Chen et al. (2016). Untangling the Relatedness among Correlations, Part II: Inter-Subject Correlation Group Analysis through Linear Mixed-Effects Modeling¶
Chen GC, Taylor PA, Shin Y-W, Reynolds RC, Cox RW (2016). Untangling the Relatedness among Correlations, Part II: Inter-Subject Correlation Group Analysis through Linear Mixed-Effects Modeling. Neuroimage 147:825-840.
Chen GC, Shin Y-W, Taylor PA, Glen DR, Reynolds RC, Israel RB, Cox RW (2016). Untangling the Relatedness among Correlations, Part I: Nonparametric Approaches to Inter-Subject Correlation Analysis at the Group Level. Neuroimage 142:248-259. Corrigendum
See also
Tag |
Label |
---|---|
FMRI paradigm: |
naturalistic |
FMRI dset: |
EPI |
Anatomical dset: |
MPRAGE |
Subject population: |
human |
Subject characteristic: |
control |
Subject age: |
adult |
Template space: |
Talairach |
Template align method: |
nonlinear |
Tissue segmentation: |
FreeSurfer |
Tissue regression: |
fANATICOR |
Comments: |
FreeSurfer segmentation; |
|
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | #!/bin/tcsh
# --------------------------------------------------------------------
# Script: s.2016_ChenEtal_01_init.tcsh
#
# From:
# Chen GC, Taylor PA, Shin Y-W, Reynolds RC, Cox RW (2016). Untangling
# the Relatedness among Correlations, Part II: Inter-Subject
# Correlation Group Analysis through Linear Mixed-Effects
# Modeling. Neuroimage (in press).
#
# Originally run using: AFNI_16.1.16
#
# ** Note: this code is a "fixed" version, with the selection of WM
# ** regions updated *not* to include voxels with value '16' in line 34.
#
# --------------------------------------------------------------------
# Commands run prior to afni_proc.py, each in appropriate
# directories for the data sets for each subject
# Run FreeSurfer on the anatomical, and then use
# SUMA to convert the FS output to NIFTI for AFNI to use.
recon-all -all -subject $subj -i $anat
@SUMA_Make_Spec_FS -sid $subj -NIFTI
# Select the ventricle maps from the FS output.
3dcalc -a aparc+aseg.nii -datum byte -prefix FSmask_vent.nii \
-expr 'amongst(a,4,43)'
# Select the WM maps from the FS output.
3dcalc -a aparc+aseg.nii -datum byte -prefix FSmask_WM.nii \
-expr 'amongst(a,2,7,41,46,251,252,253,254,255)'
|
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | #!/bin/tcsh
# --------------------------------------------------------------------
# Script: s.2016_ChenEtal_02_ap.tcsh
#
# From:
# Chen GC, Taylor PA, Shin Y-W, Reynolds RC, Cox RW (2016). Untangling
# the Relatedness among Correlations, Part II: Inter-Subject
# Correlation Group Analysis through Linear Mixed-Effects
# Modeling. Neuroimage (in press).
#
# Originally run using: AFNI_16.1.16
# --------------------------------------------------------------------
# FMRI processing script, ISC movie data.
# Assumes previously run FS and SUMA commands, respectively:
# $ recon-all -all -subject $subj -i $anat
# $ @SUMA_Make_Spec_FS -sid $subj -NIFTI
# Set top level directory structure
set subj = $1
set topdir = TOP_LEVEL_FILE_LOCATION
set task = movie
set fsroot = $topdir/freesurfer/subjects
set outroot = $topdir/subject_results/$task.6
# Input directory: unprocessed FMRI data
set indir = $topdir/orig.data
# Input directory: FreeSurfer + @SUMA_MakeSpec_FS results
set fsindir = $fsroot/$subj/SUMA
# Output directory: name for output
set outdir = $outroot/$subj
# Input data: list of partitioned EPIs (movie clips)
set epi_dpattern = "movie*.HEAD"
# Input data: FreeSurfer results (anatomy, ventricle and WM maps)
set fsanat = ${subj}_SurfVol.nii
set fsvent = FSmask_vent.nii
set fswm = FSmask_WM.nii
afni_proc.py -subj_id $subj.$task \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat $fsindir/$fsanat \
-anat_follower_ROI aaseg anat $fsindir/aparc.a2009s+aseg_rank.nii \
-anat_follower_ROI aeseg epi $fsindir/aparc.a2009s+aseg_rank.nii \
-anat_follower_ROI FSvent epi $fsindir/$fsvent \
-anat_follower_ROI FSWMe epi $fsindir/$fswm \
-anat_follower_erode FSvent FSWMe \
-dsets $epi_dpattern \
-tcat_remove_first_trs 0 \
-tlrc_base TT_N27+tlrc \
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-regress_ROI_PC FSvent 3 \
-regress_make_corr_vols aeseg FSvent \
-regress_anaticor_fast \
-regress_anaticor_label FSWMe \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.1 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no
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