# FEAT version number
set fmri(version) 5.98

# 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) 7

# 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) "/Users/hal/Desktop/tte-2a/s10_chab/r1/fullproc.feat"

# TR(s)
set fmri(tr) 2

# Total volumes
set fmri(npts) 323

# 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) 1

# 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) 5

# 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

# 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) 2
set fmri(evs_real) 4
set fmri(evs_vox) 0

# Number of contrasts
set fmri(ncon_orig) 4
set fmri(ncon_real) 4

# 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) 1

# 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) 6

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

# 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

# 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) "/Users/Hal/Desktop/ttE-2acopy/s10_chab/r1/fullproc.feat"

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

# Subject's structural image for analysis 1
set highres_files(1) "/Users/hal/Desktop/tte-2a/s10_chab/struct/s10_chab_msbrain"

# EV 1 title
set fmri(evtitle1) "b1 Tension"

# 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) 3

# 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) "/Users/Hal/Desktop/tte-2a/s10_chab/r1/beh/s10_chab_r1_b1.txt"

# 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

# EV 2 title
set fmri(evtitle2) "b2 Sound"

# 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) 3

# 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) "/Users/Hal/Desktop/tte-2a/s10_chab/r1/beh/s10_chab_r1_b2.txt"

# 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

# 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) "b1 Tension"

# 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

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

# Title for contrast_real 2
set fmri(conname_real.2) "b2  Sound"

# 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

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

# Title for contrast_real 3
set fmri(conname_real.3) "b1-b2 (Tension>Sound)"

# Real contrast_real vector 3 element 1
set fmri(con_real3.1) 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) -1.0

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

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

# Title for contrast_real 4
set fmri(conname_real.4) "b2-b1 (Sound>Tension)"

# Real contrast_real vector 4 element 1
set fmri(con_real4.1) -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) 1.0

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

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

# Title for contrast_orig 1
set fmri(conname_orig.1) "b1 Tension"

# 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

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

# Title for contrast_orig 2
set fmri(conname_orig.2) "b2  Sound"

# 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

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

# Title for contrast_orig 3
set fmri(conname_orig.3) "b1-b2 (Tension>Sound)"

# Real contrast_orig vector 3 element 1
set fmri(con_orig3.1) 1.0

# Real contrast_orig vector 3 element 2
set fmri(con_orig3.2) -1.0

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

# Title for contrast_orig 4
set fmri(conname_orig.4) "b2-b1 (Sound>Tension)"

# Real contrast_orig vector 4 element 1
set fmri(con_orig4.1) -1.0

# Real contrast_orig vector 4 element 2
set fmri(con_orig4.2) 1.0

# 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 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 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 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

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

##########################################################
# Now options that don't appear in the GUI

# Alternative example_func image (not derived from input 4D dataset)
set fmri(alternative_example_func) ""

# Alternative (to BETting) mask image
set fmri(alternative_mask) ""

# Initial structural space registration initialisation transform
set fmri(init_initial_highres) ""

# Structural space registration initialisation transform
set fmri(init_highres) ""

# Standard space registration initialisation transform
set fmri(init_standard) ""

# For full FEAT analysis: overwrite existing .feat output dir?
set fmri(overwrite_yn) 0