Hi - you have sent a setup file for a second-level analysis containing
only two sessions - presumably from just one of your subjects. You would
not generally expect to see activations from just two sessions using the
mixed-effects model, but third-level results should still be ok (though
note that the examples on the FEAT manual web page suggest doing the
second-level differently).

Regards, Steve.


On Wed, 11 Aug 2004, Alexandra Fort wrote:

> Dear all,
>
> I have run a problem using feat...
> My study involves 10 subjects and 2 sessions for each subject with an
> event-related design.
>
> When I run a first level analyis (creating feats for each session,
> registering to the standard template), all seems ok.
>
> In a second level analysis, I try to combine session 1 and 2 of each subject
> (input are lower level-feat directories) but here, I don't have any
> activation whatever the subject or the contrast...
>
> This lack of activation is very surprising since when I run the anaysis
> before (my computer crashed and I loosed the data...) I get something at the
> 2nd and third level, so I guess I'm doing something wrong but what ...?
>
> Any suggestions would be greatly appreciated...
>
> Thank
>
> Alexandra
>
> ------------------------------------------------
>
> Here are the design for the 2nd level analysis tested for one subject:
>
> # 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/magnum/af/data/mri/MRdata/sub02-AB"
>
> # TR(s)
> set fmri(tr) 3
>
> # Total volumes
> set fmri(npts) 2
>
> # Delete volumes
> set fmri(ndelete) 0
>
> # Number of first-level analyses
> set fmri(multiple) 2
>
> # 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) 2
>
> # 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) 0.05
>
> # Z threshold
> set fmri(z_thresh) 1.8
>
> # 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/rh-7.1/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) 4
>
> # 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
>
> # 4D AVW data or FEAT directory (1)
> set feat_files(1) "/home/magnum/af/data/mri/MRdata/sub02-run1.feat"
>
> # 4D AVW data or FEAT directory (2)
> set feat_files(2) "/home/magnum/af/data/mri/MRdata/sub02-run2.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
>
> # 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
>
> # 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) "sub02"
>
> # 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
>

 Stephen M. Smith  DPhil
 Associate Director, FMRIB and Analysis Research Coordinator

 Oxford University Centre for Functional MRI of the Brain
 John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
 +44 (0) 1865 222726  (fax 222717)

 [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve