afni.nimh.nih.gov

Hello,

(I am also posting this to the FSL listserv to get their perspective as well)
I am analyzing a fast event related design, and the best way for me to understand the analysis is by making two software packages do the same thing. However, despite my best efforts I cannot get the GLM output for both AFNI and FSL to come close. I am wondering if I'm violating some idiosyncrasy of either package making the results divergent.

Details:
preprocessing steps::
motion correction::: 3dvolreg (AFNI)
spatial smoothing::: susan (FSL)
temporal filtering::: 3dbandpass highpass: 0.01 lowpass: 99999 (with the signal mean added back in: [afni.nimh.nih.gov]) (AFNI)
global normalization::: mean signal across run = 10,000 (FSL)

typical output from each GLM uncorrected(?) zstat (see below to see how I got AFNI zstat) file (single subject thresholded at z=2.33).
FSL zstat file= featdir/stats/zstat#.nii.gz
AFNI # of sig voxels=500
FSL # of sig voxels=1000
overlap of AFNI and FSL sig voxels= 80

I used the 4d-volume output from these preprocessing steps and put them into AFNI's 3dDeconvolve/REMLfit and FSL's FEAT.
I added the mean signal back in and globally normalized the signal to 10,000 because FSL's FILM (prewhitening) function appears to expect that scale of intensities. Does 3dDeconvolve/REMLfit have similar assumptions about the input? Do the data need to be scaled or saved as a certain datatype (i.e. float, int, double, etc.)?

Below is the snippet of code I used to run 3dDeconvolve/REMLfit (written in BASH) and the .fsf file passed into feat. I convolved with single gamma function and I made AFNI's gamma function match FSL's gamma function using this thread: (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=FSL&D=0&X=20D3C05165200516F9&Y=steve%40fmrib.ox.ac.uk&P=787303).

One thing that I know is different between the GLMs is that I used the temporal derivative in FSL, but I didn't know how to do something similar in AFNI. Additionally, I don't know how FSL accounts for drifts (specifically my impression is that AFNI uses the -polort option to account for drifts, but I don't know how FSL does it).

Thank you for your help!
James

AFNI GLM:
3dDeconvolve -input ${FLANKER_NIFTI} \
-nfirst 0 \
-polort A \
-num_stimts 10 \
-basis_normall 1 \
-mask ${outDir}/mask/*_mask.nii.gz \
-stim_times 1 ${timing_array[0]} 'GAM(6.0024,0.9996)' -stim_label 1 con \
-stim_times 2 ${timing_array[1]} 'GAM(6.0024,0.9996)' -stim_label 2 errors \
-stim_times 3 ${timing_array[2]} 'GAM(6.0024,0.9996)' -stim_label 3 inc \
-stim_times 4 ${timing_array[3]} 'GAM(6.0024,0.9996)' -stim_label 4 neu \
-stim_file 5 ${motion_file}[0] -stim_label 5 roll \
-stim_file 6 ${motion_file}[1] -stim_label 6 pitch \
-stim_file 7 ${motion_file}[2] -stim_label 7 yaw \
-stim_file 8 ${motion_file}[3] -stim_label 8 I_S \
-stim_file 9 ${motion_file}[4] -stim_label 9 R_L \
-stim_file 10 ${motion_file}[5] -stim_label 10 A_P \
-num_glt 7 \
-glt_label 1 con_ave -gltsym 'SYM: con' \
-glt_label 2 errors_ave -gltsym 'SYM: errors' \
-glt_label 3 inc_ave -gltsym 'SYM: inc' \
-glt_label 4 neu_ave -gltsym 'SYM: neu' \
-glt_label 5 con-neu -gltsym 'SYM: +con -neu' \
-glt_label 6 inc-neu -gltsym 'SYM: +inc -neu' \
-glt_label 7 con-inc -gltsym 'SYM: +con -inc' \
-tout -fout -bucket sub${subNum}_bucket -xjpeg sub${subNum}_glm_matrix.jpg -x1D_stop &&\
3dREMLfit -matrix sub${subNum}_bucket.xmat.1D \
-input ${FLANKER_NIFTI} \
-mask ${outDir}/mask/*_mask.nii.gz \
-fout -tout -Rbuck sub${subNum}_bucket_REML -Rvar sub${subNum}_bucket_REMLvar -verb

I change the Tstat output into Zstat using the following command:
3dmerge -1zscore -datum float -prefix Zmap.nii Tmap.nii (http://afni.nimh.nih.gov/afni/community/board/read.php?1,67177,67218)
I DID NOT use the coef file, I used the Tstat file.

FSL GLM

# FEAT version number
set fmri(version) 6.00

# Are we in MELODIC?
set fmri(inmelodic) 0

# Analysis level
# 1 : First-level analysis
# 2 : Higher-level analysis
set fmri(level) 1

# Which stages to run
# 0 : No first-level analysis (registration and/or group stats only)
# 7 : Full first-level analysis
# 1 : Pre-Stats
# 3 : Pre-Stats + Stats
# 2 : Stats
# 6 : Stats + Post-stats
# 4 : Post-stats
set fmri(analysis) 6

# Use relative filenames
set fmri(relative_yn) 0

# Balloon help
set fmri(help_yn) 1

# Run Featwatcher
set fmri(featwatcher_yn) 1

# Cleanup first-level standard-space images
set fmri(sscleanup_yn) 0

# Output directory
set fmri(outputdir) "OUTPUT_DIRECTORY"

# TR(s)
set fmri(tr) 2.0000000000

# Total volumes
set fmri(npts) 315

# Delete volumes
set fmri(ndelete) 0

# Perfusion tag/control order
set fmri(tagfirst) 1

# Number of first-level analyses
set fmri(multiple) 1

# Higher-level input type
# 1 : Inputs are lower-level FEAT directories
# 2 : Inputs are cope images from FEAT directories
set fmri(inputtype) 1

# Carry out pre-stats processing?
set fmri(filtering_yn) 0

# Brain/background threshold, %
set fmri(brain_thresh) 10

# Critical z for design efficiency calculation
set fmri(critical_z) 5.3

# Noise level
set fmri(noise) 0.66

# Noise AR(1)
set fmri(noisear) 0.34

# Post-stats-only directory copying
# 0 : Overwrite original post-stats results
# 1 : Copy original FEAT directory for new Contrasts, Thresholding, Rendering
set fmri(newdir_yn) 0

# Motion correction
# 0 : None
# 1 : MCFLIRT
set fmri(mc) 1

# Spin-history (currently obsolete)
set fmri(sh_yn) 0

# B0 fieldmap unwarping?
set fmri(regunwarp_yn) 0

# EPI dwell time (ms)
set fmri(dwell) 0.7

# EPI TE (ms)
set fmri(te) 35

# % Signal loss threshold
set fmri(signallossthresh) 10

# Unwarp direction
set fmri(unwarp_dir) y-

# Slice timing correction
# 0 : None
# 1 : Regular up (0, 1, 2, 3, ...)
# 2 : Regular down
# 3 : Use slice order file
# 4 : Use slice timings file
# 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )
set fmri(st) 0

# Slice timings file
set fmri(st_file) ""

# BET brain extraction
set fmri(bet_yn) 1

# Spatial smoothing FWHM (mm)
set fmri(smooth) 5

# Intensity normalization
set fmri(norm_yn) 0

# Perfusion subtraction
set fmri(perfsub_yn) 0

# Highpass temporal filtering
set fmri(temphp_yn) 1

# Lowpass temporal filtering
set fmri(templp_yn) 0

# MELODIC ICA data exploration
set fmri(melodic_yn) 0

# Carry out main stats?
set fmri(stats_yn) 1

# Carry out prewhitening?
set fmri(prewhiten_yn) 1

# Add motion parameters to model
# 0 : No
# 1 : Yes
set fmri(motionevs) 0
set fmri(motionevsbeta) ""
set fmri(scriptevsbeta) ""

# Robust outlier detection in FLAME?
set fmri(robust_yn) 0

# Higher-level modelling
# 3 : Fixed effects
# 0 : Mixed Effects: Simple OLS
# 2 : Mixed Effects: FLAME 1
# 1 : Mixed Effects: FLAME 1+2
set fmri(mixed_yn) 2

# Number of EVs
set fmri(evs_orig) 4
set fmri(evs_real) 8
set fmri(evs_vox) 0

# Number of contrasts
set fmri(ncon_orig) 7
set fmri(ncon_real) 7

# Number of F-tests
set fmri(nftests_orig) 0
set fmri(nftests_real) 0

# Add constant column to design matrix? (obsolete)
set fmri(constcol) 0

# Carry out post-stats steps?
set fmri(poststats_yn) 1

# Pre-threshold masking?
set fmri(threshmask) ""

# Thresholding
# 0 : None
# 1 : Uncorrected
# 2 : Voxel
# 3 : Cluster
set fmri(thresh) 3

# P threshold
set fmri(prob_thresh) 0.05

# Z threshold
set fmri(z_thresh) 2.3

# Z min/max for colour rendering
# 0 : Use actual Z min/max
# 1 : Use preset Z min/max
set fmri(zdisplay) 0

# Z min in colour rendering
set fmri(zmin) 2

# Z max in colour rendering
set fmri(zmax) 8

# Colour rendering type
# 0 : Solid blobs
# 1 : Transparent blobs
set fmri(rendertype) 1

# Background image for higher-level stats overlays
# 1 : Mean highres
# 2 : First highres
# 3 : Mean functional
# 4 : First functional
# 5 : Standard space template
set fmri(bgimage) 1

# Create time series plots
set fmri(tsplot_yn) 1

# Registration?
set fmri(reg_yn) 1

# Registration to initial structural
set fmri(reginitial_highres_yn) 0

# Search space for registration to initial structural
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(reginitial_highres_search) 90

# Degrees of Freedom for registration to initial structural
set fmri(reginitial_highres_dof) 3

# Registration to main structural
set fmri(reghighres_yn) 0

# Search space for registration to main structural
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(reghighres_search) 90

# Degrees of Freedom for registration to main structural
set fmri(reghighres_dof) BBR

# Registration to standard image?
set fmri(regstandard_yn) 1

# Use alternate reference images?
set fmri(alternateReference_yn) 0

# Standard image
set fmri(regstandard) "/usr/local/fsl/data/standard/MNI152_T1_2mm_brain"

# Search space for registration to standard space
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(regstandard_search) 90

# Degrees of Freedom for registration to standard space
set fmri(regstandard_dof) 12

# Do nonlinear registration from structural to standard space?
set fmri(regstandard_nonlinear_yn) 0

# Control nonlinear warp field resolution
set fmri(regstandard_nonlinear_warpres) 10

# High pass filter cutoff
set fmri(paradigm_hp) 100

# Total voxels
set fmri(totalVoxels) 39997440


# Number of lower-level copes feeding into higher-level analysis
set fmri(ncopeinputs) 0

# 4D AVW data or FEAT directory (1)
set feat_files(1) "TEMPLATE_DATA"

# Add confound EVs text file
set fmri(confoundevs) 0

# EV 1 title
set fmri(evtitle1) "con"

# Basic waveform shape (EV 1)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
# 10 : Empty (all zeros)
set fmri(shape1) 3

# Convolution (EV 1)
# 0 : None
# 1 : Gaussian
# 2 : Gamma
# 3 : Double-Gamma HRF
# 4 : Gamma basis functions
# 5 : Sine basis functions
# 6 : FIR basis functions
set fmri(convolve1) 2

# Convolve phase (EV 1)
set fmri(convolve_phase1) 0

# Apply temporal filtering (EV 1)
set fmri(tempfilt_yn1) 1

# Add temporal derivative (EV 1)
set fmri(deriv_yn1) 1

# Custom EV file (EV 1)
set fmri(custom1) "CON_EV"

# Gamma sigma (EV 1)
set fmri(gammasigma1) 3

# Gamma delay (EV 1)
set fmri(gammadelay1) 6

# Orthogonalise EV 1 wrt EV 0
set fmri(ortho1.0) 0

# Orthogonalise EV 1 wrt EV 1
set fmri(ortho1.1) 0

# Orthogonalise EV 1 wrt EV 2
set fmri(ortho1.2) 0

# Orthogonalise EV 1 wrt EV 3
set fmri(ortho1.3) 0

# Orthogonalise EV 1 wrt EV 4
set fmri(ortho1.4) 0

# EV 2 title
set fmri(evtitle2) "inc"

# Basic waveform shape (EV 2)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
# 10 : Empty (all zeros)
set fmri(shape2) 3

# Convolution (EV 2)
# 0 : None
# 1 : Gaussian
# 2 : Gamma
# 3 : Double-Gamma HRF
# 4 : Gamma basis functions
# 5 : Sine basis functions
# 6 : FIR basis functions
set fmri(convolve2) 2

