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Subject:

Re: Command line question

From:

Joe Devlin <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 22 May 2003 08:28:09 +0100

Content-Type:

MULTIPART/MIXED

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (39 lines) , analysis.sh (1 lines) , part1.fsf (1 lines) , part2.fsf (1 lines) , part3.fsf (1 lines)

Hi Darren,

> I have been using FSL-FEAT from the GUI.  Now, I would like to execute
> a number of FEAT jobs from the command line using a script.  I am going
> to be creating a number of .fsf files that will contain the entire
> setup for that scan (for instance S02Q1.fsf).  How do I go about
> writing a script to execute those without going through the GUI?

Good idea.  I think this is a really good practice. It's so easy to write
and requires minimal effort to run the analyses that I would encourage
everyone to at least try this.  It also precludes making careless
mistakes idiosyncratically which means that oen can exactly replicate a
previous analysis or run another with only slight variation.  *end of
soapbox*

I have attached a script that I use to automate FEAT analyses.
It's in four parts.  The main part is a file
called analysis.sh which is a ksh script.  It makes certain assumptions
about how your files are stored on disk and named but as long as you have
a standardized convention, it's easy to modify.  Otherwise it sets up a
basic analysis, including preprocessing.  THere is a section, currently
commented out, which includes motion params as covariates of no interest
in the model.  Hopefully the whole thing is pretty self-explanatory and
easy to customize.  I've used this (or versions of this) script for
analyses where the model was basically fixed per subject, customized
models per subject, sparse sampling analyses, etc.  It's very flexible.
Steve made the *.fsf files very easy to script by using a TCL-style
interface and commenting the file fairly extensively.  Nice job, Steve.

The other three files are simply sections of *.fsf files which don't
change much across studies.  Parts 1 and 2 can be editted by hand, if
necessary but part3 is simply the set of contrasts you're interested in.
It's quite wordy so I tend to use the gui to set up a single analysis and
then save the design.fsf file, delete all the stuff up to the contrasts,
and then save that as part3.fsf.

