Hi again Vina,
I have had a look at your data, and I am afraid that the problem is in
FNIRT not being able to quite handle your particular data.
The problem is the presence of a quite high signal in non-brain tissue
(I am never quite sure what that stuff is. I tend to call it gunk, but
I suspect meninges might be a better term) very close to the brain in
the parieto-occipital areas. This is something you often see in
structural scans, but the intensity in those non-brain bits are
typically lower than in brain-tissue proper. If you look at e.g. the
1mm MNI152 non-linear template you will see that this signal is
present there as well, but with an intensity that is ~half of that in
brain tissue. In your data (in the parieto-occipital areas) it has
instead an intensity ~twice that of brain tissue, and that is why an
intensity base method (such as fnirt) struggles to register it to the
template.
I have seen data like this before, and I don't really know why it
looks that way. In your data one component is clearly a quite large
intensity inhomogeneity (intensities in the frontal cortex is ~half of
that in occipital cortex), but fnirt has a model for that and ought to
be able to handle it if that was the only cause. I can only guess that
there may be differences between your sequence and that used to
collect the data for the MNI152 template that means that the signal in
whatever tissue that is has a much higher relative intensity. If any
"physicsy" person reads this he/she might give you a better explanation.
So, long term I think that it would be useful for you to have a chat
with your physicists and see if you can think of a sequence that
doesn't have this problem. Short term I think you are better off using
flirt (affine transform) for the data you have already collected.
Good luck Jesper
On 6 Jan 2009, at 02:34, Vina Goghari wrote:
> Hello,
> I am using non-linear registration and I am not getting a good
> registration compared to the linear registration using FEAT for a
> single subject, single run. I am attaching my .fsf for the non-
> linear registration. Am I specifying something incorrect?
>
> Thanks,
> Vina
> # FEAT version number
> set fmri(version) 5.98
>
> # 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) 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
>
> # TR(s)
> set fmri(tr) 2.0
> set fmri(outputdir) "/pkg/bliss_all_labs/tricam/MERIT/MERIT_001/feat/
> delay/MERIT_001_SRRTA"
> set fmri(npts) 232
>
> # 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) 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) 5
>
> # Slice timings file
> set fmri(st_file) ""
>
> # BET brain extraction
> set fmri(bet_yn) 1
>
> # Spatial smoothing FWHM (mm)
> set fmri(smooth) 7.0
>
> # 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) 1
>
> # 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
>
> # 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) 6
> set fmri(evs_real) 12
> set fmri(evs_vox) 0
>
> # Number of contrasts
> set fmri(ncon_orig) 12
> set fmri(ncon_real) 12
>
> # 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) 1
>
> # 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) 1
>
> # Search space for registration to main structural
> # 0 : No search
> # 90 : Normal search
> # 180 : Full search
> set fmri(reghighres_search) 180
>
> # Degrees of Freedom for registration to main structural
> set fmri(reghighres_dof) 7
>
> # Registration to standard image?
> set fmri(regstandard_yn) 1
>
> # Standard image
> set fmri(regstandard) "/opt/bliss/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) 180
>
> # 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) 1
>
> # Control nonlinear warp field resolution
> set fmri(regstandard_nonlinear_warpres) 10
>
>
> # 4D AVW data or FEAT directory (1)
> set feat_files(1) /labs/tricam/MERIT/MERIT_001/func/
> MERIT_001_SRRTA.nii*
>
> # High resolution image for subject
> set highres_files(1) /labs/tricam/MERIT/MERIT_001/struct/
> MERIT_001_Struct_brain.nii
>
> set fmri(custom1) /labs/tricam/MERIT/MERIT_001/evs/
> MERIT_001_SRRTA_GC.txt
>
> set fmri(custom2) /labs/tricam/MERIT/MERIT_001/evs/