# Convolve phase (EV 2)
set fmri(convolve_phase2) 0

# Apply temporal filtering (EV 2)
set fmri(tempfilt_yn2) 1

# Add temporal derivative (EV 2)
set fmri(deriv_yn2) 1

# Custom EV file (EV 2)
set fmri(custom2) "INC_EV"

# Gamma sigma (EV 2)
set fmri(gammasigma2) 3

# Gamma delay (EV 2)
set fmri(gammadelay2) 6

# Orthogonalise EV 2 wrt EV 0
set fmri(ortho2.0) 0

# Orthogonalise EV 2 wrt EV 1
set fmri(ortho2.1) 0

# Orthogonalise EV 2 wrt EV 2
set fmri(ortho2.2) 0

# Orthogonalise EV 2 wrt EV 3
set fmri(ortho2.3) 0

# Orthogonalise EV 2 wrt EV 4
set fmri(ortho2.4) 0

# EV 3 title
set fmri(evtitle3) "neu"

# Basic waveform shape (EV 3)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
# 10 : Empty (all zeros)
set fmri(shape3) 3

# Convolution (EV 3)
# 0 : None
# 1 : Gaussian
# 2 : Gamma
# 3 : Double-Gamma HRF
# 4 : Gamma basis functions
# 5 : Sine basis functions
# 6 : FIR basis functions
set fmri(convolve3) 2

# Convolve phase (EV 3)
set fmri(convolve_phase3) 0

# Apply temporal filtering (EV 3)
set fmri(tempfilt_yn3) 1

# Add temporal derivative (EV 3)
set fmri(deriv_yn3) 1

# Custom EV file (EV 3)
set fmri(custom3) "NEU_EV"

# Gamma sigma (EV 3)
set fmri(gammasigma3) 3

# Gamma delay (EV 3)
set fmri(gammadelay3) 6

# Orthogonalise EV 3 wrt EV 0
set fmri(ortho3.0) 0

# Orthogonalise EV 3 wrt EV 1
set fmri(ortho3.1) 0

# Orthogonalise EV 3 wrt EV 2
set fmri(ortho3.2) 0

# Orthogonalise EV 3 wrt EV 3
set fmri(ortho3.3) 0

# Orthogonalise EV 3 wrt EV 4
set fmri(ortho3.4) 0

# EV 4 title
set fmri(evtitle4) "err"

# Basic waveform shape (EV 4)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
# 10 : Empty (all zeros)
set fmri(shape4) 3

# Convolution (EV 4)
# 0 : None
# 1 : Gaussian
# 2 : Gamma
# 3 : Double-Gamma HRF
# 4 : Gamma basis functions
# 5 : Sine basis functions
# 6 : FIR basis functions
set fmri(convolve4) 2

# Convolve phase (EV 4)
set fmri(convolve_phase4) 0

# Apply temporal filtering (EV 4)
set fmri(tempfilt_yn4) 1

# Add temporal derivative (EV 4)
set fmri(deriv_yn4) 1

# Custom EV file (EV 4)
set fmri(custom4) "ERR_EV"

# Gamma sigma (EV 4)
set fmri(gammasigma4) 3

# Gamma delay (EV 4)
set fmri(gammadelay4) 6

# Orthogonalise EV 4 wrt EV 0
set fmri(ortho4.0) 0

# Orthogonalise EV 4 wrt EV 1
set fmri(ortho4.1) 0

# Orthogonalise EV 4 wrt EV 2
set fmri(ortho4.2) 0

# Orthogonalise EV 4 wrt EV 3
set fmri(ortho4.3) 0

# Orthogonalise EV 4 wrt EV 4
set fmri(ortho4.4) 0

# Contrast & F-tests mode
# real : control real EVs
# orig : control original EVs
set fmri(con_mode_old) orig
set fmri(con_mode) orig

# Display images for contrast_real 1
set fmri(conpic_real.1) 1

# Title for contrast_real 1
set fmri(conname_real.1) "con"

# Real contrast_real vector 1 element 1
set fmri(con_real1.1) 1

# Real contrast_real vector 1 element 2
set fmri(con_real1.2) 0

# Real contrast_real vector 1 element 3
set fmri(con_real1.3) 0

# Real contrast_real vector 1 element 4
set fmri(con_real1.4) 0

# Real contrast_real vector 1 element 5
set fmri(con_real1.5) 0

# Real contrast_real vector 1 element 6
set fmri(con_real1.6) 0

# Real contrast_real vector 1 element 7
set fmri(con_real1.7) 0

# Real contrast_real vector 1 element 8
set fmri(con_real1.8) 0

# Display images for contrast_real 2
set fmri(conpic_real.2) 1

# Title for contrast_real 2
set fmri(conname_real.2) "inc"

# Real contrast_real vector 2 element 1
set fmri(con_real2.1) 0

# Real contrast_real vector 2 element 2
set fmri(con_real2.2) 0

# Real contrast_real vector 2 element 3
set fmri(con_real2.3) 1.0

# Real contrast_real vector 2 element 4
set fmri(con_real2.4) 0

# Real contrast_real vector 2 element 5
set fmri(con_real2.5) 0

# Real contrast_real vector 2 element 6
set fmri(con_real2.6) 0

# Real contrast_real vector 2 element 7
set fmri(con_real2.7) 0

# Real contrast_real vector 2 element 8
set fmri(con_real2.8) 0

# Display images for contrast_real 3
set fmri(conpic_real.3) 1

# Title for contrast_real 3
set fmri(conname_real.3) "neu"

# Real contrast_real vector 3 element 1
set fmri(con_real3.1) 0

# Real contrast_real vector 3 element 2
set fmri(con_real3.2) 0

# Real contrast_real vector 3 element 3
set fmri(con_real3.3) 0

# Real contrast_real vector 3 element 4
set fmri(con_real3.4) 0

# Real contrast_real vector 3 element 5
set fmri(con_real3.5) 1.0

# Real contrast_real vector 3 element 6
set fmri(con_real3.6) 0

# Real contrast_real vector 3 element 7
set fmri(con_real3.7) 0

# Real contrast_real vector 3 element 8
set fmri(con_real3.8) 0

# Display images for contrast_real 4
set fmri(conpic_real.4) 1

# Title for contrast_real 4
set fmri(conname_real.4) "err"

# Real contrast_real vector 4 element 1
set fmri(con_real4.1) 0

# Real contrast_real vector 4 element 2
set fmri(con_real4.2) 0

# Real contrast_real vector 4 element 3
set fmri(con_real4.3) 0

# Real contrast_real vector 4 element 4
set fmri(con_real4.4) 0

# Real contrast_real vector 4 element 5
set fmri(con_real4.5) 0

# Real contrast_real vector 4 element 6
set fmri(con_real4.6) 0

# Real contrast_real vector 4 element 7
set fmri(con_real4.7) 1.0

# Real contrast_real vector 4 element 8
set fmri(con_real4.8) 0

# Display images for contrast_real 5
set fmri(conpic_real.5) 1

# Title for contrast_real 5
set fmri(conname_real.5) "con-inc"

# Real contrast_real vector 5 element 1
set fmri(con_real5.1) 1.0

# Real contrast_real vector 5 element 2
set fmri(con_real5.2) 0

# Real contrast_real vector 5 element 3
set fmri(con_real5.3) -1.0

# Real contrast_real vector 5 element 4
set fmri(con_real5.4) 0

# Real contrast_real vector 5 element 5
set fmri(con_real5.5) 0

# Real contrast_real vector 5 element 6
set fmri(con_real5.6) 0

# Real contrast_real vector 5 element 7
set fmri(con_real5.7) 0

# Real contrast_real vector 5 element 8
set fmri(con_real5.8) 0

# Display images for contrast_real 6
set fmri(conpic_real.6) 1

# Title for contrast_real 6
set fmri(conname_real.6) "con-neu"

# Real contrast_real vector 6 element 1
set fmri(con_real6.1) 1.0

# Real contrast_real vector 6 element 2
set fmri(con_real6.2) 0

# Real contrast_real vector 6 element 3
set fmri(con_real6.3) 0

# Real contrast_real vector 6 element 4
set fmri(con_real6.4) 0

