Hi,
I'm piecing together a second level FEAT, but as I load it into the GUI
I get the following error.
invalid command name "V"
invalid command name "V"
while executing
"V 1 wrt EV 4"
(file
"/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_all.fsf"
line 422)
invoked from within
"source ${filename}"
(procedure "feat5:load" line 22)
invoked from within
"feat5:load .r 1
/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_all.fsf"
("uplevel" body line 1)
invoked from within
"uplevel #0 $cmd $args"
Unfortunately I can't really parse it out, could I please get some help
making sense of this?
cheers
martin
PS: I attach the script
--
--------------------------------------------
“Well! I’ve often seen a cat without a grin,” thought Alice, “but a grin without a cat! It’s the most curious thing I ever saw in my life!” [Lewis Carroll, Alice in Wonderland]
--------------------------------------------
Martin M. Monti
Princeton University
Department of Psychology
Green Hall 3-S-8
(609) 258-5679
www.webmartin.net
--------------------------------------------
# FEAT version number
set fmri(version) 5.63
# 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 + Post-stats
# 4 : Post-stats
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
# Cleanup first-level standard-space images
set fmri(sscleanup_yn) 0
# Output directory
set fmri(outputdir) "DB_All"
# TR(s)
set fmri(tr) 3
# Total volumes
set fmri(npts) 36
# Delete volumes
set fmri(ndelete) 0
# Perfusion tag/control order
set fmri(tagfirst) 1
# Number of first-level analyses
set fmri(multiple) 36
# Higher-level input type
# 1 : Inputs are lower-level FEAT directories
# 2 : Inputs are cope images from FEAT directories
set fmri(inputtype) 2
# Carry out pre-stats processing?
set fmri(filtering_yn) 0
# Brain/background threshold, %
set fmri(brain_thresh) 10
# Critical z for design efficiency calculation
set fmri(critical_z) 5.3
# Noise level
set fmri(noise) 0.66
# Noise AR(1)
set fmri(noisear) 0.34
# 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) 0
# Slice timings file
set fmri(st_file) ""
# BET brain extraction
set fmri(bet_yn) 1
# Spatial smoothing FWHM (mm)
set fmri(smooth) 5
# Intensity normalization
set fmri(norm_yn) 0
# Perfusion subtraction
set fmri(perfsub_yn) 0
# Highpass temporal filtering
set fmri(temphp_yn) 1
# Lowpass temporal filtering
set fmri(templp_yn) 0
# MELODIC ICA data exploration
set fmri(melodic_yn) 0
# Carry out main stats?
set fmri(stats_yn) 1
# Carry out prewhitening?
set fmri(prewhiten_yn) 1
# Add motion parameters to model
# 0 : No
# 1 : Yes, orthogonalise rest of model wrt motion
# 2 : Yes, orthogonalise motion wrt rest of model
# 3 : Yes, don't orthogonalise
set fmri(motionevs) 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) 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) 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
# Registration?
set fmri(reg_yn) 0
# Registration to initial structural
set fmri(reginitial_highres_yn) 0
# Search space for registration to initial structural
# 0 : No search
# 90 : Normal search
# 180 : Full search
set fmri(reginitial_highres_search) 90
# Degrees of Freedom for registration to initial structural
set fmri(reginitial_highres_dof) 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/csbmb/pkg/FSL/fsl/bindist/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) 0
# 4D AVW data or FEAT directory (1)
set feat_files(1) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope1.nii.gz"
# 4D AVW data or FEAT directory (2)
set feat_files(2) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope2.nii.gz"
# 4D AVW data or FEAT directory (3)
set feat_files(3) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope3.nii.gz"
# 4D AVW data or FEAT directory (4)
set feat_files(4) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope4.nii.gz"
# 4D AVW data or FEAT directory (5)
set feat_files(5) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope5.nii.gz"
# 4D AVW data or FEAT directory (6)
set feat_files(6) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope6.nii.gz"
# 4D AVW data or FEAT directory (7)
set feat_files(7) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope7.nii.gz"
# 4D AVW data or FEAT directory (8)
set feat_files(8) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope8.nii.gz"
# 4D AVW data or FEAT directory (9)
set feat_files(9) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic1.feat/stats/cope9.nii.gz"
# 4D AVW data or FEAT directory (10)
set feat_files(10) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope1.nii.gz"
# 4D AVW data or FEAT directory (11)
set feat_files(11) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope2.nii.gz"
# 4D AVW data or FEAT directory (12)
set feat_files(12) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope3.nii.gz"
# 4D AVW data or FEAT directory (13)
set feat_files(13) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope4.nii.gz"
# 4D AVW data or FEAT directory (14)
set feat_files(14) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope5.nii.gz"
# 4D AVW data or FEAT directory (15)
set feat_files(15) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope6.nii.gz"
# 4D AVW data or FEAT directory (16)
set feat_files(16) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope7.nii.gz"
# 4D AVW data or FEAT directory (17)
set feat_files(17) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope8.nii.gz"
# 4D AVW data or FEAT directory (18)
set feat_files(18) "/mounts/jukebox_static/osherson/mmonti/LingLog2/FSL/DB/Scripts/DB_Logic2.feat/stats/cope9.nii.gz"
# 4D AVW d
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