> MERIT_001_SRRTA_RC.txt
>
> set fmri(custom3) /labs/tricam/MERIT/MERIT_001/evs/
> MERIT_001_SRRTA_GD.txt
>
> set fmri(custom4) /labs/tricam/MERIT/MERIT_001/evs/
> MERIT_001_SRRTA_RD.txt
>
> set fmri(custom5) /labs/tricam/MERIT/MERIT_001/evs/
> MERIT_001_SRRTA_GP.txt
>
> set fmri(custom6) /labs/tricam/MERIT/MERIT_001/evs/
> MERIT_001_SRRTA_RP.txt
>
> # High pass filter cutoff
> set fmri(paradigm_hp) 50
>
> # Number of lower-level copes feeding into higher-level analysis
> set fmri(ncopeinputs) 0
>
> # Add confound EVs text file
> set fmri(confoundevs) 0
>
> # EV 1 title
> set fmri(evtitle1) "GC"
>
> # 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
> 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
>
> # 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
>
> # Orthogonalise EV 1 wrt EV 4
> set fmri(ortho1.4) 0
>
> # Orthogonalise EV 1 wrt EV 5
> set fmri(ortho1.5) 0
>
> # Orthogonalise EV 1 wrt EV 6
> set fmri(ortho1.6) 0
>
> # EV 2 title
> set fmri(evtitle2) "RC"
>
> # 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
> 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
>
> # 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
>
> # Orthogonalise EV 2 wrt EV 4
> set fmri(ortho2.4) 0
>
> # Orthogonalise EV 2 wrt EV 5
> set fmri(ortho2.5) 0
>
> # Orthogonalise EV 2 wrt EV 6
> set fmri(ortho2.6) 0
>
> # EV 3 title
> set fmri(evtitle3) "GD"
>
> # 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
> set fmri(convolve3) 3
>
> # 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
>
> # 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
>
> # Orthogonalise EV 3 wrt EV 4
> set fmri(ortho3.4) 0
>
> # Orthogonalise EV 3 wrt EV 5
> set fmri(ortho3.5) 0
>
> # Orthogonalise EV 3 wrt EV 6
> set fmri(ortho3.6) 0
>
> # EV 4 title
> set fmri(evtitle4) "RD"
>
> # Basic waveform shape (EV 4)
> # 0 : Square
> # 1 : Sinusoid
> # 2 : Custom (1 entry per volume)
> # 3 : Custom (3 column format)
> # 4 : Interaction
> # 10 : Empty (all zeros)
> set fmri(shape4) 3
>
> # Convolution (EV 4)
> # 0 : None
> # 1 : Gaussian
> # 2 : Gamma
> # 3 : Double-Gamma HRF
> # 4 : Gamma basis functions
> # 5 : Sine basis functions
> # 6 : FIR basis functions
> set fmri(convolve4) 3
>
> # Convolve phase (EV 4)
> set fmri(convolve_phase4) 0
>
> # Apply temporal filtering (EV 4)
> set fmri(tempfilt_yn4) 1
>
> # Add temporal derivative (EV 4)
> set fmri(deriv_yn4) 1
>
> # Orthogonalise EV 4 wrt EV 0
> set fmri(ortho4.0) 0
>
> # Orthogonalise EV 4 wrt EV 1
> set fmri(ortho4.1) 0
>
> # Orthogonalise EV 4 wrt EV 2
> set fmri(ortho4.2) 0
>
> # Orthogonalise EV 4 wrt EV 3
> set fmri(ortho4.3) 0
>
> # Orthogonalise EV 4 wrt EV 4
> set fmri(ortho4.4) 0
>
> # Orthogonalise EV 4 wrt EV 5
> set fmri(ortho4.5) 0
>
> # Orthogonalise EV 4 wrt EV 6
> set fmri(ortho4.6) 0
>
> # EV 5 title
> set fmri(evtitle5) "GP"
>
> # Basic waveform shape (EV 5)
> # 0 : Square
> # 1 : Sinusoid
> # 2 : Custom (1 entry per volume)
> # 3 : Custom (3 column format)
> # 4 : Interaction
> # 10 : Empty (all zeros)
> set fmri(shape5) 3
>
> # Convolution (EV 5)
> # 0 : None
> # 1 : Gaussian
> # 2 : Gamma
> # 3 : Double-Gamma HRF
> # 4 : Gamma basis functions
> # 5 : Sine basis functions
> # 6 : FIR basis functions
> set fmri(convolve5) 3
>
> # Convolve phase (EV 5)
> set fmri(convolve_phase5) 0
>
> # Apply temporal filtering (EV 5)
> set fmri(tempfilt_yn5) 1
>
> # Add temporal derivative (EV 5)
> set fmri(deriv_yn5) 1
>
> # Orthogonalise EV 5 wrt EV 0
> set fmri(ortho5.0) 0
>
> # Orthogonalise EV 5 wrt EV 1
> set fmri(ortho5.1) 0
>
> # Orthogonalise EV 5 wrt EV 2
> set fmri(ortho5.2) 0
>
> # Orthogonalise EV 5 wrt EV 3
> set fmri(ortho5.3) 0
>
> # Orthogonalise EV 5 wrt EV 4
> set fmri(ortho5.4) 0
>
> # Orthogonalise EV 5 wrt EV 5
> set fmri(ortho5.5) 0
>
> # Orthogonalise EV 5 wrt EV 6
> set fmri(ortho5.6) 0
>
> # EV 6 title
> set fmri(evtitle6) "RP"
>
> # Basic waveform shape (EV 6)
> # 0 : Square
> # 1 : Sinusoid
> # 2 : Custom (1 entry per volume)
> # 3 : Custom (3 column format)
> # 4 : Interaction
> # 10 : Empty (all zeros)
> set fmri(shape6) 3
>
> # Convolution (EV 6)
> # 0 : None
> # 1 : Gaussian
> # 2 : Gamma
