Dear FSL experts:
I'm trying to run tensorial ICA on a subset of my data (2 groups, 5 subjects each).
I specified the images, put in all the settings, and specified time series and session/subject .mat and .con files. However, when reading the output, there is an overall F test and model fit graph for the sessions/subject design, but there is no GLM test on the time series designs and there is no full model fit in the temporal mode graph.
I can't figure out what I've done wrong, but I'm guessing my GLM design files are wrong. Any help would be greatly appreciated. I've copied the design.fsf and time series .fsf below
Many thanks,
Kris
MELODIC design file
# FEAT version number
set fmri(version) 3.14
# Are we in MELODIC?
set fmri(inmelodic) 1
# 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) "/home/msgroup/Desktop/TICA_10ss_mar20"
# TR(s)
set fmri(tr) 2.000000
# Total volumes
set fmri(npts) 289
# Delete volumes
set fmri(ndelete) 4
# Perfusion tag/control order
set fmri(tagfirst) 1
# Number of first-level analyses
set fmri(multiple) 10
# 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) 2
# 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) 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) 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/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) 30777344
# 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) "/home/msgroup/Desktop/39_MS_patients/104_SDMT"
# 4D AVW data or FEAT directory (2)
set feat_files(2) "/home/msgroup/Desktop/39_MS_patients/105_SDMT"
# 4D AVW data or FEAT directory (3)
set feat_files(3) "/home/msgroup/Desktop/39_MS_patients/106_SDMT"
# 4D AVW data or FEAT directory (4)
set feat_files(4) "/home/msgroup/Desktop/39_MS_patients/109_SDMT"
# 4D AVW data or FEAT directory (5)
set feat_files(5) "/home/msgroup/Desktop/39_MS_patients/116_SDMT"
# 4D AVW data or FEAT directory (6)
set feat_files(6) "/home/msgroup/Desktop/39_MS_patients/110_SDMT"
# 4D AVW data or FEAT directory (7)
set feat_files(7) "/home/msgroup/Desktop/39_MS_patients/112_SDMT"
# 4D AVW data or FEAT directory (8)
set feat_files(8) "/home/msgroup/Desktop/39_MS_patients/113_SDMT"
# 4D AVW data or FEAT directory (9)
set feat_files(9) "/home/msgroup/Desktop/39_MS_patients/114_SDMT"
# 4D AVW data or FEAT directory (10)
set feat_files(10) "/home/msgroup/Desktop/39_MS_patients/117_SDMT"
# Add confound EVs text file
set fmri(confoundevs) 0
# Resampling resolution
set fmri(regstandard_res) 4
# Variance-normalise timecourses
set fmri(varnorm) 1
# Automatic dimensionality estimation
set fmri(dim_yn) 1
# Output components
set fmri(dim) 1
# 1 : Single-session ICA
# 2 : Multi-session temporal concatenation
# 3 : Multi-session tensor TICA
set fmri(icaopt) 3
# Threshold IC maps
set fmri(thresh_yn) 1
# Mixture model threshold
set fmri(mmthresh) 0.5
# Output full stats folder
set fmri(ostats) 1
# Timeseries and subject models
set fmri(ts_model_mat) "/home/msgroup/Desktop/TICA_contrasts/sdmt_rest_final_timeseries.mat"
set fmri(ts_model_con) "/home/msgroup/Desktop/TICA_contrasts/sdmt_rest_final_timeseries.con"
set fmri(subject_model_mat) "/home/msgroup/Desktop/TICA_contrasts/10_1grp_con.mat"
set fmri(subject_model_con) "/home/msgroup/Desktop/TICA_contrasts/10_1grp_con.con"
Time series .fsf
# 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) 2
# 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) ""
# TR(s)
set fmri(tr) 2.0
# Total volumes
set fmri(npts) 289
# 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) 2
set fmri(evs_real) 2
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) 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) 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) 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) 60
# Number of lower-level copes feeding into higher-level analysis
set fmri(ncopeinputs) 0
# EV 1 title
set fmri(evtitle1) "sdmt"
# 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) 0
# 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) 0
# Skip (EV 1)
set fmri(skip1) 2
# Off (EV 1)
set fmri(off1) 26.0
# On (EV 1)
set fmri(on1) 27.0
# Phase (EV 1)
set fmri(phase1) 26
# Stop (EV 1)
set fmri(stop1) 583
# 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
# EV 2 title
set fmri(evtitle2) "rest"
# 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) 0
# 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) 0
# Skip (EV 2)
set fmri(skip2) 2
# Off (EV 2)
set fmri(off2) 27.0
# On (EV 2)
set fmri(on2) 26.0
# Phase (EV 2)
set fmri(phase2) 0
# Stop (EV 2)
set fmri(stop2) 583
# 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
# 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) "sdmt>rest"
# 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) -1.0
# Display images for contrast_real 2
set fmri(conpic_real.2) 1
# Title for contrast_real 2
set fmri(conname_real.2) "rest>sdmt"
# Real contrast_real vector 2 element 1
set fmri(con_real2.1) -1.0
# Real contrast_real vector 2 element 2
set fmri(con_real2.2) 1.0
# Display images for contrast_real 3
set fmri(conpic_real.3) 1
# Title for contrast_real 3
set fmri(conname_real.3) "sdmt"
# 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
# Display images for contrast_real 4
set fmri(conpic_real.4) 1
# Title for contrast_real 4
set fmri(conname_real.4) "rest"
# 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) 1.0
# Display images for contrast_orig 1
set fmri(conpic_orig.1) 1
# Title for contrast_orig 1
set fmri(conname_orig.1) "sdmt>rest"
# 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) -1.0
# Display images for contrast_orig 2
set fmri(conpic_orig.2) 1
# Title for contrast_orig 2
set fmri(conname_orig.2) "rest>sdmt"
# Real contrast_orig vector 2 element 1
set fmri(con_orig2.1) -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) "sdmt"
# 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) 0
# Display images for contrast_orig 4
set fmri(conpic_orig.4) 1
# Title for contrast_orig 4
set fmri(conname_orig.4) "rest"
# 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) 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
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