Joe



#!/bin/ksh # # Specify the location of the EPI files to analyse # ORIG=~/scratch/ # # Specify the directories to analyse # DIRS="6235 6236 6247 6248 6302 6314 6334 6335 6346 6347 6348" # # Specify the sessions to analyse # SESS="A B" # # Regressors: Explanatory variables # EVS="cond1 cond2 cond3 cond4 cond5 cond6 cond7 cond10" #---------------------------------------------------------------- # Details of the model can be specified below #---------------------------------------------------------------- for D in $DIRS; do print "Analysing subject" $D # # This looks for a structural scan which has already been skull stripped # (ie BETed) called *_brain) # STRUCT=$(ls $ORIG/$D/*_brain.hdr) # # Create subject and session specific analysis # for S in $SESS; do # Create a new FEAT setup file based on the model cat part1.fsf > model.fsf # Set the number of volumes per session NVOL=$(avwnvols $ORIG/$D/session_$S) print "set fmri(npts) $NVOL" >>model.fsf # Second part of file cat part2.fsf >> model.fsf print "# 4D AVW data or FEAT directory (1)" >> model.fsf print "set feat_files(1) \"$ORIG/$D/session_${S}.hdr\"" >> model.fsf print "" >> model.fsf print "# Subject's structural image for analysis 1" >> model.fsf print "set highres_files(1) \"$STRUCT\"" >> model.fsf # Put in the EVs ((IDX=1)) for E in $EVS; do print "# Basic waveform shape (EV "$IDX")" >> model.fsf print "set fmri(shape"$IDX") 3" >> model.fsf print "set fmri(convolve"$IDX") 2" >> model.fsf print "set fmri(convolve_phase"$IDX") 0" >> model.fsf print "set fmri(tempfilt_yn"$IDX") 1" >> model.fsf print "set fmri(deriv_yn"$IDX") 1" >> model.fsf EV=$(ls $ORIG/$D/${E}${S}.txt) print "set fmri(custom"$IDX") \"$EV\"" >> model.fsf print "set fmri(gammasigma"$IDX") 3" >> model.fsf print "set fmri(gammadelay"$IDX") 6" >> model.fsf print "set fmri(ortho"$IDX".0) 0" >> model.fsf ((IDX=$IDX+1)) done # Put in the motion params. To include the motion params, you need # to run motion correction *before* setting up this analysis and then # parse the motion files into one-column format EV files. Uncomment # to include motion params in the current analysis. ALso don't forget # to adjust the number of EVs in part2.fsf. # # COVS="trans_x trans_y trans_z rot_x rot_y rot_z" # ((IDX=9)) # for C in $COVS; do # print "# Basic waveform shape (EV "$IDX")" >> model.fsf # print "set fmri(shape"$IDX") 2" >> model.fsf # print "set fmri(convolve"$IDX") 0" >> model.fsf # print "set fmri(convolve_phase"$IDX") 0" >> model.fsf # print "set fmri(tempfilt_yn"$IDX") 1" >> model.fsf # print "set fmri(deriv_yn"$IDX") 0" >> model.fsf # print "set fmri(custom"$IDX")" "\""$ORIG/$D/$C.session_$S"\"" >> model.fsf # print "set fmri(ortho"$IDX".0) 0" >> model.fsf # ((IDX=$IDX+1)) # done # Put in the contrast cat part3.fsf >> model.fsf # Run the model print "Session $S" feat model.fsf > log.$S # Clean up any files? done print "" done
# FEAT version number set fmri(version) 5.03 # Analysis level 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 + Contrasts, Thresholding, Rendering # 4 : Contrasts, Thresholding, Rendering set fmri(analysis) 7 # Delay before starting (hours) set fmri(delay) 0 # Use relative filenames set fmri(relative_yn) 0 # Balloon help set fmri(help_yn) 0 # Output directory set fmri(outputdir) "" # TR(s) set fmri(tr) 3.0 # Total volumes
# Delete volumes set fmri(ndelete) 4 # Number of first-level analyses set fmri(multiple) 1 # Carry out pre-stats processing? set fmri(filtering_yn) 1 # 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 set fmri(st) 0 # Slice timings file set fmri(st_file) "" # Motion correction # 0 : None # 1 : MCFLIRT set fmri(mc) 1 # 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 # Number of EVs set fmri(evs_orig) 8 set fmri(evs_real) 16 # Number of contrasts set fmri(ncon_orig) 6 set fmri(ncon_real) 6 # Number of F-tests set fmri(nftests_orig) 0 set fmri(nftests_real) 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) 1 # 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 # Registration? set fmri(reg_yn) 1 # 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) 1 # 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) 120
# 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) "Unrel > consonants" # 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 # Real contrast_real vector 1 element 13 set fmri(con_real1.13) -1 # Real contrast_real vector 1 element 14 set fmri(con_real1.14) 0 # Real contrast_real vector 1 element 15 set fmri(con_real1.15) 0 # Real contrast_real vector 1 element 16 set fmri(con_real1.16) 0 # Real contrast_real vector 1 element 17 set fmri(con_real1.17) 0 # Real contrast_real vector 1 element 18 set fmri(con_real1.18) 0 # Real contrast_real vector 1 element 19 set fmri(con_real1.19) 0 # Real contrast_real vector 1 element 20 set fmri(con_real1.20) 0 # Real contrast_real vector 1 element 21 set fmri(con_real1.21) 0 # Real contrast_real vector 1 element 22 set fmri(con_real1.22) 0 # Display images for contrast_real 2 set fmri(conpic_real.2) 1 # Title for contrast_real 2 set fmri(conname_real.2) "Ortho priming" # Real contrast_real vector 2 element 1 set fmri(con_real2.1) 1 # Real contrast_real vector 2 element 2 set fmri(con_real2.2) 0 # Real contrast_real vector 2 element 3 set fmri(con_real2.3) -1 # Real contrast_real vector 2 element 4 set fmri(con_real2.4) 0 # Real contrast_real vector 2 element 5 set fmri(con_real2.5) 0 # Real contrast_real vector 2 element 6 set fmri(con_real2.6) 0 # 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 # Real contrast_real vector 2 element 13 set fmri(con_real2.13) 0 # Real contrast_real vector 2 element 14 set fmri(con_real2.14) 0 # Real contrast_real vector 2 element 15 set fmri(con_real2.15) 0 # Real contrast_real vector 2 element 16 set fmri(con_real2.16) 0 # Real contrast_real vector 2 element 17 set fmri(con_real2.17) 0 # Real contrast_real vector 2 element 18 set fmri(con_real2.18) 0 # Real contrast_real vector 2 element 19 set fmri(con_real2.19) 0 # Real contrast_real vector 2 element 20 set fmri(con_real2.20) 0 # Real contrast_real vector 2 element 21 set fmri(con_real2.21) 0 # Real contrast_real vector 2 element 22 set fmri(con_real2.22) 0 # Display images for contrast_real 3 set fmri(conpic_real.3) 1 # Title for contrast_real 3 set fmri(conname_real.3) "Morph priming" # 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 # Real contrast_real vector 3 element 3 set fmri(con_real3.3) 0 # Real contrast_real vector 3 element 4 set fmri(con_real3.4) 0 # Real contrast_real vector 3 element 5 set fmri(con_real3.5) -1 # Real contrast_real vector 3 element 6 set fmri(con_real3.6) 0 # 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 # Real contrast_real vector 3 element 13 set fmri(con_real3.13) 0 # Real contrast_real vector 3 element 14 set fmri(con_real3.14) 0 # Real contrast_real vector 3 element 15 set fmri(con_real3.15) 0 # Real contrast_real vector 3 element 16 set fmri(con_real3.16) 0 # Real contrast_real vector 3 element 17 set fmri(con_real3.17) 0 # Real contrast_real vector 3 element 18 set fmri(con_real3.18) 0 # Real contrast_real vector 3 element 19 set fmri(con_real3.19) 0 # Real contrast_real vector 3 element 20 set fmri(con_real3.20) 0 # Real contrast_real vector 3 element 21 set fmri(con_real3.21) 0 # Real contrast_real vector 3 element 22 set fmri(con_real3.22) 0 # Display images for contrast_real 4 set fmri(conpic_real.4) 1 # Title for contrast_real 4 set fmri(conname_real.4) "Sem priming" # Real contrast_real vector 4 element 1 set fmri(con_real4.1) 1 # 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) 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) -1 # 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 # Real contrast_real vector 4 element 13 set fmri(con_real4.13) 0 # Real contrast_real vector 4 element 14 set fmri(con_real4.14) 0 # Real contrast_real vector 4 element 15 set fmri(con_real4.15) 0 # Real contrast_real vector 4 element 16 set fmri(con_real4.16) 0 # Real contrast_real vector 4 element 17 