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Commit 88ea57ec authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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RF: Move feat1 design.fsf to git rather than external data set, add F test to 

FEAT analysis
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1 merge request!31RF: Move feat1 design.fsf to git rather than external data set, add F test to FEAT analysis
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fsl_course/feat1/design.fsf 0 → 100755
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# FEAT version number
set fmri(version) 6.00
# 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-processing
# 2 : Statistics
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) 0
# Cleanup first-level standard-space images
set fmri(sscleanup_yn) 0
# Output directory
set fmri(outputdir) "/vols/Data/fsldev/dataSets/fsl_course_data/fmri/fmri_fluency/fmri.feat"
# TR(s)
set fmri(tr) 4.200000
# Total volumes
set fmri(npts) 106
# 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) 2
# 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
# 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) 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) 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
set fmri(motionevs) 0
set fmri(motionevsbeta) ""
set fmri(scriptevsbeta) ""
# 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) 2
set fmri(evs_real) 4
set fmri(evs_vox) 0
# Number of contrasts
set fmri(ncon_orig) 5
set fmri(ncon_real) 5
# Number of F-tests
set fmri(nftests_orig) 1
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) 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
# Create time series plots
set fmri(tsplot_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) 90
# Degrees of Freedom for registration to main structural
set fmri(reghighres_dof) 7
# Registration to standard image?
set fmri(regstandard_yn) 1
# Use alternate reference images?
set fmri(alternateReference_yn) 0
# Standard image
set fmri(regstandard) "/opt/fmrib/fsl-alpha/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) 90
# 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) 0
# Control nonlinear warp field resolution
set fmri(regstandard_nonlinear_warpres) 10
# High pass filter cutoff
set fmri(paradigm_hp) 90
# Total voxels
set fmri(totalVoxels) 18235392
# 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) "/vols/Data/fsldev/dataSets/fsl_course_data/fmri/fmri_fluency/fmri"
# Add confound EVs text file
set fmri(confoundevs) 0
# Subject's structural image for analysis 1
set highres_files(1) "/vols/Data/fsldev/dataSets/fsl_course_data/fmri/fmri_fluency/structural_brain"
# EV 1 title
set fmri(evtitle1) "Gen"
# 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
# Custom EV file (EV 1)
set fmri(custom1) "/vols/Data/fsldev/dataSets/fsl_course_data/fmri/fmri_fluency/word_generation.txt"
# 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
# EV 2 title
set fmri(evtitle2) "Shad"
# 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
# Custom EV file (EV 2)
set fmri(custom2) "/vols/Data/fsldev/dataSets/fsl_course_data/fmri/fmri_fluency/word_shadowing.txt"
# 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
# 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) "Generation"
# 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
# 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) "Shadow"
# 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
# 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) "Mean"
# 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
# F-test 1 element 3
set fmri(ftest_real1.3) 0
# Display images for contrast_real 4
set fmri(conpic_real.4) 1
# Title for contrast_real 4
set fmri(conname_real.4) "Shad > Gen"
# 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) 1
# Real contrast_real vector 4 element 4
set fmri(con_real4.4) 0
# F-test 1 element 4
set fmri(ftest_real1.4) 0
# Display images for contrast_real 5
set fmri(conpic_real.5) 1
# Title for contrast_real 5
set fmri(conname_real.5) "Gen > Shad"
# 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) -1
# Real contrast_real vector 5 element 4
set fmri(con_real5.4) 0
# F-test 1 element 5
set fmri(ftest_real1.5) 0
# Display images for contrast_orig 1
set fmri(conpic_orig.1) 1
# Title for contrast_orig 1
set fmri(conname_orig.1) "Generation"
# 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
# F-test 1 element 1
set fmri(ftest_orig1.1) 1
# Display images for contrast_orig 2
set fmri(conpic_orig.2) 1
# Title for contrast_orig 2
set fmri(conname_orig.2) "Shadow"
# 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
# F-test 1 element 2
set fmri(ftest_orig1.2) 1
# Display images for contrast_orig 3
set fmri(conpic_orig.3) 1
# Title for contrast_orig 3
set fmri(conname_orig.3) "Mean"
# 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
# F-test 1 element 3
set fmri(ftest_orig1.3) 0
# Display images for contrast_orig 4
set fmri(conpic_orig.4) 1
# Title for contrast_orig 4
set fmri(conname_orig.4) "Shad > Gen"
# 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) 1
# F-test 1 element 4
set fmri(ftest_orig1.4) 0
# Display images for contrast_orig 5
set fmri(conpic_orig.5) 1
# Title for contrast_orig 5
set fmri(conname_orig.5) "Gen > Shad"
# 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) -1
# F-test 1 element 5
set fmri(ftest_orig1.5) 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
##########################################################
# Now options that don't appear in the GUI
# 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
fsl_course/feat1/feedsRun1.py
+ 2
− 2
View file @ 88ea57ec
...@@ -19,7 +19,7 @@ fslDir = os.environ['FSLDIR'] ...@@ -19,7 +19,7 @@ fslDir = os.environ['FSLDIR']
# copy FSF to test location and update paths # copy FSF to test location and update paths
origFeatDir = op.join(dataDir, "fsl_course_data/fmri/fmri_fluency") origFeatDir = op.join(dataDir, "fsl_course_data/fmri/fmri_fluency")
origFSF = op.join(origFeatDir, "design.fsf") origFSF = op.join(os.getcwd(), "design.fsf")
origFSLDir = "/opt/fmrib/fsl-alpha" origFSLDir = "/opt/fmrib/fsl-alpha"
origDataDir = "/vols/Data/fsldev/dataSets" origDataDir = "/vols/Data/fsldev/dataSets"
...@@ -32,6 +32,6 @@ util.run(cmd) ...@@ -32,6 +32,6 @@ util.run(cmd)
# run FEAT with new FSF # run FEAT with new FSF
util.run("unset SGE_ROOT; feat {0}".format(op.join(outDir, "design.fsf"))) util.run("unset SGE_ROOT; feat {0}".format(newFSF))
sys.exit(0) sys.exit(0)
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