Hello Everybody
First of all I am new to the fMRI analisy using FSL (I was using SPM99
before) so please excuse me if my question would be naïve. I have two
groups of subjects, namely males and females. When I do 2nd level analysis
for the entire group (males+females) I get robust activations that go up to
7 in z score. But if I try to perform contrast analisys (males-females
contrast 1,-1) I get no activations whatsoever. Also when I include only
one group in the contrast (cotrast 1,0 or 0,1)I end up with no activation.
I am completely puzzled by this. I am using simple OLS to save time and
also I set thresholding to uncorrected, P=0.01. I include the setting for
both the entire group analysis (yielding robust activations) and contrast
analysis (yielding no activations) below.
Thank you for any help in advance
Michal Kuniecki
Analisis for entire group:
# FEAT version number
set fmri(version) 5.1
# 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-Stats
# 3 : Pre-Stats + Stats
# 2 : Stats
# 6 : Stats + Contrasts, Thresholding, Rendering
# 4 : Contrasts, Thresholding, Rendering
set fmri(analysis) 6
# Delay before starting (hours)
set fmri(delay) 0
# Use relative filenames
set fmri(relative_yn) 0
# Balloon help
set fmri(help_yn) 1
# Run Featwatcher
set fmri(featwatcher_yn) 1
# Output directory
set fmri(outputdir) "/usr/local/analisys/!OUTPUT"
# TR(s)
set fmri(tr) 3
# Total volumes
set fmri(npts) 44
# Delete volumes
set fmri(ndelete) 0
# Number of first-level analyses
set fmri(multiple) 44
# 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
# 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
# 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) ""
# Motion correction
# 0 : None
# 1 : MCFLIRT
set fmri(mc) 1
# Spin-history (currently obsolete)
set fmri(sh_yn) 0
# BET brain extraction
set fmri(bet_yn) 1
# Spatial smoothing FWHM (mm)
set fmri(smooth) 5
# Intensity normalization
set fmri(norm_yn) 0
# Highpass temporal filtering
set fmri(temphp_yn) 1
# Lowpass temporal filtering
set fmri(templp_yn) 0
# Carry out main stats?
set fmri(stats_yn) 1
# Carry out prewhitening?
set fmri(prewhiten_yn) 1
# Higher-level mixed effects choice
# 0 : Simple OLS
# 1 : FLAME (full)
# 2 : FLAME (stage 1 only)
set fmri(mixed_yn) 1
# Number of EVs
set fmri(evs_orig) 1
set fmri(evs_real) 1
# 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) 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) 0.01
# 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) 1
# Z max in colour rendering
set fmri(zmax) 15
# 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
# Registration?
set fmri(reg_yn) 0
# B0 fieldmap unwarping?
set fmri(regunwarp_yn) 0
# Dwell/Asymmetry ratio
set fmri(dwellasym) -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) 12
# Do nonlinear registration to initial structural?
set fmri(reginitial_highres_nonlinear_yn) 0
# 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) 12
# Do nonlinear registration to main structural?
set fmri(reghighres_nonlinear_yn) 0
# Registration to standard image?
set fmri(regstandard_yn) 1
# Standard image
set fmri(regstandard) "/usr/local/fsl/etc/standard/avg152T1_brain.hdr"