set fmri(con_real4.17) 0 # Real contrast_real vector 4 element 18 set fmri(con_real4.18) 0 # Real contrast_real vector 4 element 19 set fmri(con_real4.19) 0 # Real contrast_real vector 4 element 20 set fmri(con_real4.20) 0 # Real contrast_real vector 4 element 21 set fmri(con_real4.21) 0 # Real contrast_real vector 4 element 22 set fmri(con_real4.22) 0 # Display images for contrast_real 5 set fmri(conpic_real.5) 1 # Title for contrast_real 5 set fmri(conname_real.5) "Identity priming" # Real contrast_real vector 5 element 1 set fmri(con_real5.1) 1 # 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) 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) -1 # 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 # Real contrast_real vector 5 element 13 set fmri(con_real5.13) 0 # Real contrast_real vector 5 element 14 set fmri(con_real5.14) 0 # Real contrast_real vector 5 element 15 set fmri(con_real5.15) 0 # Real contrast_real vector 5 element 16 set fmri(con_real5.16) 0 # Real contrast_real vector 5 element 17 set fmri(con_real5.17) 0 # Real contrast_real vector 5 element 18 set fmri(con_real5.18) 0 # Real contrast_real vector 5 element 19 set fmri(con_real5.19) 0 # Real contrast_real vector 5 element 20 set fmri(con_real5.20) 0 # Real contrast_real vector 5 element 21 set fmri(con_real5.21) 0 # Real contrast_real vector 5 element 22 set fmri(con_real5.22) 0 # Display images for contrast_real 6 set fmri(conpic_real.6) 1 # Title for contrast_real 6 set fmri(conname_real.6) "Pseudoword identity priming" # 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) 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) 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) -1 # Real contrast_real vector 6 element 12 set fmri(con_real6.12) 0 # Real contrast_real vector 6 element 13 set fmri(con_real6.13) 0 # Real contrast_real vector 6 element 14 set fmri(con_real6.14) 0 # Real contrast_real vector 6 element 15 set fmri(con_real6.15) 1 # Real contrast_real vector 6 element 16 set fmri(con_real6.16) 0 # Real contrast_real vector 6 element 17 set fmri(con_real6.17) 0 # Real contrast_real vector 6 element 18 set fmri(con_real6.18) 0 # Real contrast_real vector 6 element 19 set fmri(con_real6.19) 0 # Real contrast_real vector 6 element 20 set fmri(con_real6.20) 0 # Real contrast_real vector 6 element 21 set fmri(con_real6.21) 0 # Real contrast_real vector 6 element 22 set fmri(con_real6.22) 0 # Display images for contrast_orig 1 set fmri(conpic_orig.1) 1 # Title for contrast_orig 1 set fmri(conname_orig.1) "Unrel > consonants" # 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 # Real contrast_orig vector 1 element 7 set fmri(con_orig1.7) -1 # Real contrast_orig vector 1 element 8 set fmri(con_orig1.8) 0 # Real contrast_orig vector 1 element 9 set fmri(con_orig1.9) 0 # Real contrast_orig vector 1 element 10 set fmri(con_orig1.10) 0 # Real contrast_orig vector 1 element 11 set fmri(con_orig1.11) 0 # Real contrast_orig vector 1 element 12 set fmri(con_orig1.12) 0 # Real contrast_orig vector 1 element 13 set fmri(con_orig1.13) 0 # Real contrast_orig vector 1 element 14 set fmri(con_orig1.14) 0 # Display images for contrast_orig 2 set fmri(conpic_orig.2) 1 # Title for contrast_orig 2 set fmri(conname_orig.2) "Ortho priming" # Real contrast_orig vector 2 element 1 set fmri(con_orig2.1) 1 # Real contrast_orig vector 2 element 2 set fmri(con_orig2.2) -1 # Real contrast_orig vector 2 element 3 set fmri(con_orig2.3) 0 # 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 # Real contrast_orig vector 2 element 7 set fmri(con_orig2.7) 0 # Real contrast_orig vector 2 element 8 set fmri(con_orig2.8) 0 # Real contrast_orig vector 2 element 9 set fmri(con_orig2.9) 0 # Real contrast_orig vector 2 element 10 set fmri(con_orig2.10) 0 # Real contrast_orig vector 2 element 11 set fmri(con_orig2.11) 0 # Real contrast_orig vector 2 element 12 set fmri(con_orig2.12) 0 # Real contrast_orig vector 2 element 13 set fmri(con_orig2.13) 0 # Real contrast_orig vector 2 element 