> # 3 : Double-Gamma HRF
> # 4 : Gamma basis functions
> # 5 : Sine basis functions
> # 6 : FIR basis functions
> set fmri(convolve6) 3
>
> # Convolve phase (EV 6)
> set fmri(convolve_phase6) 0
>
> # Apply temporal filtering (EV 6)
> set fmri(tempfilt_yn6) 1
>
> # Add temporal derivative (EV 6)
> set fmri(deriv_yn6) 1
>
> # Orthogonalise EV 6 wrt EV 0
> set fmri(ortho6.0) 0
>
> # Orthogonalise EV 6 wrt EV 1
> set fmri(ortho6.1) 0
>
> # Orthogonalise EV 6 wrt EV 2
> set fmri(ortho6.2) 0
>
> # Orthogonalise EV 6 wrt EV 3
> set fmri(ortho6.3) 0
>
> # Orthogonalise EV 6 wrt EV 4
> set fmri(ortho6.4) 0
>
> # Orthogonalise EV 6 wrt EV 5
> set fmri(ortho6.5) 0
>
> # Orthogonalise EV 6 wrt EV 6
> set fmri(ortho6.6) 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) "GC"
>
> # 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
>
> # Real contrast_real vector 1 element 7
> set fmri(con_real1.7) 0
>
> # Real contrast_real vector 1 element 8
> set fmri(con_real1.8) 0
>
> # Real contrast_real vector 1 element 9
> set fmri(con_real1.9) 0
>
> # Real contrast_real vector 1 element 10
> set fmri(con_real1.10) 0
>
> # Real contrast_real vector 1 element 11
> set fmri(con_real1.11) 0
>
> # Real contrast_real vector 1 element 12
> set fmri(con_real1.12) 0
>
> # Display images for contrast_real 2
> set fmri(conpic_real.2) 1
>
> # Title for contrast_real 2
> set fmri(conname_real.2) "RC"
>
> # 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) 1.0
>
> # 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
>
> # Real contrast_real vector 2 element 7
> set fmri(con_real2.7) 0
>
> # Real contrast_real vector 2 element 8
> set fmri(con_real2.8) 0
>
> # Real contrast_real vector 2 element 9
> set fmri(con_real2.9) 0
>
> # Real contrast_real vector 2 element 10
> set fmri(con_real2.10) 0
>
> # Real contrast_real vector 2 element 11
> set fmri(con_real2.11) 0
>
> # Real contrast_real vector 2 element 12
> set fmri(con_real2.12) 0
>
> # Display images for contrast_real 3
> set fmri(conpic_real.3) 1
>
> # Title for contrast_real 3
> set fmri(conname_real.3) "C"
>
> # 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
>
> # Real contrast_real vector 3 element 3
> set fmri(con_real3.3) 1.0
>
> # 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) 0
>
> # Real contrast_real vector 3 element 6
> set fmri(con_real3.6) 0
>
> # Real contrast_real vector 3 element 7
> set fmri(con_real3.7) 0
>
> # Real contrast_real vector 3 element 8
> set fmri(con_real3.8) 0
>
> # Real contrast_real vector 3 element 9
> set fmri(con_real3.9) 0
>
> # Real contrast_real vector 3 element 10
> set fmri(con_real3.10) 0
>
> # Real contrast_real vector 3 element 11
> set fmri(con_real3.11) 0
>
> # Real contrast_real vector 3 element 12
> set fmri(con_real3.12) 0
>
> # Display images for contrast_real 4
> set fmri(conpic_real.4) 1
>
> # Title for contrast_real 4
> set fmri(conname_real.4) "GD"
>
> # 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) 0
>
> # Real contrast_real vector 4 element 3
> set fmri(con_real4.3) 0
>
> # Real contrast_real vector 4 element 4
> set fmri(con_real4.4) 0
>
> # Real contrast_real vector 4 element 5
> set fmri(con_real4.5) 1.0
>
> # Real contrast_real vector 4 element 6
> set fmri(con_real4.6) 0
>
> # Real contrast_real vector 4 element 7
> set fmri(con_real4.7) 0
>
> # Real contrast_real vector 4 element 8
> set fmri(con_real4.8) 0
>
> # Real contrast_real vector 4 element 9
> set fmri(con_real4.9) 0
>
> # Real contrast_real vector 4 element 10
> set fmri(con_real4.10) 0
>
> # Real contrast_real vector 4 element 11
> set fmri(con_real4.11) 0
>
> # Real contrast_real vector 4 element 12
> set fmri(con_real4.12) 0
>
> # Display images for contrast_real 5
> set fmri(conpic_real.5) 1
>
> # Title for contrast_real 5
> set fmri(conname_real.5) "RD"
>
> # Real contrast_real vector 5 element 1
> set fmri(con_real5.1) 0
>
> # Real contrast_real vector 5 element 2
> set fmri(con_real5.2) 0
>
> # Real contrast_real vector 5 element 3
> set fmri(con_real5.3) 0
>
> # Real contrast_real vector 5 element 4
> set fmri(con_real5.4) 0
>
> # Real contrast_real vector 5 element 5
> set fmri(con_real5.5) 0