# 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 to standard space?
set fmri(regstandard_nonlinear_yn) 0
# High pass filter cutoff
set fmri(paradigm_hp) 100
# Number of lower-level copes feeding into higher-level analysis
set fmri(ncopeinputs) 1
# Use lower-level cope 1 for higher-level analysis
set fmri(copeinput.1) 1
# 4D AVW data or FEAT directory (1)
set feat_files(1) "/usr/local/analisys/x!BIENIEK_POZx.feat"
# 4D AVW data or FEAT directory (2)
set feat_files(2) "/usr/local/analisys/x!CHMIELEWSKA_POZx.feat"
# 4D AVW data or FEAT directory (3)
set feat_files(3) "/usr/local/analisys/x!CHMIELEWSKI_POZx.feat"
# 4D AVW data or FEAT directory (4)
set feat_files(4) "/usr/local/analisys/x!CISON_POZx.feat"
# 4D AVW data or FEAT directory (5)
set feat_files(5) "/usr/local/analisys/x!CURYLO_POZx.feat"
# 4D AVW data or FEAT directory (6)
set feat_files(6) "/usr/local/analisys/x!DOKTOR_POZx.feat"
# 4D AVW data or FEAT directory (7)
set feat_files(7) "/usr/local/analisys/x!DRAGULA_POZx.feat"
# 4D AVW data or FEAT directory (8)
set feat_files(8) "/usr/local/analisys/x!DZIEDZIC_POZx.feat"
# 4D AVW data or FEAT directory (9)
set feat_files(9) "/usr/local/analisys/x!HABER_POZx.feat"
# 4D AVW data or FEAT directory (10)
set feat_files(10) "/usr/local/analisys/x!HELLER_POZx.feat"
# 4D AVW data or FEAT directory (11)
set feat_files(11) "/usr/local/analisys/x!KALTENBEK_POZx.feat"
# 4D AVW data or FEAT directory (12)
set feat_files(12) "/usr/local/analisys/x!KAPEL_POZx.feat"
# 4D AVW data or FEAT directory (13)
set feat_files(13) "/usr/local/analisys/x!KLAPA_POZx.feat"
# 4D AVW data or FEAT directory (14)
set feat_files(14) "/usr/local/analisys/x!KOWALSKA_POZx.feat"
# 4D AVW data or FEAT directory (15)
set feat_files(15) "/usr/local/analisys/x!KRAWCZYK_POZx.feat"
# 4D AVW data or FEAT directory (16)
set feat_files(16) "/usr/local/analisys/x!KROLASIK_POZx.feat"
# 4D AVW data or FEAT directory (17)
set feat_files(17) "/usr/local/analisys/x!KULA_POZx.feat"
# 4D AVW data or FEAT directory (18)
set feat_files(18) "/usr/local/analisys/x!KURPIEL_POZx.feat"
# 4D AVW data or FEAT directory (19)
set feat_files(19) "/usr/local/analisys/x!KWOKA_POZx.feat"
# 4D AVW data or FEAT directory (20)
set feat_files(20) "/usr/local/analisys/x!LESNIAK_POZx.feat"
# 4D AVW data or FEAT directory (21)
set feat_files(21) "/usr/local/analisys/x!MARCINKOWSKA_POZx.feat"
# 4D AVW data or FEAT directory (22)
set feat_files(22) "/usr/local/analisys/x!MISKO_POZx.feat"
# 4D AVW data or FEAT directory (23)
set feat_files(23) "/usr/local/analisys/x!MOSKALA_POZx.feat"
# 4D AVW data or FEAT directory (24)
set feat_files(24) "/usr/local/analisys/x!NIEZGODA_POZx.feat"
# 4D AVW data or FEAT directory (25)
set feat_files(25) "/usr/local/analisys/x!NOWAK_POZx.feat"
# 4D AVW data or FEAT directory (26)
set feat_files(26) "/usr/local/analisys/x!PIWOWAR_POZx.feat"
# 4D AVW data or FEAT directory (27)
set feat_files(27) "/usr/local/analisys/x!PLAZA_POZx.feat"
# 4D AVW data or FEAT directory (28)
set feat_files(28) "/usr/local/analisys/x!PLONCZYK_POZx.feat"
# 4D AVW data or FEAT directory (29)
set feat_files(29) "/usr/local/analisys/x!RYBAK_POZx.feat"
# 4D AVW data or FEAT directory (30)
set feat_files(30) "/usr/local/analisys/x!SAMITOWSKA_POZx.feat"
# 4D AVW data or FEAT directory (31)
set feat_files(31) "/usr/local/analisys/x!SENDUR_POZx.feat"
# 4D AVW data or FEAT directory (32)
set feat_files(32) "/usr/local/analisys/x!SKAWINSKA_POZx.feat"
