Dear FSL experts,
I am doing an ROI analysis in FSL and am getting parameter estimates of 0 (that I don't think should be 0) that seem to be related to autocorrelation estimation.
Background: I am using FSL to check the results of a model I fit in MATLAB. I am using ROI data so I am populating a single subject's nii image by assigning each voxel within an ROI the ROI time series. The data is already preprocessed so I am only running the FEAT 'Statstics' module. I am not prewhitening, nor doing any filtering, nor any voxel thresholding; at this point I'm only interested in parameter estimates.
After I fit the FSL GLM, I'm comparing the parameter estimates to my own GLM that I have fit in MATLAB using the same data and design. From FSL I'm taking the unique parameter estimate from each ROI. The results match almost perfectly for about half of the ROIs I am looking at. For the other half, the estimates from FSL are all zeros. These zeros correspond to entries of threshac1.nii.gz. The estimates that are zeros have a value of 0 in the threshac1.nii.gz image. The estimates that match my results all have values of 1. I've checked that the time series data is uncorrupted. I've also double checked that I'm not prewhitening so I'm not sure why the autocorrelation estimate is affecting the parameter estimates. Any idea what could be going on?
Let me know if there is any information that you need.
Thank you!
-Garren
P.S. I'm running FSL 5.0.10/FEAT 6.0.0 on a MAC. Here's my log and design.fsf file if that helps troubleshoot:
Log:
/bin/cp /tmp/feat_WdXyGB.fsf design.fsf
/usr/local/fsl/bin/feat_model design
mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;cp -r /usr/local/fsl/doc/images .files/images
/usr/local/fsl/bin/fsl_sub -T 10 -l logs -N feat0_init /usr/local/fsl/bin/feat /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat/design.fsf -D /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat -I 1 -init
34235
/usr/local/fsl/bin/fsl_sub -T 0 -l logs -N feat2_pre -j 34235 /usr/local/fsl/bin/feat /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat/design.fsf -D /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat -I 1 -prestats
34310
/usr/local/fsl/bin/fsl_sub -T 2 -l logs -N feat3_film -j 34310 /usr/local/fsl/bin/feat /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat/design.fsf -D /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat -I 1 -stats
34380
/usr/local/fsl/bin/fsl_sub -T 119 -l logs -N feat4_post -j 34380 /usr/local/fsl/bin/feat /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat/design.fsf -D /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat -poststats 0
34602
/usr/local/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j 34310,34380,34602 /usr/local/fsl/bin/feat /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat/design.fsf -D /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput.feat -stop
Initialisation
/usr/local/fsl/bin/fslmaths /Users/Garren/Dropbox/FMRI/restingstatedata/WM_edge_removed_177 prefiltered_func_data -odt float
Total original volumes = 177
/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 88 1
Preprocessing:Stage 1
Preprocessing:Stage 2
/usr/local/fsl/bin/fslmaths prefiltered_func_data filtered_func_data
/usr/local/fsl/bin/fslmaths filtered_func_data -Tmin -bin mask -odt char
/usr/local/fsl/bin/fslstats filtered_func_data -k mask -R | awk '{ print }' -
ERROR:: Empty mask image
[ This repeats ~700 times]
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
ERROR:: Empty mask image
0.000000
/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func
/bin/rm -rf prefiltered_func_data*
Stats
mkdir -p custom_timing_files ; /usr/local/fsl/bin/fslFixText /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSL/EVs/Underlined.txt custom_timing_files/ev1.txt
mkdir -p custom_timing_files ; /usr/local/fsl/bin/fslFixText /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSL/EVs/2-back.txt custom_timing_files/ev2.txt
mkdir -p custom_timing_files ; /usr/local/fsl/bin/fslFixText /Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSL/EVs/Instruction.txt custom_timing_files/ev3.txt
/usr/local/fsl/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=0.000000 --noest --con=design.con
Log directory is: stats
paradigm.getDesignMatrix().Nrows()=177
paradigm.getDesignMatrix().Ncols()=3
sizeTS=177
numTS=16054
Completed
Prewhitening and Computing PEs...
Percentage done:
1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
Saving results...
Completed
/usr/local/fsl/bin/smoothest -d 174 -m mask -r stats/res4d > stats/smoothness
WARNING: Extreme smoothness detected in X - possibly biased global estimate.
WARNING: Extreme smoothness detected in Y - possibly biased global estimate.
WARNING: Extreme smoothness detected in Z - possibly biased global estimate.
Post-stats
design.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-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) "/Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSLOutput"
# TR(s)
set fmri(tr) 2.000000
# Total volumes
set fmri(npts) 177
# 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) 2
# 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) 0
# Spin-history (currently obsolete)
set fmri(sh_yn) 0
# B0 fieldmap unwarping?
set fmri(regunwarp_yn) 0
# GDC Test
set fmri(gdc) ""
# 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) 0
# Spatial smoothing FWHM (mm)
set fmri(smooth) 0.0
# Intensity normalization
set fmri(norm_yn) 0
# Perfusion subtraction
set fmri(perfsub_yn) 0
# Highpass temporal filtering
set fmri(temphp_yn) 0
# 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) 0
# 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
# Higher-level permutations
set fmri(randomisePermutations) 5000
# Number of EVs
set fmri(evs_orig) 3
set fmri(evs_real) 3
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) 0
# P threshold
set fmri(prob_thresh) 0.05
# Z threshold
set fmri(z_thresh) 3.1
# 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) 0
# 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) 400
# Total voxels
set fmri(totalVoxels) 48079041
# 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/Garren/Dropbox/FMRI/restingstatedata/WM_edge_removed_177"
# Add confound EVs text file
set fmri(confoundevs) 0
# EV 1 title
set fmri(evtitle1) "Und"
# 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) "/Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSL/EVs/Underlined.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
# Orthogonalise EV 1 wrt EV 3
set fmri(ortho1.3) 0
# EV 2 title
set fmri(evtitle2) "2-back"
# 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) 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) "/Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSL/EVs/2-back.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
# Orthogonalise EV 2 wrt EV 3
set fmri(ortho2.3) 0
# EV 3 title
set fmri(evtitle3) "Instruction "
# 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) 2
# 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) 0
# Convolve phase (EV 3)
set fmri(convolve_phase3) 0
# Apply temporal filtering (EV 3)
set fmri(tempfilt_yn3) 0
# Add temporal derivative (EV 3)
set fmri(deriv_yn3) 0
# Custom EV file (EV 3)
set fmri(custom3) "/Users/Garren/Dropbox/FMRI/Code/varianceGLM/FSL/EVs/Instruction.txt"
# 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
# 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) "2bck_minus_Und"
# 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
# Real contrast_real vector 1 element 3
set fmri(con_real1.3) 0
# Display images for contrast_orig 1
set fmri(conpic_orig.1) 1
# Title for contrast_orig 1
set fmri(conname_orig.1) "2bck_minus_Und"
# 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
# Real contrast_orig vector 1 element 3
set fmri(con_orig1.3) 0
# 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) 0
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