diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..e43b0f9
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+.DS_Store
diff --git a/design_tem.fsf b/design_tem.fsf
index 02563b7..9d0e3d7 100755
--- a/design_tem.fsf
+++ b/design_tem.fsf
@@ -36,7 +36,7 @@ set fmri(sscleanup_yn) 0
 set fmri(outputdir) ""
 
 # TR(s)
-set fmri(tr) 3.0000000000 
+set fmri(tr) 2.0000000000
 
 # Total volumes
 set fmri(npts) 80
@@ -268,7 +268,7 @@ set fmri(regstandard_nonlinear_yn) 0
 set fmri(regstandard_nonlinear_warpres) 10 
 
 # High pass filter cutoff
-set fmri(paradigm_hp) 60
+set fmri(paradigm_hp) 40
 
 # Total voxels
 set fmri(totalVoxels) 39321600
@@ -321,10 +321,10 @@ set fmri(deriv_yn1) 1
 set fmri(skip1) 0
 
 # Off (EV 1)
-set fmri(off1) 30
+set fmri(off1) 20
 
 # On (EV 1)
-set fmri(on1) 30
+set fmri(on1) 20
 
 # Phase (EV 1)
 set fmri(phase1) 0
diff --git a/design_tem_1_5.fsf b/design_tem_1_5.fsf
new file mode 100644
index 0000000..7fb0bfa
--- /dev/null
+++ b/design_tem_1_5.fsf
@@ -0,0 +1,396 @@
+
+# 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-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
+
+# Output directory
+set fmri(outputdir) ""
+
+# TR(s)
+set fmri(tr) 3.0000000000
+
+# Total volumes
+set fmri(npts) 80
+
+# 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) 1
+
+# Slice timings file
+set fmri(st_file) ""
+
+# BET brain extraction
+set fmri(bet_yn) 0
+
+# Spatial smoothing FWHM (mm)
+set fmri(smooth) 6.0
+
+# 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) 1
+set fmri(evs_real) 2
+set fmri(evs_vox) 0
+
+# 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
+
+# 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) 90
+
+# Degrees of Freedom for registration to main structural
+set fmri(reghighres_dof) BBR
+
+# Registration to standard image?
+set fmri(regstandard_yn) 1
+
+# Use alternate reference images?
+set fmri(alternateReference_yn) 0
+
+# Standard image
+set fmri(regstandard) "/usr/local/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) 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) 40
+
+# Total voxels
+set fmri(totalVoxels) 39321600
+
+
+# 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) pathf
+
+# Add confound EVs text file
+set fmri(confoundevs) 0
+
+# Subject's structural image for analysis 1
+set highres_files(1) paths
+
+# EV 1 title
+set fmri(evtitle1) ""
+
+# 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) 0
+
+# 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) 2
+
+# 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
+
+# Skip (EV 1)
+set fmri(skip1) 0
+
+# Off (EV 1)
+set fmri(off1) 30
+
+# On (EV 1)
+set fmri(on1) 30
+
+# Phase (EV 1)
+set fmri(phase1) 0
+
+# Stop (EV 1)
+set fmri(stop1) -1
+
+# Gamma sigma (EV 1)
+set fmri(gammasigma1) 3
+
+# Gamma delay (EV 1)
+set fmri(gammadelay1) 6
+
+# Orthogonalise EV 1 wrt EV 0
+set fmri(ortho1.0) 0
+
+# Orthogonalise EV 1 wrt EV 1
+set fmri(ortho1.1) 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) ""
+
+# 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
+
+# Display images for contrast_orig 1
+set fmri(conpic_orig.1) 1
+
+# Title for contrast_orig 1
+set fmri(conname_orig.1) ""
+
+# Real contrast_orig vector 1 element 1
+set fmri(con_orig1.1) 1
+
+# Contrast masking - use >0 instead of thresholding?
+set fmri(conmask_zerothresh_yn) 0
+
+# Do contrast masking at all?
+set fmri(conmask1_1) 0
+
+##########################################################
+# 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
diff --git a/design_tem_1_5_120.fsf b/design_tem_1_5_120.fsf
new file mode 100644
index 0000000..038b029
--- /dev/null
+++ b/design_tem_1_5_120.fsf
@@ -0,0 +1,396 @@
+
+# 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-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
+
+# Output directory
+set fmri(outputdir) ""
+
+# TR(s)
+set fmri(tr) 3.0000000000
+
+# Total volumes
+set fmri(npts) 120
+
+# 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) 1
+
+# Slice timings file
+set fmri(st_file) ""
+
+# BET brain extraction
+set fmri(bet_yn) 0
+
+# Spatial smoothing FWHM (mm)
+set fmri(smooth) 6.0
+
+# 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) 1
+set fmri(evs_real) 2
+set fmri(evs_vox) 0
+
+# 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
+
+# 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) 90
+
+# Degrees of Freedom for registration to main structural
+set fmri(reghighres_dof) BBR
