Hi - just a couple of thoughts to add to Joe's anwer:
Your [1 -1] contrast is expected to give less activation that the data all
combined, as this is a subtraction of two presumably fairly similar
groups. The [1 0] and [0 1] contrasts should give only a little less
"activation" than with all the data combined - but the reduced N may be
just taking it below threshold.
You should almost certainly be using FLAME rather than OLS - it is a lot
more accurate, particularly at lower N.
Cheers, Steve.
On Wed, 3 Mar 2004, Michal Kuniecki wrote:
> 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
>
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
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