add FSL design files (lvl 1-2) for audio (individuals)

code/2nd-lvl_audio-ppa-ind.fsf

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+
+# 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) 2
+
+# Which stages to run
+# 0 : No first-level analysis (registration and/or group stats only)
+# 7 : Full first-level analysis
+# 1 : Pre-processing
+# 2 : Statistics
+set fmri(analysis) 2
+
+# Use relative filenames
+set fmri(relative_yn) 0
+
+# Balloon help
+set fmri(help_yn) 0
+
+# Run Featwatcher
+set fmri(featwatcher_yn) 0
+
+# Cleanup first-level standard-space images
+set fmri(sscleanup_yn) 0
+
+# Output directory
+set fmri(outputdir) "/data/project/studyforrest_ppa/###SUB###/2nd-lvl_audio-ppa-ind"
+
+# TR(s)
+set fmri(tr) 3
+
+# Total volumes
+set fmri(npts) 8
+
+# Delete volumes
+set fmri(ndelete) 0
+
+# Perfusion tag/control order
+set fmri(tagfirst) 1
+
+# Number of first-level analyses
+set fmri(multiple) 8
+
+# 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
+
+# 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) 3
+
+# Number of EVs
+set fmri(evs_orig) 1
+set fmri(evs_real) 1
+set fmri(evs_vox) 0
+
+# Number of contrasts
+set fmri(ncon_orig) 1
+set fmri(ncon_real) 1
+
+# 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) 0
+
+# 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) 3.4
+
+# 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) 0
+
+# 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/share/fsl/5.0/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) 111703680
+
+
+# Number of lower-level copes feeding into higher-level analysis
+set fmri(ncopeinputs) 13
+
+# Use lower-level cope 1 for higher-level analysis
+set fmri(copeinput.1) 1
+
+# Use lower-level cope 2 for higher-level analysis
+set fmri(copeinput.2) 1
+
+# Use lower-level cope 3 for higher-level analysis
+set fmri(copeinput.3) 1
+
+# Use lower-level cope 4 for higher-level analysis
+set fmri(copeinput.4) 1
+
+# Use lower-level cope 5 for higher-level analysis
+set fmri(copeinput.5) 1
+
+# Use lower-level cope 6 for higher-level analysis
+set fmri(copeinput.6) 1
+
+# Use lower-level cope 7 for higher-level analysis
+set fmri(copeinput.7) 1
+
+# Use lower-level cope 8 for higher-level analysis
+set fmri(copeinput.8) 1
+
+# Use lower-level cope 9 for higher-level analysis
+set fmri(copeinput.9) 1
+
+# Use lower-level cope 10 for higher-level analysis
+set fmri(copeinput.10) 1
+
+# Use lower-level cope 11 for higher-level analysis
+set fmri(copeinput.11) 1
+
+# Use lower-level cope 12 for higher-level analysis
+set fmri(copeinput.12) 1
+
+# Use lower-level cope 13 for higher-level analysis
+set fmri(copeinput.13) 1
+
+# 4D AVW data or FEAT directory (1)
+set feat_files(1) "/data/project/studyforrest_ppa/###SUB###/run-1_audio-ppa-ind.feat"
+
+# 4D AVW data or FEAT directory (2)
+set feat_files(2) "/data/project/studyforrest_ppa/###SUB###/run-2_audio-ppa-ind.feat"
+
+# 4D AVW data or FEAT directory (3)
+set feat_files(3) "/data/project/studyforrest_ppa/###SUB###/run-3_audio-ppa-ind.feat"
+
+# 4D AVW data or FEAT directory (4)
+set feat_files(4) "/data/project/studyforrest_ppa/###SUB###/run-4_audio-ppa-ind.feat"
+
+# 4D AVW data or FEAT directory (5)
+set feat_files(5) "/data/project/studyforrest_ppa/###SUB###/run-5_audio-ppa-ind.feat"
+
+# 4D AVW data or FEAT directory (6)
+set feat_files(6) "/data/project/studyforrest_ppa/###SUB###/run-6_audio-ppa-ind.feat"