# Real contrast_real vector 6 element 5
set fmri(con_real6.5) -1.0

# Real contrast_real vector 6 element 6
set fmri(con_real6.6) 0

# Real contrast_real vector 6 element 7
set fmri(con_real6.7) 0

# Real contrast_real vector 6 element 8
set fmri(con_real6.8) 0

# Display images for contrast_real 7
set fmri(conpic_real.7) 1

# Title for contrast_real 7
set fmri(conname_real.7) "inc-neu"

# Real contrast_real vector 7 element 1
set fmri(con_real7.1) 0

# Real contrast_real vector 7 element 2
set fmri(con_real7.2) 0

# Real contrast_real vector 7 element 3
set fmri(con_real7.3) 1.0

# Real contrast_real vector 7 element 4
set fmri(con_real7.4) 0

# Real contrast_real vector 7 element 5
set fmri(con_real7.5) -1.0

# Real contrast_real vector 7 element 6
set fmri(con_real7.6) 0

# Real contrast_real vector 7 element 7
set fmri(con_real7.7) 0

# Real contrast_real vector 7 element 8
set fmri(con_real7.8) 0

# Display images for contrast_orig 1
set fmri(conpic_orig.1) 1

# Title for contrast_orig 1
set fmri(conname_orig.1) "con"

# Real contrast_orig vector 1 element 1
set fmri(con_orig1.1) 1

# Real contrast_orig vector 1 element 2
set fmri(con_orig1.2) 0

# Real contrast_orig vector 1 element 3
set fmri(con_orig1.3) 0

# Real contrast_orig vector 1 element 4
set fmri(con_orig1.4) 0

# Display images for contrast_orig 2
set fmri(conpic_orig.2) 1

# Title for contrast_orig 2
set fmri(conname_orig.2) "inc"

# Real contrast_orig vector 2 element 1
set fmri(con_orig2.1) 0

# Real contrast_orig vector 2 element 2
set fmri(con_orig2.2) 1.0

# Real contrast_orig vector 2 element 3
set fmri(con_orig2.3) 0

# Real contrast_orig vector 2 element 4
set fmri(con_orig2.4) 0

# Display images for contrast_orig 3
set fmri(conpic_orig.3) 1

# Title for contrast_orig 3
set fmri(conname_orig.3) "neu"

# Real contrast_orig vector 3 element 1
set fmri(con_orig3.1) 0

# Real contrast_orig vector 3 element 2
set fmri(con_orig3.2) 0

# Real contrast_orig vector 3 element 3
set fmri(con_orig3.3) 1.0

# Real contrast_orig vector 3 element 4
set fmri(con_orig3.4) 0

# Display images for contrast_orig 4
set fmri(conpic_orig.4) 1

# Title for contrast_orig 4
set fmri(conname_orig.4) "err"

# Real contrast_orig vector 4 element 1
set fmri(con_orig4.1) 0

# Real contrast_orig vector 4 element 2
set fmri(con_orig4.2) 0

# Real contrast_orig vector 4 element 3
set fmri(con_orig4.3) 0

# Real contrast_orig vector 4 element 4
set fmri(con_orig4.4) 1.0

# Display images for contrast_orig 5
set fmri(conpic_orig.5) 1

# Title for contrast_orig 5
set fmri(conname_orig.5) "con-inc"

# Real contrast_orig vector 5 element 1
set fmri(con_orig5.1) 1.0

# Real contrast_orig vector 5 element 2
set fmri(con_orig5.2) -1.0

# Real contrast_orig vector 5 element 3
set fmri(con_orig5.3) 0

# Real contrast_orig vector 5 element 4
set fmri(con_orig5.4) 0

# Display images for contrast_orig 6
set fmri(conpic_orig.6) 1

# Title for contrast_orig 6
set fmri(conname_orig.6) "con-neu"

# Real contrast_orig vector 6 element 1
set fmri(con_orig6.1) 1.0

# Real contrast_orig vector 6 element 2
set fmri(con_orig6.2) 0

# Real contrast_orig vector 6 element 3
set fmri(con_orig6.3) -1.0

# Real contrast_orig vector 6 element 4
set fmri(con_orig6.4) 0

# Display images for contrast_orig 7
set fmri(conpic_orig.7) 1

# Title for contrast_orig 7
set fmri(conname_orig.7) "inc-neu"

# Real contrast_orig vector 7 element 1
set fmri(con_orig7.1) 0

# Real contrast_orig vector 7 element 2
set fmri(con_orig7.2) 1.0

# Real contrast_orig vector 7 element 3
set fmri(con_orig7.3) -1.0

# Real contrast_orig vector 7 element 4
set fmri(con_orig7.4) 0