>
> # Real contrast_real vector 5 element 6
> set fmri(con_real5.6) 0
>
> # Real contrast_real vector 5 element 7
> set fmri(con_real5.7) 1.0
>
> # Real contrast_real vector 5 element 8
> set fmri(con_real5.8) 0
>
> # Real contrast_real vector 5 element 9
> set fmri(con_real5.9) 0
>
> # Real contrast_real vector 5 element 10
> set fmri(con_real5.10) 0
>
> # Real contrast_real vector 5 element 11
> set fmri(con_real5.11) 0
>
> # Real contrast_real vector 5 element 12
> set fmri(con_real5.12) 0
>
> # Display images for contrast_real 6
> set fmri(conpic_real.6) 1
>
> # Title for contrast_real 6
> set fmri(conname_real.6) "D"
>
> # Real contrast_real vector 6 element 1
> set fmri(con_real6.1) 0
>
> # Real contrast_real vector 6 element 2
> set fmri(con_real6.2) 0
>
> # Real contrast_real vector 6 element 3
> set fmri(con_real6.3) 0
>
> # Real contrast_real vector 6 element 4
> set fmri(con_real6.4) 0
>
> # Real contrast_real vector 6 element 5
> set fmri(con_real6.5) 1.0
>
> # Real contrast_real vector 6 element 6
> set fmri(con_real6.6) 0
>
> # Real contrast_real vector 6 element 7
> set fmri(con_real6.7) 1.0
>
> # Real contrast_real vector 6 element 8
> set fmri(con_real6.8) 0
>
> # Real contrast_real vector 6 element 9
> set fmri(con_real6.9) 0
>
> # Real contrast_real vector 6 element 10
> set fmri(con_real6.10) 0
>
> # Real contrast_real vector 6 element 11
> set fmri(con_real6.11) 0
>
> # Real contrast_real vector 6 element 12
> set fmri(con_real6.12) 0
>
> # Display images for contrast_real 7
> set fmri(conpic_real.7) 1
>
> # Title for contrast_real 7
> set fmri(conname_real.7) "GP"
>
> # Real contrast_real vector 7 element 1
> set fmri(con_real7.1) 0
>
> # Real contrast_real vector 7 element 2
> set fmri(con_real7.2) 0
>
> # Real contrast_real vector 7 element 3
> set fmri(con_real7.3) 0
>
> # Real contrast_real vector 7 element 4
> set fmri(con_real7.4) 0
>
> # Real contrast_real vector 7 element 5
> set fmri(con_real7.5) 0
>
> # Real contrast_real vector 7 element 6
> set fmri(con_real7.6) 0
>
> # Real contrast_real vector 7 element 7
> set fmri(con_real7.7) 0
>
> # Real contrast_real vector 7 element 8
> set fmri(con_real7.8) 0
>
> # Real contrast_real vector 7 element 9
> set fmri(con_real7.9) 1.0
>
> # Real contrast_real vector 7 element 10
> set fmri(con_real7.10) 0
>
> # Real contrast_real vector 7 element 11
> set fmri(con_real7.11) 0
>
> # Real contrast_real vector 7 element 12
> set fmri(con_real7.12) 0
>
> # Display images for contrast_real 8
> set fmri(conpic_real.8) 1
>
> # Title for contrast_real 8
> set fmri(conname_real.8) "RP"
>
> # Real contrast_real vector 8 element 1
> set fmri(con_real8.1) 0
>
> # Real contrast_real vector 8 element 2
> set fmri(con_real8.2) 0
>
> # Real contrast_real vector 8 element 3
> set fmri(con_real8.3) 0
>
> # Real contrast_real vector 8 element 4
> set fmri(con_real8.4) 0
>
> # Real contrast_real vector 8 element 5
> set fmri(con_real8.5) 0
>
> # Real contrast_real vector 8 element 6
> set fmri(con_real8.6) 0
>
> # Real contrast_real vector 8 element 7
> set fmri(con_real8.7) 0
>
> # Real contrast_real vector 8 element 8
> set fmri(con_real8.8) 0
>
> # Real contrast_real vector 8 element 9
> set fmri(con_real8.9) 0
>
> # Real contrast_real vector 8 element 10
> set fmri(con_real8.10) 0
>
> # Real contrast_real vector 8 element 11
> set fmri(con_real8.11) 1.0
>
> # Real contrast_real vector 8 element 12
> set fmri(con_real8.12) 0
>
> # Display images for contrast_real 9
> set fmri(conpic_real.9) 1
>
> # Title for contrast_real 9
> set fmri(conname_real.9) "P"
>
> # Real contrast_real vector 9 element 1
> set fmri(con_real9.1) 0
>
> # Real contrast_real vector 9 element 2
> set fmri(con_real9.2) 0
>
> # Real contrast_real vector 9 element 3
> set fmri(con_real9.3) 0
>
> # Real contrast_real vector 9 element 4
> set fmri(con_real9.4) 0
>
> # Real contrast_real vector 9 element 5
> set fmri(con_real9.5) 0
>
> # Real contrast_real vector 9 element 6
> set fmri(con_real9.6) 0
>
> # Real contrast_real vector 9 element 7
> set fmri(con_real9.7) 0
>
> # Real contrast_real vector 9 element 8
> set fmri(con_real9.8) 0
>
