Deletions are marked like this. | Additions are marked like this. |
Line 2: | Line 2: |
[[FsFastTutorialV5.1|top]] | [[FsFastTutorialV5.1|previous]]| [[FsFastTutorialV5.1/FsFastDirStruct|next (Directory Structure)]] |
|
Line 8: | Line 5: |
= FSFAST Tutorial Data Description = | = Surface-based Interhemispheric Registration = |
Line 10: | Line 7: |
The functional data were collected as part of the Functional Biomedical Research Network (fBIRN, www.nbirn.net). |
Greve, D.N., Sabuncu, M.R., Shafee, R., Schmansky, N., Buckner, R.L., and Fischl, B. (2011). Automatic surface-based interhemispheric registration with FreeSurfer (Quebec City, Canada: 17th Annual Meeting of the Organization on Human Brain Mapping, June 2011). http://www.nmr.mgh.harvard.edu/martinos/publications/posters/HBM-2011/HBM11-Greve.pdf |
Line 12: | Line 13: |
* Working-memory paradigm with distractors * 18 subjects * Each subject has 1 run (except sess01 which has 4 runs) * Collected at MGH Bay 4 (3T Siemens) * FreeSurfer anatomical analyses |
== Installation == |
Line 18: | Line 15: |
= Functional Paradigm = | Note: you only need to do this installation if you have version 5.1 or lower |
Line 20: | Line 17: |
The paradigm was designed to study the effects of emotional stimuli on the ability to recall items stored in working memory. * Blocked design * Each block consisted of 3 phases 1. Encode (16 sec) - 8 stick figures to remember (no response) 1. Distractor (16 sec) - 8 distractor images (response whether there is a face in the image) a. Emotional - Distractors are emotionally disturbing a. Neutral - Distractors are emotionally neutral 1. Probe (16 sec) - 8 pairs of stick figures. Subject responds as to which of the pair was in the original Encode. * Between each block was a 16 sec scrambled image used as baseline. {{attachment:wmparadigm.jpg}} The above yields 5 conditions: 1. Encode 1. Emotional Distractor 1. Neutral Distractor 1. Probe following Emotional Distractor 1. Probe following Neutral Distractor The scrambled image will be modeled as a baseline, not as a condition. = Functional Data = * Original data: each subject had 8 runs * This data: each subject has 1 run (except for sess01 who has 4) * Each run lasts 142 time points * TR = 2 sec. * There is one run of rest data for 13 subjects * There is a B0 map for each subject = Anatomical Data = * FreeSurfer analysis has been run for all 18 subjects = Getting the Data (not necessary for the Boston FreeSurfer Course) = You can get the analyzed functional data (10G) from: |
Download these files |
Line 59: | Line 19: |
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz |
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.mcc.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.linxu |
Line 62: | Line 27: |
You can get the structural data (5G) from: |
Copy surfreg, xhemireg, mris_preproc into $FREESURFER_HOME/bin Copy mri_convert.linux into $FREESURFER_HOME/bin/mri_convert # Untar fsaverage_sym.tar.gz into your $SUBJECTS_DIR cd $SUBJECTS_DIR tar xvfz fsaverage_sym.tar.gz # Untar fsaverage_sym.mcc.tar.gz into $FREESURFER_HOME/average/mult-comp-cor/ cd $FREESURFER_HOME/average/mult-comp-cor/ tar xvfz fsaverage_sym.mcc.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 == 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 |
Line 64: | Line 47: |
wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz |
foreach subject (subjectlist) surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi end |
Line 67: | Line 53: |
= Organizing the Tutorial (not necessary for the Boston FreeSurfer Course) = cd to a place on your network where you have enough space to unpack the tutorial data. |
# Create a stack of subjects |
Line 74: | Line 55: |
cd /place/with/space }}} Untar the data {{{ tar xvfz fsfast-tutorial.tar.gz tar xvfz fsfast-tutorial.subjects.tar.gz |
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 ... |
Line 82: | Line 63: |
You will need to set the TUTORIAL_DATA environment variable. In tcsh or csh |
# Smooth |
Line 85: | Line 65: |
setenv TUTORIAL_DATA /place/with/space |
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 |
Line 88: | Line 69: |
You will also need to link the FreeSurfer anatomical subjeccts (data in fsfast-tutorial.subjects) into your $SUBJECTS_DIR. You should set the FSFAST output format to be compressed NIFTI (nii.gz): |
# Analyze |
Line 93: | Line 71: |
setenv FSF_OUTPUT_FORMAT nii.gz |
mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 \ --osgm --surf fsaverage_sym lh |
Line 96: | Line 75: |
[[FsFastTutorialV5.1|top]] | [[FsFastTutorialV5.1|previous]]| [[FsFastTutorialV5.1/FsFastDirStruct|next (Directory Structure)]] |
# View {{{ tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh }}} # Correct for MC (need new version of mri_glmfit-sim) {{{ mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 \ --cwpvalthresh .5 --cache 2 abs \ --subject-override fsaverage }}} == 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 }}} |
Contents
1. Surface-based Interhemispheric Registration
Greve, D.N., Sabuncu, M.R., Shafee, R., Schmansky, N., Buckner, R.L., and Fischl, B. (2011). Automatic surface-based interhemispheric registration with FreeSurfer (Quebec City, Canada: 17th Annual Meeting of the Organization on Human Brain Mapping, June 2011). http://www.nmr.mgh.harvard.edu/martinos/publications/posters/HBM-2011/HBM11-Greve.pdf
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/transfer/outgoing/flat/greve/surfreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.mcc.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.linxu
Copy surfreg, xhemireg, mris_preproc into $FREESURFER_HOME/bin Copy mri_convert.linux into $FREESURFER_HOME/bin/mri_convert
# Untar fsaverage_sym.tar.gz into your $SUBJECTS_DIR cd $SUBJECTS_DIR tar xvfz fsaverage_sym.tar.gz
# Untar fsaverage_sym.mcc.tar.gz into $FREESURFER_HOME/average/mult-comp-cor/ cd $FREESURFER_HOME/average/mult-comp-cor/ tar xvfz fsaverage_sym.mcc.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 MC (need new version of mri_glmfit-sim)
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 \ --cwpvalthresh .5 --cache 2 abs \ --subject-override fsaverage
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