# 4D AVW data or FEAT directory (33)
set feat_files(33) "/usr/local/analisys/x!SKRZYPULEC_POZx.feat"
# 4D AVW data or FEAT directory (34)
set feat_files(34) "/usr/local/analisys/x!SMIALEK_POZx.feat"
# 4D AVW data or FEAT directory (35)
set feat_files(35) "/usr/local/analisys/x!SOBIECKI_POZx.feat"
# 4D AVW data or FEAT directory (36)
set feat_files(36) "/usr/local/analisys/x!SUSZEK_POZx.feat"
# 4D AVW data or FEAT directory (37)
set feat_files(37) "/usr/local/analisys/x!SZUMINSKA_POZx.feat"
# 4D AVW data or FEAT directory (38)
set feat_files(38) "/usr/local/analisys/x!TOMERA_POZx.feat"
# 4D AVW data or FEAT directory (39)
set feat_files(39) "/usr/local/analisys/x!WASZKIEWICZ_POZx.feat"
# 4D AVW data or FEAT directory (40)
set feat_files(40) "/usr/local/analisys/x!WILK_POZx.feat"
# 4D AVW data or FEAT directory (41)
set feat_files(41) "/usr/local/analisys/x!WOJTUSIKL_POZx.feat"
# 4D AVW data or FEAT directory (42)
set feat_files(42) "/usr/local/analisys/x!WOJTUSIKZ_POZx.feat"
# 4D AVW data or FEAT directory (43)
set feat_files(43) "/usr/local/analisys/x!WROBEL_POZx.feat"
# 4D AVW data or FEAT directory (44)
set feat_files(44) "/usr/local/analisys/x!ZULICKI_POZx.feat"
# Basic waveform shape (EV 1)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
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
set fmri(ortho1.0) 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
# Higher-level EV value for EV 1 and input 3
set fmri(evg3.1) 1
# Higher-level EV value for EV 1 and input 4
set fmri(evg4.1) 1
# Higher-level EV value for EV 1 and input 5
set fmri(evg5.1) 1
# Higher-level EV value for EV 1 and input 6
set fmri(evg6.1) 1
# Higher-level EV value for EV 1 and input 7
set fmri(evg7.1) 1
# Higher-level EV value for EV 1 and input 8
set fmri(evg8.1) 1
# Higher-level EV value for EV 1 and input 9
set fmri(evg9.1) 1
# Higher-level EV value for EV 1 and input 10
set fmri(evg10.1) 1
# Higher-level EV value for EV 1 and input 11
set fmri(evg11.1) 1
# Higher-level EV value for EV 1 and input 12
set fmri(evg12.1) 1
# Higher-level EV value for EV 1 and input 13
set fmri(evg13.1) 1
# Higher-level EV value for EV 1 and input 14
set fmri(evg14.1) 1
# Higher-level EV value for EV 1 and input 15
set fmri(evg15.1) 1
# Higher-level EV value for EV 1 and input 16
set fmri(evg16.1) 1
# Higher-level EV value for EV 1 and input 17
set fmri(evg17.1) 1
# Higher-level EV value for EV 1 and input 18
set fmri(evg18.1) 1
# Higher-level EV value for EV 1 and input 19
set fmri(evg19.1) 1
# Higher-level EV value for EV 1 and input 20
set fmri(evg20.1) 1
# Higher-level EV value for EV 1 and input 21
set fmri(evg21.1) 1
# Higher-level EV value for EV 1 and input 22
set fmri(evg22.1) 1
# Higher-level EV value for EV 1 and input 23
set fmri(evg23.1) 1
# Higher-level EV value for EV 1 and input 24
set fmri(evg24.1) 1
# Higher-level EV value for EV 1 and input 25
set fmri(evg25.1) 1
# Higher-level EV value for EV 1 and input 26
set fmri(evg26.1) 1
# Higher-level EV value for EV 1 and input 27
set fmri(evg27.1) 1
# Higher-level EV value for EV 1 and input 28
set fmri(evg28.1) 1
# Higher-level EV value for EV 1 and input 29
set fmri(evg29.1) 1
# Higher-level EV value for EV 1 and input 30
set fmri(evg30.1) 1
# Higher-level EV value for EV 1 and input 31
set fmri(evg31.1) 1
# Higher-level EV value for EV 1 and input 32
set fmri(evg32.1) 1
# Higher-level EV value for EV 1 and input 33
set fmri(evg33.1) 1