> # Real contrast_real vector 9 element 9
> set fmri(con_real9.9) 1.0
>
> # Real contrast_real vector 9 element 10
> set fmri(con_real9.10) 0
>
> # Real contrast_real vector 9 element 11
> set fmri(con_real9.11) 1.0
>
> # Real contrast_real vector 9 element 12
> set fmri(con_real9.12) 0
>
> # Display images for contrast_real 10
> set fmri(conpic_real.10) 1
>
> # Title for contrast_real 10
> set fmri(conname_real.10) "RCvsGC"
>
> # Real contrast_real vector 10 element 1
> set fmri(con_real10.1) -1.0
>
> # Real contrast_real vector 10 element 2
> set fmri(con_real10.2) 0
>
> # Real contrast_real vector 10 element 3
> set fmri(con_real10.3) 1.0
>
> # Real contrast_real vector 10 element 4
> set fmri(con_real10.4) 0
>
> # Real contrast_real vector 10 element 5
> set fmri(con_real10.5) 0
>
> # Real contrast_real vector 10 element 6
> set fmri(con_real10.6) 0
>
> # Real contrast_real vector 10 element 7
> set fmri(con_real10.7) 0
>
> # Real contrast_real vector 10 element 8
> set fmri(con_real10.8) 0
>
> # Real contrast_real vector 10 element 9
> set fmri(con_real10.9) 0
>
> # Real contrast_real vector 10 element 10
> set fmri(con_real10.10) 0
>
> # Real contrast_real vector 10 element 11
> set fmri(con_real10.11) 0
>
> # Real contrast_real vector 10 element 12
> set fmri(con_real10.12) 0
>
> # Display images for contrast_real 11
> set fmri(conpic_real.11) 1
>
> # Title for contrast_real 11
> set fmri(conname_real.11) "RDvsGD"
>
> # Real contrast_real vector 11 element 1
> set fmri(con_real11.1) 0
>
> # Real contrast_real vector 11 element 2
> set fmri(con_real11.2) 0
>
> # Real contrast_real vector 11 element 3
> set fmri(con_real11.3) 0
>
> # Real contrast_real vector 11 element 4
> set fmri(con_real11.4) 0
>
> # Real contrast_real vector 11 element 5
> set fmri(con_real11.5) -1.0
>
> # Real contrast_real vector 11 element 6
> set fmri(con_real11.6) 0
>
> # Real contrast_real vector 11 element 7
> set fmri(con_real11.7) 1.0
>
> # Real contrast_real vector 11 element 8
> set fmri(con_real11.8) 0
>
> # Real contrast_real vector 11 element 9
> set fmri(con_real11.9) 0
>
> # Real contrast_real vector 11 element 10
> set fmri(con_real11.10) 0
>
> # Real contrast_real vector 11 element 11
> set fmri(con_real11.11) 0
>
> # Real contrast_real vector 11 element 12
> set fmri(con_real11.12) 0
>
> # Display images for contrast_real 12
> set fmri(conpic_real.12) 1
>
> # Title for contrast_real 12
> set fmri(conname_real.12) "RPvsGP"
>
> # Real contrast_real vector 12 element 1
> set fmri(con_real12.1) 0
>
> # Real contrast_real vector 12 element 2
> set fmri(con_real12.2) 0
>
> # Real contrast_real vector 12 element 3
> set fmri(con_real12.3) 0
>
> # Real contrast_real vector 12 element 4
> set fmri(con_real12.4) 0
>
> # Real contrast_real vector 12 element 5
> set fmri(con_real12.5) 0
>
> # Real contrast_real vector 12 element 6
> set fmri(con_real12.6) 0
>
> # Real contrast_real vector 12 element 7
> set fmri(con_real12.7) 0
>
> # Real contrast_real vector 12 element 8
> set fmri(con_real12.8) 0
>
> # Real contrast_real vector 12 element 9
> set fmri(con_real12.9) -1.0
>
> # Real contrast_real vector 12 element 10
> set fmri(con_real12.10) 0
>
> # Real contrast_real vector 12 element 11
> set fmri(con_real12.11) 1.0
>
> # Real contrast_real vector 12 element 12
> set fmri(con_real12.12) 0
>
> # Display images for contrast_orig 1
> set fmri(conpic_orig.1) 1
>
> # Title for contrast_orig 1
> set fmri(conname_orig.1) "GC"
>
> # 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
>
> # Real contrast_orig vector 1 element 4
> set fmri(con_orig1.4) 0
>
> # Real contrast_orig vector 1 element 5
> set fmri(con_orig1.5) 0
>
> # Real contrast_orig vector 1 element 6
> set fmri(con_orig1.6) 0
>
> # Display images for contrast_orig 2
> set fmri(conpic_orig.2) 1
>
> # Title for contrast_orig 2
> set fmri(conname_orig.2) "RC"
>
> # 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) 1.0
>
> # Real contrast_orig vector 2 element 3
> set fmri(con_orig2.3) 0
>
> # Real contrast_orig vector 2 element 4
> set fmri(con_orig2.4) 0
>
> # Real contrast_orig vector 2 element 5
> set fmri(con_orig2.5) 0