# Contrast masking - use >0 instead of thresholding?
set fmri(conmask_zerothresh_yn) 0

# Mask real contrast/F-test 1 with real contrast/F-test 2?
set fmri(conmask1_2) 0

# Mask real contrast/F-test 1 with real contrast/F-test 3?
set fmri(conmask1_3) 0

# Mask real contrast/F-test 1 with real contrast/F-test 4?
set fmri(conmask1_4) 0

# Mask real contrast/F-test 1 with real contrast/F-test 5?
set fmri(conmask1_5) 0

# Mask real contrast/F-test 1 with real contrast/F-test 6?
set fmri(conmask1_6) 0

# Mask real contrast/F-test 1 with real contrast/F-test 7?
set fmri(conmask1_7) 0

# Mask real contrast/F-test 2 with real contrast/F-test 1?
set fmri(conmask2_1) 0

# Mask real contrast/F-test 2 with real contrast/F-test 3?
set fmri(conmask2_3) 0

# Mask real contrast/F-test 2 with real contrast/F-test 4?
set fmri(conmask2_4) 0

# Mask real contrast/F-test 2 with real contrast/F-test 5?
set fmri(conmask2_5) 0

# Mask real contrast/F-test 2 with real contrast/F-test 6?
set fmri(conmask2_6) 0

# Mask real contrast/F-test 2 with real contrast/F-test 7?
set fmri(conmask2_7) 0

# Mask real contrast/F-test 3 with real contrast/F-test 1?
set fmri(conmask3_1) 0

# Mask real contrast/F-test 3 with real contrast/F-test 2?
set fmri(conmask3_2) 0

# Mask real contrast/F-test 3 with real contrast/F-test 4?
set fmri(conmask3_4) 0

# Mask real contrast/F-test 3 with real contrast/F-test 5?
set fmri(conmask3_5) 0

# Mask real contrast/F-test 3 with real contrast/F-test 6?
set fmri(conmask3_6) 0

# Mask real contrast/F-test 3 with real contrast/F-test 7?
set fmri(conmask3_7) 0

# Mask real contrast/F-test 4 with real contrast/F-test 1?
set fmri(conmask4_1) 0

# Mask real contrast/F-test 4 with real contrast/F-test 2?
set fmri(conmask4_2) 0

# Mask real contrast/F-test 4 with real contrast/F-test 3?
set fmri(conmask4_3) 0

# Mask real contrast/F-test 4 with real contrast/F-test 5?
set fmri(conmask4_5) 0

# Mask real contrast/F-test 4 with real contrast/F-test 6?
set fmri(conmask4_6) 0

# Mask real contrast/F-test 4 with real contrast/F-test 7?
set fmri(conmask4_7) 0

# Mask real contrast/F-test 5 with real contrast/F-test 1?
set fmri(conmask5_1) 0

# Mask real contrast/F-test 5 with real contrast/F-test 2?
set fmri(conmask5_2) 0

# Mask real contrast/F-test 5 with real contrast/F-test 3?
set fmri(conmask5_3) 0

# Mask real contrast/F-test 5 with real contrast/F-test 4?
set fmri(conmask5_4) 0

# Mask real contrast/F-test 5 with real contrast/F-test 6?
set fmri(conmask5_6) 0

# Mask real contrast/F-test 5 with real contrast/F-test 7?
set fmri(conmask5_7) 0

# Mask real contrast/F-test 6 with real contrast/F-test 1?
set fmri(conmask6_1) 0

# Mask real contrast/F-test 6 with real contrast/F-test 2?
set fmri(conmask6_2) 0

# Mask real contrast/F-test 6 with real contrast/F-test 3?
set fmri(conmask6_3) 0

# Mask real contrast/F-test 6 with real contrast/F-test 4?
set fmri(conmask6_4) 0

# Mask real contrast/F-test 6 with real contrast/F-test 5?
set fmri(conmask6_5) 0

# Mask real contrast/F-test 6 with real contrast/F-test 7?
set fmri(conmask6_7) 0

# Mask real contrast/F-test 7 with real contrast/F-test 1?
set fmri(conmask7_1) 0

# Mask real contrast/F-test 7 with real contrast/F-test 2?
set fmri(conmask7_2) 0

# Mask real contrast/F-test 7 with real contrast/F-test 3?
set fmri(conmask7_3) 0

# Mask real contrast/F-test 7 with real contrast/F-test 4?
set fmri(conmask7_4) 0

# Mask real contrast/F-test 7 with real contrast/F-test 5?
set fmri(conmask7_5) 0

# Mask real contrast/F-test 7 with real contrast/F-test 6?
set fmri(conmask7_6) 0

# Do contrast masking at all?
set fmri(conmask1_1) 0