjectlist)
  surfreg --s $subject --t myatlas.i1 --lh
  surfreg --s $subject --t myatlas.i1 --xhemi --lh
end

# Make second iteration (<5min)

make_average_subject --out myatlas.i2 \
  --surf-reg myatlas.i1.sphere.reg \
  --subjects subjectlist \
  --xhemi \
  --no-vol --template-only 

# Reg to second iteration. Note: if you want test the symmetry, use --lhrh

foreach subject (subjectlist)
  surfreg --s $subject --t myatlas.i2 --lh
  surfreg --s $subject --t myatlas.i2 --xhemi --lh
end

# Make final iteration (1-2 hours)

 make_average_subject --out myatlas.i3 \
  --surf-reg myatlas.i2.sphere.reg \
  --subjects subjectlist \
  --xhemi --hemi lh