>
> # Real contrast_orig vector 2 element 6
> set fmri(con_orig2.6) 0
>
> # Display images for contrast_orig 3
> set fmri(conpic_orig.3) 1
>
> # Title for contrast_orig 3
> set fmri(conname_orig.3) "C"
>
> # 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) 1.0
>
> # Real contrast_orig vector 3 element 3
> set fmri(con_orig3.3) 0
>
> # Real contrast_orig vector 3 element 4
> set fmri(con_orig3.4) 0
>
> # Real contrast_orig vector 3 element 5
> set fmri(con_orig3.5) 0
>
> # Real contrast_orig vector 3 element 6
> set fmri(con_orig3.6) 0
>
> # Display images for contrast_orig 4
> set fmri(conpic_orig.4) 1
>
> # Title for contrast_orig 4
> set fmri(conname_orig.4) "GD"
>
> # 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) 0
>
> # Real contrast_orig vector 4 element 3
> set fmri(con_orig4.3) 1.0
>
> # Real contrast_orig vector 4 element 4
> set fmri(con_orig4.4) 0
>
> # Real contrast_orig vector 4 element 5
> set fmri(con_orig4.5) 0
>
> # Real contrast_orig vector 4 element 6
> set fmri(con_orig4.6) 0
>
> # Display images for contrast_orig 5
> set fmri(conpic_orig.5) 1
>
> # Title for contrast_orig 5
> set fmri(conname_orig.5) "RD"
>
> # Real contrast_orig vector 5 element 1
> set fmri(con_orig5.1) 0
>
> # Real contrast_orig vector 5 element 2
> set fmri(con_orig5.2) 0
>
> # Real contrast_orig vector 5 element 3
> set fmri(con_orig5.3) 0
>
> # Real contrast_orig vector 5 element 4
> set fmri(con_orig5.4) 1.0
>
> # Real contrast_orig vector 5 element 5
> set fmri(con_orig5.5) 0
>
> # Real contrast_orig vector 5 element 6
> set fmri(con_orig5.6) 0
>
> # Display images for contrast_orig 6
> set fmri(conpic_orig.6) 1
>
> # Title for contrast_orig 6
> set fmri(conname_orig.6) "D"
>
> # Real contrast_orig vector 6 element 1
> set fmri(con_orig6.1) 0
>
> # Real contrast_orig vector 6 element 2
> set fmri(con_orig6.2) 0
>
> # Real contrast_orig vector 6 element 3
> set fmri(con_orig6.3) 1.0
>
> # Real contrast_orig vector 6 element 4
> set fmri(con_orig6.4) 1.0
>
> # Real contrast_orig vector 6 element 5
> set fmri(con_orig6.5) 0
>
> # Real contrast_orig vector 6 element 6
> set fmri(con_orig6.6) 0
>
> # Display images for contrast_orig 7
> set fmri(conpic_orig.7) 1
>
> # Title for contrast_orig 7
> set fmri(conname_orig.7) "GP"
>
> # Real contrast_orig vector 7 element 1
> set fmri(con_orig7.1) 0
>
> # Real contrast_orig vector 7 element 2
> set fmri(con_orig7.2) 0
>
> # Real contrast_orig vector 7 element 3
> set fmri(con_orig7.3) 0
>
> # Real contrast_orig vector 7 element 4
> set fmri(con_orig7.4) 0
>
> # Real contrast_orig vector 7 element 5
> set fmri(con_orig7.5) 1.0
>
> # Real contrast_orig vector 7 element 6
> set fmri(con_orig7.6) 0
>
> # Display images for contrast_orig 8
> set fmri(conpic_orig.8) 1
>
> # Title for contrast_orig 8
> set fmri(conname_orig.8) "RP"
>
> # Real contrast_orig vector 8 element 1
> set fmri(con_orig8.1) 0
>
> # Real contrast_orig vector 8 element 2
> set fmri(con_orig8.2) 0
>
> # Real contrast_orig vector 8 element 3
> set fmri(con_orig8.3) 0
>
> # Real contrast_orig vector 8 element 4
> set fmri(con_orig8.4) 0
>
> # Real contrast_orig vector 8 element 5
> set fmri(con_orig8.5) 0
>
> # Real contrast_orig vector 8 element 6
> set fmri(con_orig8.6) 1.0
>
> # Display images for contrast_orig 9
> set fmri(conpic_orig.9) 1
>
> # Title for contrast_orig 9
> set fmri(conname_orig.9) "P"
>
> # Real contrast_orig vector 9 element 1
> set fmri(con_orig9.1) 0
>
> # Real contrast_orig vector 9 element 2
> set fmri(con_orig9.2) 0
>
> # Real contrast_orig vector 9 element 3
> set fmri(con_orig9.3) 0
>
> # Real contrast_orig vector 9 element 4
> set fmri(con_orig9.4) 0
>
> # Real contrast_orig vector 9 element 5
> set fmri(con_orig9.5) 1.0
>
> # Real contrast_orig vector 9 element 6
> set fmri(con_orig9.6) 1.0
>
> # Display images for contrast_orig 10
> set fmri(conpic_orig.10) 1
>
> # Title for contrast_orig 10
> set fmri(conname_orig.10) "RCvsGC"
>
> # Real contrast_orig vector 10 element 1
> set fmri(con_orig10.1) -1.0
>
> # Real contrast_orig vector 10 element 2
> set fmri(con_orig10.2) 1.0
>
> # Real contrast_orig vector 10 element 3
