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[[FsFastTutorialV5.1|top]] | [[FsFastTutorialV5.1|previous]]| [[FsFastTutorialV5.1/FsFastDirStruct|next (Directory Structure)]]
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= FSFAST Tutorial Data Description = = Surface-based Interhemispheric Registration =
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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
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 * 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 ==
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= Functional Paradigm = Note: you only need to do this installation if you have version 5.1 or lower
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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
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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
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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
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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
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= 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
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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 ...
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You will need to set the TUTORIAL_DATA environment variable. In tcsh
or csh
# Smooth
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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
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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
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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
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[[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
}}}

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

Xhemi (last edited 2019-07-11 13:37:50 by 172)