+
+# 4D AVW data or FEAT directory (7)
+set feat_files(7) "/data/project/studyforrest_ppa/###SUB###/run-7_audio-ppa-ind.feat"
+
+# 4D AVW data or FEAT directory (8)
+set feat_files(8) "/data/project/studyforrest_ppa/###SUB###/run-8_audio-ppa-ind.feat"
+
+# Add confound EVs text file
+set fmri(confoundevs) 0
+
+# EV 1 title
+set fmri(evtitle1) ""
+
+# 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) 2
+
+# 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) 0
+
+# Convolve phase (EV 1)
+set fmri(convolve_phase1) 0
+
+# Apply temporal filtering (EV 1)
+set fmri(tempfilt_yn1) 0
+
+# Add temporal derivative (EV 1)
+set fmri(deriv_yn1) 0
+
+# Custom EV file (EV 1)
+set fmri(custom1) "dummy"
+
+# Orthogonalise EV 1 wrt EV 0
+set fmri(ortho1.0) 0
+
+# Orthogonalise EV 1 wrt EV 1
+set fmri(ortho1.1) 0
+
+# Higher-level EV value for EV 1 and input 1
+set fmri(evg1.1) 1
+
+# Higher-level EV value for EV 1 and input 2
+set fmri(evg2.1) 1.0
+
+# Higher-level EV value for EV 1 and input 3
+set fmri(evg3.1) 1.0
+
+# Higher-level EV value for EV 1 and input 4
+set fmri(evg4.1) 1.0
+
+# Higher-level EV value for EV 1 and input 5
+set fmri(evg5.1) 1.0
+
+# Higher-level EV value for EV 1 and input 6
+set fmri(evg6.1) 1.0
+
+# Higher-level EV value for EV 1 and input 7
+set fmri(evg7.1) 1.0
+
+# Higher-level EV value for EV 1 and input 8
+set fmri(evg8.1) 1.0
+
+# Group membership for input 1
+set fmri(groupmem.1) 1
+
+# Group membership for input 2
+set fmri(groupmem.2) 1
+
+# Group membership for input 3
+set fmri(groupmem.3) 1
+
+# Group membership for input 4
+set fmri(groupmem.4) 1
+
+# Group membership for input 5
+set fmri(groupmem.5) 1
+
+# Group membership for input 6
+set fmri(groupmem.6) 1
+
+# Group membership for input 7
+set fmri(groupmem.7) 1
+
+# Group membership for input 8
+set fmri(groupmem.8) 1
+
+# Contrast & F-tests mode
+# real : control real EVs
+# orig : control original EVs
+set fmri(con_mode_old) real
+set fmri(con_mode) real
+
+# Display images for contrast_real 1
+set fmri(conpic_real.1) 1
+
+# Title for contrast_real 1
+set fmri(conname_real.1) "group mean"
+
+# Real contrast_real vector 1 element 1
+set fmri(con_real1.1) 1
+
+# Contrast masking - use >0 instead of thresholding?
+set fmri(conmask_zerothresh_yn) 0
+
+# Do contrast masking at all?
+set fmri(conmask1_1) 0
+
+##########################################################
+# Now options that don't appear in the GUI
+
+# 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) 1

code/generate_2nd-lvl-design_audio-ppa-ind.sh

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+#!/bin/bash
+
+set -e
+set -u
+
+cat << EOT > code/compute_2nd-lvl_audio-ppa-ind.submit
+# auto-generate file (generate_2nd_level_design.sh) -- do not modify!
+universe = vanilla
+output = condor_logs/\$(CLUSTER).\$(PROCESS).out
+error = condor_logs/\$(CLUSTER).\$(PROCESS).err
+log = condor_logs/\$(CLUSTER).\$(PROCESS).log
+getenv = True
+request_cpus = 1
+request_memory = 5000
+should_transfer_files = NO
+transfer_executable = False
+initialdir = /data/project/studyforrest_ppa
+executable = \$ENV(FSLDIR)/bin/feat
+
+EOT
+
+label="2nd-lvl_audio-ppa-ind"
+
+for sub in sub-*; do
+  subid=$(echo "$sub" | cut -d '-' -f2-)
+  sed -e "s/###SUB###/sub-${subid}/g" code/2nd-lvl_audio-ppa-ind.fsf > "$sub/${label}.fsf"
+  printf "arguments = $sub/${label}.fsf\nqueue\n" >> code/compute_2nd-lvl_audio-ppa-ind.submit
+done