# Higher-level EV value for EV 1 and input 34
set fmri(evg34.1) 1
# Higher-level EV value for EV 1 and input 35
set fmri(evg35.1) 1
# Higher-level EV value for EV 1 and input 36
set fmri(evg36.1) 1
# Higher-level EV value for EV 1 and input 37
set fmri(evg37.1) 1
# Higher-level EV value for EV 1 and input 38
set fmri(evg38.1) 1
# Higher-level EV value for EV 1 and input 39
set fmri(evg39.1) 1
# Higher-level EV value for EV 1 and input 40
set fmri(evg40.1) 1
# Higher-level EV value for EV 1 and input 41
set fmri(evg41.1) 1
# Higher-level EV value for EV 1 and input 42
set fmri(evg42.1) 1
# Higher-level EV value for EV 1 and input 43
set fmri(evg43.1) 1
# Higher-level EV value for EV 1 and input 44
set fmri(evg44.1) 1
# Number of higher-level groups
set fmri(ngroups) 1
# 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
# Group membership for input 9
set fmri(groupmem.9) 1
# Group membership for input 10
set fmri(groupmem.10) 1
# Group membership for input 11
set fmri(groupmem.11) 1
# Group membership for input 12
set fmri(groupmem.12) 1
# Group membership for input 13
set fmri(groupmem.13) 1
# Group membership for input 14
set fmri(groupmem.14) 1
# Group membership for input 15
set fmri(groupmem.15) 1
# Group membership for input 16
set fmri(groupmem.16) 1
# Group membership for input 17
set fmri(groupmem.17) 1
# Group membership for input 18
set fmri(groupmem.18) 1
# Group membership for input 19
set fmri(groupmem.19) 1
# Group membership for input 20
set fmri(groupmem.20) 1
# Group membership for input 21
set fmri(groupmem.21) 1
# Group membership for input 22
set fmri(groupmem.22) 1
# Group membership for input 23
set fmri(groupmem.23) 1
# Group membership for input 24
set fmri(groupmem.24) 1
# Group membership for input 25
set fmri(groupmem.25) 1
# Group membership for input 26
set fmri(groupmem.26) 1
# Group membership for input 27
set fmri(groupmem.27) 1
# Group membership for input 28
set fmri(groupmem.28) 1
# Group membership for input 29
set fmri(groupmem.29) 1
# Group membership for input 30
set fmri(groupmem.30) 1
# Group membership for input 31
set fmri(groupmem.31) 1
# Group membership for input 32
set fmri(groupmem.32) 1
# Group membership for input 33
set fmri(groupmem.33) 1
# Group membership for input 34
set fmri(groupmem.34) 1
# Group membership for input 35
set fmri(groupmem.35) 1
# Group membership for input 36
set fmri(groupmem.36) 1
# Group membership for input 37
set fmri(groupmem.37) 1
# Group membership for input 38
set fmri(groupmem.38) 1
# Group membership for input 39
set fmri(groupmem.39) 1
# Group membership for input 40
set fmri(groupmem.40) 1
# Group membership for input 41
set fmri(groupmem.41) 1
# Group membership for input 42
set fmri(groupmem.42) 1
# Group membership for input 43
set fmri(groupmem.43) 1
# Group membership for input 44
set fmri(groupmem.44) 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) ""
# 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
Analisis with selective contrasts:
# FEAT version number
set fmri(version) 5.1
# 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-Stats
# 3 : Pre-Stats + Stats
# 2 : Stats
# 6 : Stats + Contrasts, Thresholding, Rendering
# 4 : Contrasts, Thresholding, Rendering
set fmri(analysis) 6
# Delay before starting (hours)
set fmri(delay) 0
# Use relative filenames
set fmri(relative_yn) 0
# Balloon help
set fmri(help_yn) 1
# Run Featwatcher
set fmri(featwatcher_yn) 1
# Output directory
set fmri(outputdir) "/home/michal/poz"
