Hello everyone,
I tried to run a 1st level analysis with the FEAT fsl gui. It seems that there were no errors, and I got the cope files and other necessary outputs. However, nothing happened in the post-stats tab, and it seems like no contrast maps have been generated in the html output.
Any idea what could be the reason for that? I attach the design template fsf file as saved from the gui.
Thank you very much
Design template
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) 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/liorabramson/Documents/fsl_analyses”
TR(s)
set fmri(tr) 2.000000
Total volumes
set fmri(npts) 126
Delete volumes
set fmri(ndelete) 4
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) 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
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) 0.0
EPI TE (ms)
set fmri(te) 0.0
% 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) 6.0
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
Higher-level permutations
set fmri(randomisePermutations) 5000
Number of EVs
set fmri(evs_orig) 3
set fmri(evs_real) 6
set fmri(evs_vox) 0
Number of contrasts
set fmri(ncon_orig) 3
set fmri(ncon_real) 3
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) 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) 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/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) 6
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) 136336410
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/liorabramson/Documents/fsl_analyses/input/sub-002_task-cond1_run-1_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold”
Add confound EVs text file
set fmri(confoundevs) 1
Confound EVs text file for analysis 1
set confoundev_files(1) “/Users/liorabramson/Documents/fsl_analyses/input/confound_lowdof_task-cond1_dropfirst4TRs.txt”
EV 1 title
set fmri(evtitle1) “plus”
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
8 : Alternate Double-Gamma
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/liorabramson/Documents/fsl_analyses/input/s2_alone_plus.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) “noise”
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
8 : Alternate Double-Gamma
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/liorabramson/Documents/fsl_analyses/input/s2_alone_noise.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) “minus”
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) 3
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
8 : Alternate Double-Gamma
set fmri(convolve3) 2
Convolve phase (EV 3)
set fmri(convolve_phase3) 0
Apply temporal filtering (EV 3)
set fmri(tempfilt_yn3) 1
Add temporal derivative (EV 3)
set fmri(deriv_yn3) 1
Custom EV file (EV 3)
set fmri(custom3) “/Users/liorabramson/Documents/fsl_analyses/input/s2_alone_minus.txt”
Gamma sigma (EV 3)
set fmri(gammasigma3) 3
Gamma delay (EV 3)
set fmri(gammadelay3) 6
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) “”
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
Real contrast_real vector 1 element 5
set fmri(con_real1.5) 0
Real contrast_real vector 1 element 6
set fmri(con_real1.6) 0
Display images for contrast_real 2
set fmri(conpic_real.2) 1
Title for contrast_real 2
set fmri(conname_real.2) “”
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
Real contrast_real vector 2 element 4
set fmri(con_real2.4) 0
Real contrast_real vector 2 element 5
set fmri(con_real2.5) 0
Real contrast_real vector 2 element 6
set fmri(con_real2.6) 0
Display images for contrast_real 3
set fmri(conpic_real.3) 1
Title for contrast_real 3
set fmri(conname_real.3) “”
Real contrast_real vector 3 element 1
set fmri(con_real3.1) 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) 0
Real contrast_real vector 3 element 4
set fmri(con_real3.4) 0
Real contrast_real vector 3 element 5
set fmri(con_real3.5) 1
Real contrast_real vector 3 element 6
set fmri(con_real3.6) 0
Display images for contrast_orig 1
set fmri(conpic_orig.1) 1
Title for contrast_orig 1
set fmri(conname_orig.1) “”
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
Real contrast_orig vector 1 element 3
set fmri(con_orig1.3) 0
Display images for contrast_orig 2
set fmri(conpic_orig.2) 1
Title for contrast_orig 2
set fmri(conname_orig.2) “”
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
Real contrast_orig vector 2 element 3
set fmri(con_orig2.3) 0
Display images for contrast_orig 3
set fmri(conpic_orig.3) 1
Title for contrast_orig 3
set fmri(conname_orig.3) “”
Real contrast_orig vector 3 element 1
set fmri(con_orig3.1) 0
Real contrast_orig vector 3 element 2
set fmri(con_orig3.2) 0
Real contrast_orig vector 3 element 3
set fmri(con_orig3.3) 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 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 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
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