14 set fmri(con_orig2.14) 0 # Display images for contrast_orig 3 set fmri(conpic_orig.3) 1 # Title for contrast_orig 3 set fmri(conname_orig.3) "Morph priming" # Real contrast_orig vector 3 element 1 set fmri(con_orig3.1) 1 # Real contrast_orig vector 3 element 2 set fmri(con_orig3.2) 0 # Real contrast_orig vector 3 element 3 set fmri(con_orig3.3) -1 # 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 # Real contrast_orig vector 3 element 7 set fmri(con_orig3.7) 0 # Real contrast_orig vector 3 element 8 set fmri(con_orig3.8) 0 # Real contrast_orig vector 3 element 9 set fmri(con_orig3.9) 0 # Real contrast_orig vector 3 element 10 set fmri(con_orig3.10) 0 # Real contrast_orig vector 3 element 11 set fmri(con_orig3.11) 0 # Real contrast_orig vector 3 element 12 set fmri(con_orig3.12) 0 # Real contrast_orig vector 3 element 13 set fmri(con_orig3.13) 0 # Real contrast_orig vector 3 element 14 set fmri(con_orig3.14) 0 # Display images for contrast_orig 4 set fmri(conpic_orig.4) 1 # Title for contrast_orig 4 set fmri(conname_orig.4) "Sem priming" # Real contrast_orig vector 4 element 1 set fmri(con_orig4.1) 1 # 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) 0 # Real contrast_orig vector 4 element 4 set fmri(con_orig4.4) -1 # 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 # Real contrast_orig vector 4 element 7 set fmri(con_orig4.7) 0 # Real contrast_orig vector 4 element 8 set fmri(con_orig4.8) 0 # Real contrast_orig vector 4 element 9 set fmri(con_orig4.9) 0 # Real contrast_orig vector 4 element 10 set fmri(con_orig4.10) 0 # Real contrast_orig vector 4 element 11 set fmri(con_orig4.11) 0 # Real contrast_orig vector 4 element 12 set fmri(con_orig4.12) 0 # Real contrast_orig vector 4 element 13 set fmri(con_orig4.13) 0 # Real contrast_orig vector 4 element 14 set fmri(con_orig4.14) 0 # Display images for contrast_orig 5 set fmri(conpic_orig.5) 1 # Title for contrast_orig 5 set fmri(conname_orig.5) "Identity priming" # Real contrast_orig vector 5 element 1 set fmri(con_orig5.1) 1 # 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) 0 # Real contrast_orig vector 5 element 5 set fmri(con_orig5.5) -1 # Real contrast_orig vector 5 element 6 set fmri(con_orig5.6) 0 # Real contrast_orig vector 5 element 7 set fmri(con_orig5.7) 0 # Real contrast_orig vector 5 element 8 set fmri(con_orig5.8) 0 # Real contrast_orig vector 5 element 9 set fmri(con_orig5.9) 0 # Real contrast_orig vector 5 element 10 set fmri(con_orig5.10) 0 # Real contrast_orig vector 5 element 11 set fmri(con_orig5.11) 0 # Real contrast_orig vector 5 element 12 set fmri(con_orig5.12) 0 # Real contrast_orig vector 5 element 13 set fmri(con_orig5.13) 0 # Real contrast_orig vector 5 element 14 set fmri(con_orig5.14) 0 # Display images for contrast_orig 6 set fmri(conpic_orig.6) 1 # Title for contrast_orig 6 set fmri(conname_orig.6) "Pseudoword identity priming" # 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) 0 # Real contrast_orig vector 6 element 4 set fmri(con_orig6.4) 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) -1 # Real contrast_orig vector 6 element 7 set fmri(con_orig6.7) 0 # Real contrast_orig vector 6 element 8 set fmri(con_orig6.8) 1 # Real contrast_orig vector 6 element 9 set fmri(con_orig6.9) 0 # Real contrast_orig vector 6 element 10 set fmri(con_orig6.10) 0 # Real contrast_orig vector 6 element 11 set fmri(con_orig6.11) 0 # Real contrast_orig vector 6 element 12 set fmri(con_orig6.12) 0 # Real contrast_orig vector 6 element 13 set fmri(con_orig6.13) 0 # Real contrast_orig vector 6 element 14 set fmri(con_orig6.14) 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 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 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 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 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 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 # Do contrast masking at all? set fmri(conmask1_1) 0

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