# TR(s)
set fmri(tr) 3
# Total volumes
set fmri(npts) 44
# Delete volumes
set fmri(ndelete) 0
# Number of first-level analyses
set fmri(multiple) 44
# 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
# 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
# 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) ""
# Motion correction
# 0 : None
# 1 : MCFLIRT
set fmri(mc) 1
# Spin-history (currently obsolete)
set fmri(sh_yn) 0
# BET brain extraction
set fmri(bet_yn) 1
# Spatial smoothing FWHM (mm)
set fmri(smooth) 5
# Intensity normalization
set fmri(norm_yn) 0
# Highpass temporal filtering
set fmri(temphp_yn) 1
# Lowpass temporal filtering
set fmri(templp_yn) 0
# Carry out main stats?
set fmri(stats_yn) 1
# Carry out prewhitening?
set fmri(prewhiten_yn) 1
# Higher-level mixed effects choice
# 0 : Simple OLS
# 1 : FLAME (full)
# 2 : FLAME (stage 1 only)
set fmri(mixed_yn) 0
# Number of EVs
set fmri(evs_orig) 2
set fmri(evs_real) 2
# Number of contrasts
set fmri(ncon_orig) 1
set fmri(ncon_real) 3
# Number of F-tests
set fmri(nftests_orig) 0
set fmri(nftests_real) 1
# 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) 1
# P threshold
set fmri(prob_thresh) 0.01
# 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) 1
# Z max in colour rendering
set fmri(zmax) 15
# 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
# Registration?
set fmri(reg_yn) 0
# B0 fieldmap unwarping?
set fmri(regunwarp_yn) 0
# Dwell/Asymmetry ratio
set fmri(dwellasym) -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) 12
# Do nonlinear registration to initial structural?
set fmri(reginitial_highres_nonlinear_yn) 0
# 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) 12
# Do nonlinear registration to main structural?
set fmri(reghighres_nonlinear_yn) 0
# Registration to standard image?
set fmri(regstandard_yn) 1
# Standard image
set fmri(regstandard) "/usr/local/fsl/etc/standard/avg152T1_brain.hdr"
# 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 to standard space?
set fmri(regstandard_nonlinear_yn) 0
# High pass filter cutoff
set fmri(paradigm_hp) 100
# Number of lower-level copes feeding into higher-level analysis
set fmri(ncopeinputs) 1
# Use lower-level cope 1 for higher-level analysis
set fmri(copeinput.1) 1
# 4D AVW data or FEAT directory (1)
set feat_files(1) "/usr/local/analisys/poz/K_CHMIELEWSKA_POZx.feat"
# 4D AVW data or FEAT directory (2)
set feat_files(2) "/usr/local/analisys/poz/K_CURYLO_POZx.feat"
# 4D AVW data or FEAT directory (3)
set feat_files(3) "/usr/local/analisys/poz/K_DOKTOR_POZx.feat"
# 4D AVW data or FEAT directory (4)
set feat_files(4) "/usr/local/analisys/poz/K_KALTENBEK_POZx.feat"
# 4D AVW data or FEAT directory (5)
set feat_files(5) "/usr/local/analisys/poz/K_KOWALSKA_POZx.feat"
# 4D AVW data or FEAT directory (6)
set feat_files(6) "/usr/local/analisys/poz/K_KROLASIK_POZx.feat"
# 4D AVW data or FEAT directory (7)
set feat_files(7) "/usr/local/analisys/poz/K_LESNIAK_POZx.feat"
# 4D AVW data or FEAT directory (8)
set feat_files(8) "/usr/local/analisys/poz/K_MARCINKOWSKA_POZx.feat"
# 4D AVW data or FEAT directory (9)
set feat_files(9) "/usr/local/analisys/poz/K_MISKO_POZx.feat"
# 4D AVW data or FEAT directory (10)
set feat_files(10) "/usr/local/analisys/poz/K_NOWAK_POZx.feat"
# 4D AVW data or FEAT directory (11)
set feat_files(11) "/usr/local/analisys/poz/K_PIWOWAR_POZx.feat"
# 4D AVW data or FEAT directory (12)
set feat_files(12) "/usr/local/analisys/poz/K_PLAZA_POZx.feat"
# 4D AVW data or FEAT directory (13)
set feat_files(13) "/usr/local/analisys/poz/K_PLONCZYK_POZx.feat"
# 4D AVW data or FEAT directory (14)
set feat_files(14) "/usr/local/analisys/poz/K_SAMITOWSKA_POZx.feat"
# 4D AVW data or FEAT directory (15)
set feat_files(15) "/usr/local/analisys/poz/K_SENDUR_POZx.feat"
# 4D AVW data or FEAT directory (16)
set feat_files(16) "/usr/local/analisys/poz/K_SKAWINSKA_POZx.feat"
# 4D AVW data or FEAT directory (17)
set feat_files(17) "/usr/local/analisys/poz/K_SKRZYPULEC_POZx.feat"