+
+# Registration to standard image?
+set fmri(regstandard_yn) 1
+
+# Use alternate reference images?
+set fmri(alternateReference_yn) 0
+
+# Standard image
+set fmri(regstandard) "/usr/local/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) 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) 40
+
+# Total voxels
+set fmri(totalVoxels) 39321600
+
+
+# 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) pathf
+
+# Add confound EVs text file
+set fmri(confoundevs) 0
+
+# Subject's structural image for analysis 1
+set highres_files(1) paths
+
+# EV 1 title
+set fmri(evtitle1) ""
+
+# 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) 0
+
+# 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) 2
+
+# 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
+
+# Skip (EV 1)
+set fmri(skip1) 0
+
+# Off (EV 1)
+set fmri(off1) 30
+
+# On (EV 1)
+set fmri(on1) 30
+
+# Phase (EV 1)
+set fmri(phase1) 0
+
+# Stop (EV 1)
+set fmri(stop1) -1
+
+# Gamma sigma (EV 1)
+set fmri(gammasigma1) 3
+
+# Gamma delay (EV 1)
+set fmri(gammadelay1) 6
+
+# Orthogonalise EV 1 wrt EV 0
+set fmri(ortho1.0) 0
+
+# Orthogonalise EV 1 wrt EV 1
+set fmri(ortho1.1) 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) ""
+
+# 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
+
+# Display images for contrast_orig 1
+set fmri(conpic_orig.1) 1
+
+# Title for contrast_orig 1
+set fmri(conname_orig.1) ""
+
+# Real contrast_orig vector 1 element 1
+set fmri(con_orig1.1) 1
+
+# Contrast masking - use >0 instead of thresholding?
+set fmri(conmask_zerothresh_yn) 0
+
+# Do contrast masking at all?
+set fmri(conmask1_1) 0
+
+##########################################################
+# 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
diff --git a/design_tem_1_5_120_o.fsf b/design_tem_1_5_120_o.fsf
new file mode 100644
index 0000000..28b6a11
--- /dev/null
+++ b/design_tem_1_5_120_o.fsf
@@ -0,0 +1,505 @@
+
+# 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-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
+
+# Output directory
+set fmri(outputdir) ""
+
+# TR(s)
+set fmri(tr) 3.0000000000
+
+# Total volumes
+set fmri(npts) 120
+
+# 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) 1
+
+# Slice timings file
+set fmri(st_file) ""
+
+# BET brain extraction
+set fmri(bet_yn) 0
+
+# Spatial smoothing FWHM (mm)
+set fmri(smooth) 6.0
+
+# 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) 2
+set fmri(ncon_real) 2
+
+# 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
+
+# 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) 90
+
+# Degrees of Freedom for registration to main structural
+set fmri(reghighres_dof) BBR
+
+# Registration to standard image?
+set fmri(regstandard_yn) 1
+
+# Use alternate reference images?
+set fmri(alternateReference_yn) 0
+
+# Standard image
+set fmri(regstandard) "/usr/local/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) 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) 60
+
+# Total voxels
+set fmri(totalVoxels) 39321600
+
+
+# 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) pathf
+
+# Add confound EVs text file
+set fmri(confoundevs) 0
+
+# Subject's structural image for analysis 1
+set highres_files(1) paths
+
+# EV 1 title
+set fmri(evtitle1) "i"
+
+# 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) 0
+
+# 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) 2
+
+# 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
+
+# Skip (EV 1)
+set fmri(skip1) 0
+
+# Off (EV 1)
+set fmri(off1) 30
+
+# On (EV 1)
+set fmri(on1) 30
+
+# Phase (EV 1)
+set fmri(phase1) 0
+
+# Stop (EV 1)
+set fmri(stop1) -1
+
+# Gamma sigma (EV 1)
+set fmri(gammasigma1) 3
+
+# Gamma delay (EV 1)
+set fmri(gammadelay1) 6
+
+# 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) "d"
+
+# 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) 0
+
+# 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) 2
+
+# Convolve phase (EV 2)
+set fmri(convolve_phase2) 30
+
+# Apply temporal filtering (EV 2)
+set fmri(tempfilt_yn2) 1
+
+# Add temporal derivative (EV 2)
+set fmri(deriv_yn2) 1
+
+# Skip (EV 2)
+set fmri(skip2) 0
+
+# Off (EV 2)
+set fmri(off2) 30
+
+# On (EV 2)
+set fmri(on2) 30
+
+# Phase (EV 2)
+set fmri(phase2) 0
+
+# Stop (EV 2)
+set fmri(stop2) -1
+
+# Gamma sigma (EV 2)
+set fmri(gammasigma2) 3
+
+# Gamma delay (EV 2)
+set fmri(gammadelay2) 6
+
+# 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) "i"
+