> set fmri(con_orig10.3) 0
>
> # Real contrast_orig vector 10 element 4
> set fmri(con_orig10.4) 0
>
> # Real contrast_orig vector 10 element 5
> set fmri(con_orig10.5) 0
>
> # Real contrast_orig vector 10 element 6
> set fmri(con_orig10.6) 0
>
> # Display images for contrast_orig 11
> set fmri(conpic_orig.11) 1
>
> # Title for contrast_orig 11
> set fmri(conname_orig.11) "RDvsGD"
>
> # Real contrast_orig vector 11 element 1
> set fmri(con_orig11.1) 0
>
> # Real contrast_orig vector 11 element 2
> set fmri(con_orig11.2) 0
>
> # Real contrast_orig vector 11 element 3
> set fmri(con_orig11.3) -1.0
>
> # Real contrast_orig vector 11 element 4
> set fmri(con_orig11.4) 1.0
>
> # Real contrast_orig vector 11 element 5
> set fmri(con_orig11.5) 0
>
> # Real contrast_orig vector 11 element 6
> set fmri(con_orig11.6) 0
>
> # Display images for contrast_orig 12
> set fmri(conpic_orig.12) 1
>
> # Title for contrast_orig 12
> set fmri(conname_orig.12) "RPvsGP"
>
> # Real contrast_orig vector 12 element 1
> set fmri(con_orig12.1) 0
>
> # Real contrast_orig vector 12 element 2
> set fmri(con_orig12.2) 0
>
> # Real contrast_orig vector 12 element 3
> set fmri(con_orig12.3) 0
>
> # Real contrast_orig vector 12 element 4
> set fmri(con_orig12.4) 0
>
> # Real contrast_orig vector 12 element 5
> set fmri(con_orig12.5) -1.0
>
> # Real contrast_orig vector 12 element 6
> set fmri(con_orig12.6) 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 1 with real contrast/F-test 5?
> set fmri(conmask1_5) 0
>
> # Mask real contrast/F-test 1 with real contrast/F-test 6?
> set fmri(conmask1_6) 0
>
> # Mask real contrast/F-test 1 with real contrast/F-test 7?
> set fmri(conmask1_7) 0
>
> # Mask real contrast/F-test 1 with real contrast/F-test 8?
> set fmri(conmask1_8) 0
>
> # Mask real contrast/F-test 1 with real contrast/F-test 9?
> set fmri(conmask1_9) 0
>
> # Mask real contrast/F-test 1 with real contrast/F-test 10?
> set fmri(conmask1_10) 0
>
> # Mask real contrast/F-test 1 with real contrast/F-test 11?
> set fmri(conmask1_11) 0
>
> # Mask real contrast/F-test 1 with real contrast/F-test 12?
> set fmri(conmask1_12) 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 2 with real contrast/F-test 5?
> set fmri(conmask2_5) 0
>
> # Mask real contrast/F-test 2 with real contrast/F-test 6?
> set fmri(conmask2_6) 0
>
> # Mask real contrast/F-test 2 with real contrast/F-test 7?
> set fmri(conmask2_7) 0
>
> # Mask real contrast/F-test 2 with real contrast/F-test 8?
> set fmri(conmask2_8) 0
>
> # Mask real contrast/F-test 2 with real contrast/F-test 9?
> set fmri(conmask2_9) 0
>
> # Mask real contrast/F-test 2 with real contrast/F-test 10?
> set fmri(conmask2_10) 0
>
> # Mask real contrast/F-test 2 with real contrast/F-test 11?
> set fmri(conmask2_11) 0
>
> # Mask real contrast/F-test 2 with real contrast/F-test 12?
> set fmri(conmask2_12) 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 3 with real contrast/F-test 5?
> set fmri(conmask3_5) 0
>
> # Mask real contrast/F-test 3 with real contrast/F-test 6?
> set fmri(conmask3_6) 0
>
> # Mask real contrast/F-test 3 with real contrast/F-test 7?
> set fmri(conmask3_7) 0
>
> # Mask real contrast/F-test 3 with real contrast/F-test 8?
> set fmri(conmask3_8) 0
>
> # Mask real contrast/F-test 3 with real contrast/F-test 9?
> set fmri(conmask3_9) 0
>
> # Mask real contrast/F-test 3 with real contrast/F-test 10?
> set fmri(conmask3_10) 0
>
> # Mask real contrast/F-test 3 with real contrast/F-test 11?
> set fmri(conmask3_11) 0
>
> # Mask real contrast/F-test 3 with real contrast/F-test 12?
> set fmri(conmask3_12) 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
>
> # Mask real contrast/F-test 4 with real contrast/F-test 5?
> set fmri(conmask4_5) 0
>
> # Mask real contrast/F-test 4 with real contrast/F-test 6?
> set fmri(conmask4_6) 0
>
> # Mask real contrast/F-test 4 with real contrast/F-test 7?
> set fmri(conmask4_7) 0
>
> # Mask real contrast/F-test 4 with real contrast/F-test 8?
> set fmri(conmask4_8) 0
>
> # Mask real contrast/F-test 4 with real contrast/F-test 9?
> set fmri(conmask4_9) 0
>
> # Mask real contrast/F-test 4 with real contrast/F-test 10?