# 4D AVW data or FEAT directory (18)
set feat_files(18) "/usr/local/analisys/poz/K_SZUMINSKA_POZx.feat"
# 4D AVW data or FEAT directory (19)
set feat_files(19) "/usr/local/analisys/poz/K_TOMERA_POZx.feat"
# 4D AVW data or FEAT directory (20)
set feat_files(20) "/usr/local/analisys/poz/K_WASZKIEWICZ_POZx.feat"
# 4D AVW data or FEAT directory (21)
set feat_files(21) "/usr/local/analisys/poz/K_WOJTUSIKZ_POZx.feat"
# 4D AVW data or FEAT directory (22)
set feat_files(22) "/usr/local/analisys/poz/M_BIENIEK_POZx.feat"
# 4D AVW data or FEAT directory (23)
set feat_files(23) "/usr/local/analisys/poz/M_CHMIELEWSKI_POZx.feat"
# 4D AVW data or FEAT directory (24)
set feat_files(24) "/usr/local/analisys/poz/M_CISON_POZx.feat"
# 4D AVW data or FEAT directory (25)
set feat_files(25) "/usr/local/analisys/poz/M_DRAGULA_POZx.feat"
# 4D AVW data or FEAT directory (26)
set feat_files(26) "/usr/local/analisys/poz/M_DZIEDZIC_POZx.feat"
# 4D AVW data or FEAT directory (27)
set feat_files(27) "/usr/local/analisys/poz/M_HABER_POZx.feat"
# 4D AVW data or FEAT directory (28)
set feat_files(28) "/usr/local/analisys/poz/M_HELLER_POZx.feat"
# 4D AVW data or FEAT directory (29)
set feat_files(29) "/usr/local/analisys/poz/M_KAPEL_POZx.feat"
# 4D AVW data or FEAT directory (30)
set feat_files(30) "/usr/local/analisys/poz/M_KLAPA_POZx.feat"
# 4D AVW data or FEAT directory (31)
set feat_files(31) "/usr/local/analisys/poz/M_KRAWCZYK_POZx.feat"
# 4D AVW data or FEAT directory (32)
set feat_files(32) "/usr/local/analisys/poz/M_KULA_POZx.feat"
# 4D AVW data or FEAT directory (33)
set feat_files(33) "/usr/local/analisys/poz/M_KURPIEL_POZx.feat"
# 4D AVW data or FEAT directory (34)
set feat_files(34) "/usr/local/analisys/poz/M_KWOKA_POZx.feat"
# 4D AVW data or FEAT directory (35)
set feat_files(35) "/usr/local/analisys/poz/M_MOSKALA_POZx.feat"
# 4D AVW data or FEAT directory (36)
set feat_files(36) "/usr/local/analisys/poz/M_NIEZGODA_POZx.feat"
# 4D AVW data or FEAT directory (37)
set feat_files(37) "/usr/local/analisys/poz/M_RYBAK_POZx.feat"
# 4D AVW data or FEAT directory (38)
set feat_files(38) "/usr/local/analisys/poz/M_SMIALEK_POZx.feat"
# 4D AVW data or FEAT directory (39)
set feat_files(39) "/usr/local/analisys/poz/M_SOBIECKI_POZx.feat"
# 4D AVW data or FEAT directory (40)
set feat_files(40) "/usr/local/analisys/poz/M_SUSZEK_POZx.feat"
# 4D AVW data or FEAT directory (41)
set feat_files(41) "/usr/local/analisys/poz/M_WILK_POZx.feat"
# 4D AVW data or FEAT directory (42)
set feat_files(42) "/usr/local/analisys/poz/M_WOJTUSIKL_POZx.feat"
# 4D AVW data or FEAT directory (43)
set feat_files(43) "/usr/local/analisys/poz/M_WROBEL_POZx.feat"
# 4D AVW data or FEAT directory (44)
set feat_files(44) "/usr/local/analisys/poz/M_ZULICKI_POZx.feat"
# Basic waveform shape (EV 1)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
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
set fmri(ortho1.0) 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
# Higher-level EV value for EV 1 and input 3
set fmri(evg3.1) 1
# Higher-level EV value for EV 1 and input 4
set fmri(evg4.1) 1
# Higher-level EV value for EV 1 and input 5
set fmri(evg5.1) 1
# Higher-level EV value for EV 1 and input 6
set fmri(evg6.1) 1
# Higher-level EV value for EV 1 and input 7
set fmri(evg7.1) 1
# Higher-level EV value for EV 1 and input 8
set fmri(evg8.1) 1
# Higher-level EV value for EV 1 and input 9
set fmri(evg9.1) 1
# Higher-level EV value for EV 1 and input 10
set fmri(evg10.1) 1
# Higher-level EV value for EV 1 and input 11
set fmri(evg11.1) 1
# Higher-level EV value for EV 1 and input 12
set fmri(evg12.1) 1
# Higher-level EV value for EV 1 and input 13
set fmri(evg13.1) 1
# Higher-level EV value for EV 1 and input 14
set fmri(evg14.1) 1
# Higher-level EV value for EV 1 and input 15
set fmri(evg15.1) 1
# Higher-level EV value for EV 1 and input 16
set fmri(evg16.1) 1
# Higher-level EV value for EV 1 and input 17
set fmri(evg17.1) 1
