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# Smooth |
# Smooth. This example smooths by 10mm on the surface. This is only an # example and your data might be better off being smoothed more or # less. There is no way to determine what the optimal smoothing level is. |
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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 |
mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 10\ --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm10.mgh |
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mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 \ | mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 \ |
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tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh | tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm10/osgm/sig.mgh |
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mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 \ | mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 \ |
Contents
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. This example smooths by 10mm on the surface. This is only an # example and your data might be better off being smoothed more or # less. There is no way to determine what the optimal smoothing level is.
mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 10\ --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm10.mgh
# Analyze
mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 \ --osgm --surf fsaverage_sym lh
# View
tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm10/osgm/sig.mgh
# Correct for multiple comparisons
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 \ --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