> set fmri(conmask4_10) 0
>
> # Mask real contrast/F-test 4 with real contrast/F-test 11?
> set fmri(conmask4_11) 0
>
> # Mask real contrast/F-test 4 with real contrast/F-test 12?
> set fmri(conmask4_12) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 1?
> set fmri(conmask5_1) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 2?
> set fmri(conmask5_2) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 3?
> set fmri(conmask5_3) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 4?
> set fmri(conmask5_4) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 6?
> set fmri(conmask5_6) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 7?
> set fmri(conmask5_7) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 8?
> set fmri(conmask5_8) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 9?
> set fmri(conmask5_9) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 10?
> set fmri(conmask5_10) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 11?
> set fmri(conmask5_11) 0
>
> # Mask real contrast/F-test 5 with real contrast/F-test 12?
> set fmri(conmask5_12) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 1?
> set fmri(conmask6_1) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 2?
> set fmri(conmask6_2) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 3?
> set fmri(conmask6_3) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 4?
> set fmri(conmask6_4) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 5?
> set fmri(conmask6_5) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 7?
> set fmri(conmask6_7) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 8?
> set fmri(conmask6_8) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 9?
> set fmri(conmask6_9) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 10?
> set fmri(conmask6_10) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 11?
> set fmri(conmask6_11) 0
>
> # Mask real contrast/F-test 6 with real contrast/F-test 12?
> set fmri(conmask6_12) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 1?
> set fmri(conmask7_1) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 2?
> set fmri(conmask7_2) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 3?
> set fmri(conmask7_3) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 4?
> set fmri(conmask7_4) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 5?
> set fmri(conmask7_5) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 6?
> set fmri(conmask7_6) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 8?
> set fmri(conmask7_8) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 9?
> set fmri(conmask7_9) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 10?
> set fmri(conmask7_10) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 11?
> set fmri(conmask7_11) 0
>
> # Mask real contrast/F-test 7 with real contrast/F-test 12?
> set fmri(conmask7_12) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 1?
> set fmri(conmask8_1) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 2?
> set fmri(conmask8_2) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 3?
> set fmri(conmask8_3) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 4?
> set fmri(conmask8_4) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 5?
> set fmri(conmask8_5) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 6?
> set fmri(conmask8_6) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 7?
> set fmri(conmask8_7) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 9?
> set fmri(conmask8_9) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 10?
> set fmri(conmask8_10) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 11?
> set fmri(conmask8_11) 0
>
> # Mask real contrast/F-test 8 with real contrast/F-test 12?
> set fmri(conmask8_12) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 1?
> set fmri(conmask9_1) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 2?
> set fmri(conmask9_2) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 3?
> set fmri(conmask9_3) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 4?
> set fmri(conmask9_4) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 5?
> set fmri(conmask9_5) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 6?
> set fmri(conmask9_6) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 7?
> set fmri(conmask9_7) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 8?
> set fmri(conmask9_8) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 10?
> set fmri(conmask9_10) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 11?
> set fmri(conmask9_11) 0
>
> # Mask real contrast/F-test 9 with real contrast/F-test 12?
> set fmri(conmask9_12) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 1?
> set fmri(conmask10_1) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 2?
> set fmri(conmask10_2) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 3?
> set fmri(conmask10_3) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 4?
> set fmri(conmask10_4) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 5?
> set fmri(conmask10_5) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 6?
> set fmri(conmask10_6) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 7?
> set fmri(conmask10_7) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 8?
> set fmri(conmask10_8) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 9?
> set fmri(conmask10_9) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 11?
> set fmri(conmask10_11) 0
>
> # Mask real contrast/F-test 10 with real contrast/F-test 12?
> set fmri(conmask10_12) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 1?
> set fmri(conmask11_1) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 2?
> set fmri(conmask11_2) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 3?
> set fmri(conmask11_3) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 4?
> set fmri(conmask11_4) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 5?
> set fmri(conmask11_5) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 6?
> set fmri(conmask11_6) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 7?
> set fmri(conmask11_7) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 8?
> set fmri(conmask11_8) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 9?
> set fmri(conmask11_9) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 10?
> set fmri(conmask11_10) 0
>
> # Mask real contrast/F-test 11 with real contrast/F-test 12?
> set fmri(conmask11_12) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 1?
> set fmri(conmask12_1) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 2?
> set fmri(conmask12_2) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 3?
> set fmri(conmask12_3) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 4?
> set fmri(conmask12_4) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 5?
> set fmri(conmask12_5) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 6?
> set fmri(conmask12_6) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 7?
> set fmri(conmask12_7) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 8?
> set fmri(conmask12_8) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 9?
> set fmri(conmask12_9) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 10?
> set fmri(conmask12_10) 0
>
> # Mask real contrast/F-test 12 with real contrast/F-test 11?
> set fmri(conmask12_11) 0
>
> # Do contrast masking at all?
> set fmri(conmask1_1) 0
>
> ##########################################################
> # Now options that don't appear in the GUI
>
> # Alternative example_func image (not derived from input 4D dataset)
> set fmri(alternative_example_func) ""
>
> # 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
|