# Higher-level EV value for EV 1 and input 18
set fmri(evg18.1) 1
# Higher-level EV value for EV 1 and input 19
set fmri(evg19.1) 1
# Higher-level EV value for EV 1 and input 20
set fmri(evg20.1) 1
# Higher-level EV value for EV 1 and input 21
set fmri(evg21.1) 1
# Higher-level EV value for EV 1 and input 22
set fmri(evg22.1) 0
# Higher-level EV value for EV 1 and input 23
set fmri(evg23.1) 0
# Higher-level EV value for EV 1 and input 24
set fmri(evg24.1) 0
# Higher-level EV value for EV 1 and input 25
set fmri(evg25.1) 0
# Higher-level EV value for EV 1 and input 26
set fmri(evg26.1) 0
# Higher-level EV value for EV 1 and input 27
set fmri(evg27.1) 0
# Higher-level EV value for EV 1 and input 28
set fmri(evg28.1) 0
# Higher-level EV value for EV 1 and input 29
set fmri(evg29.1) 0
# Higher-level EV value for EV 1 and input 30
set fmri(evg30.1) 0
# Higher-level EV value for EV 1 and input 31
set fmri(evg31.1) 0
# Higher-level EV value for EV 1 and input 32
set fmri(evg32.1) 0
# Higher-level EV value for EV 1 and input 33
set fmri(evg33.1) 0
# Higher-level EV value for EV 1 and input 34
set fmri(evg34.1) 0
# Higher-level EV value for EV 1 and input 35
set fmri(evg35.1) 0
# Higher-level EV value for EV 1 and input 36
set fmri(evg36.1) 0
# Higher-level EV value for EV 1 and input 37
set fmri(evg37.1) 0
# Higher-level EV value for EV 1 and input 38
set fmri(evg38.1) 0
# Higher-level EV value for EV 1 and input 39
set fmri(evg39.1) 0
# Higher-level EV value for EV 1 and input 40
set fmri(evg40.1) 0
# Higher-level EV value for EV 1 and input 41
set fmri(evg41.1) 0
# Higher-level EV value for EV 1 and input 42
set fmri(evg42.1) 0
# Higher-level EV value for EV 1 and input 43
set fmri(evg43.1) 0
# Higher-level EV value for EV 1 and input 44
set fmri(evg44.1) 0
# Basic waveform shape (EV 2)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
set fmri(shape2) 2
# 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) 0
# Convolve phase (EV 2)
set fmri(convolve_phase2) 0
# Apply temporal filtering (EV 2)
set fmri(tempfilt_yn2) 0
# Add temporal derivative (EV 2)
set fmri(deriv_yn2) 0
# Custom EV file (EV 2)
set fmri(custom2) "dummy"
# Orthogonalise EV 2
set fmri(ortho2.0) 0
# Higher-level EV value for EV 2 and input 1
set fmri(evg1.2) 0
# Higher-level EV value for EV 2 and input 2
set fmri(evg2.2) 0
# Higher-level EV value for EV 2 and input 3
set fmri(evg3.2) 0
# Higher-level EV value for EV 2 and input 4
set fmri(evg4.2) 0
# Higher-level EV value for EV 2 and input 5
set fmri(evg5.2) 0
# Higher-level EV value for EV 2 and input 6
set fmri(evg6.2) 0
# Higher-level EV value for EV 2 and input 7
set fmri(evg7.2) 0
# Higher-level EV value for EV 2 and input 8
set fmri(evg8.2) 0
# Higher-level EV value for EV 2 and input 9
set fmri(evg9.2) 0
# Higher-level EV value for EV 2 and input 10
set fmri(evg10.2) 0
# Higher-level EV value for EV 2 and input 11
set fmri(evg11.2) 0
# Higher-level EV value for EV 2 and input 12
set fmri(evg12.2) 0
# Higher-level EV value for EV 2 and input 13
set fmri(evg13.2) 0
# Higher-level EV value for EV 2 and input 14
set fmri(evg14.2) 0
# Higher-level EV value for EV 2 and input 15
set fmri(evg15.2) 0
# Higher-level EV value for EV 2 and input 16
set fmri(evg16.2) 0
# Higher-level EV value for EV 2 and input 17
set fmri(evg17.2) 0
# Higher-level EV value for EV 2 and input 18
set fmri(evg18.2) 0
# Higher-level EV value for EV 2 and input 19
set fmri(evg19.2) 0
# Higher-level EV value for EV 2 and input 20
set fmri(evg20.2) 0
# Higher-level EV value for EV 2 and input 21
set fmri(evg21.2) 0
# Higher-level EV value for EV 2 and input 22
set fmri(evg22.2) 1
# Higher-level EV value for EV 2 and input 23
set fmri(evg23.2) 1
# Higher-level EV value for EV 2 and input 24
set fmri(evg24.2) 1
# Higher-level EV value for EV 2 and input 25
set fmri(evg25.2) 1
# Higher-level EV value for EV 2 and input 26
set fmri(evg26.2) 1
# Higher-level EV value for EV 2 and input 27
set fmri(evg27.2) 1
# Higher-level EV value for EV 2 and input 28
set fmri(evg28.2) 1
# Higher-level EV value for EV 2 and input 29
set fmri(evg29.2) 1
# Higher-level EV value for EV 2 and input 30
set fmri(evg30.2) 1
# Higher-level EV value for EV 2 and input 31
set fmri(evg31.2) 1
# Higher-level EV value for EV 2 and input 32
set fmri(evg32.2) 1
# Higher-level EV value for EV 2 and input 33
set fmri(evg33.2) 1
# Higher-level EV value for EV 2 and input 34
set fmri(evg34.2) 1
# Higher-level EV value for EV 2 and input 35
set fmri(evg35.2) 1
# Higher-level EV value for EV 2 and input 36
set fmri(evg36.2) 1
# Higher-level EV value for EV 2 and input 37
set fmri(evg37.2) 1
# Higher-level EV value for EV 2 and input 38
set fmri(evg38.2) 1
# Higher-level EV value for EV 2 and input 39
set fmri(evg39.2) 1
# Higher-level EV value for EV 2 and input 40
set fmri(evg40.2) 1
# Higher-level EV value for EV 2 and input 41
set fmri(evg41.2) 1
# Higher-level EV value for EV 2 and input 42
set fmri(evg42.2) 1
# Higher-level EV value for EV 2 and input 43
set fmri(evg43.2) 1
# Higher-level EV value for EV 2 and input 44
set fmri(evg44.2) 1
# Number of higher-level groups
set fmri(ngroups) 2
# 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
# Group membership for input 9
set fmri(groupmem.9) 1
# Group membership for input 10
set fmri(groupmem.10) 1
# Group membership for input 11
set fmri(groupmem.11) 1
# Group membership for input 12
set fmri(groupmem.12) 1
# Group membership for input 13
set fmri(groupmem.13) 1
# Group membership for input 14
set fmri(groupmem.14) 1
# Group membership for input 15
set fmri(groupmem.15) 1
# Group membership for input 16
set fmri(groupmem.16) 1
# Group membership for input 17
set fmri(groupmem.17) 1
# Group membership for input 18
set fmri(groupmem.18) 1
# Group membership for input 19
set fmri(groupmem.19) 1
# Group membership for input 20
set fmri(groupmem.20) 1
# Group membership for input 21
set fmri(groupmem.21) 1
# Group membership for input 22
set fmri(groupmem.22) 2
# Group membership for input 23
set fmri(groupmem.23) 2
# Group membership for input 24
set fmri(groupmem.24) 2
# Group membership for input 25
set fmri(groupmem.25) 2
# Group membership for input 26
set fmri(groupmem.26) 2
# Group membership for input 27
set fmri(groupmem.27) 2
# Group membership for input 28
set fmri(groupmem.28) 2
# Group membership for input 29
set fmri(groupmem.29) 2
# Group membership for input 30
set fmri(groupmem.30) 2
# Group membership for input 31
set fmri(groupmem.31) 2
# Group membership for input 32
set fmri(groupmem.32) 2
# Group membership for input 33
set fmri(groupmem.33) 2
# Group membership for input 34
set fmri(groupmem.34) 2
# Group membership for input 35
set fmri(groupmem.35) 2
# Group membership for input 36
set fmri(groupmem.36) 2
# Group membership for input 37
set fmri(groupmem.37) 2
# Group membership for input 38
set fmri(groupmem.38) 2
# Group membership for input 39
set fmri(groupmem.39) 2
# Group membership for input 40
set fmri(groupmem.40) 2
# Group membership for input 41
set fmri(groupmem.41) 2
# Group membership for input 42
set fmri(groupmem.42) 2
# Group membership for input 43
set fmri(groupmem.43) 2
# Group membership for input 44
set fmri(groupmem.44) 2
# 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) "K-M"
# 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) -1
# F-test 1 element 1
set fmri(ftest_real1.1) 1
# Display images for contrast_real 2
set fmri(conpic_real.2) 1
# Title for contrast_real 2
set fmri(conname_real.2) "K"
# 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) 1
# F-test 1 element 2
set fmri(ftest_real1.2) 1
# Display images for contrast_real 3
set fmri(conpic_real.3) 1
# Title for contrast_real 3
set fmri(conname_real.3) "M"
# Real contrast_real vector 3 element 1
set fmri(con_real3.1) 1
# Real contrast_real vector 3 element 2
set fmri(con_real3.2) 0
# F-test 1 element 3
set fmri(ftest_real1.3) 1
# 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
|