+# 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) -1
+
+# Real contrast_real vector 1 element 4
+set fmri(con_real1.4) 0
+
+# Display images for contrast_real 2
+set fmri(conpic_real.2) 1
+
+# Title for contrast_real 2
+set fmri(conname_real.2) "d"
+
+# 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
+
+# Display images for contrast_orig 1
+set fmri(conpic_orig.1) 1
+
+# Title for contrast_orig 1
+set fmri(conname_orig.1) "i"
+
+# 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) -1
+
+# Display images for contrast_orig 2
+set fmri(conpic_orig.2) 1
+
+# Title for contrast_orig 2
+set fmri(conname_orig.2) "d"
+
+# 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
+
+# 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 2 with real contrast/F-test 1?
+set fmri(conmask2_1) 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
diff --git a/design_tem_1_5_o.fsf b/design_tem_1_5_o.fsf
new file mode 100644
index 0000000..b06b1d1
--- /dev/null
+++ b/design_tem_1_5_o.fsf
@@ -0,0 +1,505 @@
+
+# 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-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
+
+# Output directory
+set fmri(outputdir) ""
+
+# TR(s)
+set fmri(tr) 3.0000000000
+
+# Total volumes
+set fmri(npts) 80
+
+# 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) 1
+
+# Slice timings file
+set fmri(st_file) ""
+
+# BET brain extraction
+set fmri(bet_yn) 0
+
+# Spatial smoothing FWHM (mm)
+set fmri(smooth) 6.0
+
+# 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) 2
+set fmri(ncon_real) 2
+
+# 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
+
+# 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) 90
+
+# Degrees of Freedom for registration to main structural
+set fmri(reghighres_dof) BBR
+
+# Registration to standard image?
+set fmri(regstandard_yn) 1
+
+# Use alternate reference images?
+set fmri(alternateReference_yn) 0
+
+# Standard image
+set fmri(regstandard) "/usr/local/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) 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) 60
+
+# Total voxels
+set fmri(totalVoxels) 39321600
+
+
+# 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) pathf
+
+# Add confound EVs text file
+set fmri(confoundevs) 0
+
+# Subject's structural image for analysis 1
+set highres_files(1) paths
+
+# EV 1 title
+set fmri(evtitle1) "i"
+
+# 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) 0
+
+# 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) 2
+
+# 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
+
+# Skip (EV 1)
+set fmri(skip1) 0
+
+# Off (EV 1)
+set fmri(off1) 20
+
+# On (EV 1)
+set fmri(on1) 20
+
+# Phase (EV 1)
+set fmri(phase1) 0
+
+# Stop (EV 1)
+set fmri(stop1) -1
+
+# Gamma sigma (EV 1)
+set fmri(gammasigma1) 3
+
+# Gamma delay (EV 1)
+set fmri(gammadelay1) 6
+
+# 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) "d"
+
+# 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) 0
+
+# 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) 2
+
+# Convolve phase (EV 2)
+set fmri(convolve_phase2) 20
+
+# Apply temporal filtering (EV 2)
+set fmri(tempfilt_yn2) 1
+
+# Add temporal derivative (EV 2)
+set fmri(deriv_yn2) 1
+
+# Skip (EV 2)
+set fmri(skip2) 0
+
+# Off (EV 2)
+set fmri(off2) 20
+
+# On (EV 2)
+set fmri(on2) 20
+
+# Phase (EV 2)
+set fmri(phase2) 0
+
+# Stop (EV 2)
+set fmri(stop2) -1
+
+# Gamma sigma (EV 2)
+set fmri(gammasigma2) 3
+
+# Gamma delay (EV 2)
+set fmri(gammadelay2) 6
+
+# 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) "i"
+
+# 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) -1
+
+# Real contrast_real vector 1 element 4
+set fmri(con_real1.4) 0
+
+# Display images for contrast_real 2
+set fmri(conpic_real.2) 1
+
+# Title for contrast_real 2
+set fmri(conname_real.2) "d"
+
+# 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
+
+# Display images for contrast_orig 1
+set fmri(conpic_orig.1) 1
+
+# Title for contrast_orig 1
+set fmri(conname_orig.1) "i"
+
+# 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) -1
+
+# Display images for contrast_orig 2
+set fmri(conpic_orig.2) 1
+
+# Title for contrast_orig 2
+set fmri(conname_orig.2) "d"
+
+# 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
+
+# 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 2 with real contrast/F-test 1?
+set fmri(conmask2_1) 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
diff --git a/design_tem_o.fsf b/design_tem_o.fsf
new file mode 100644
index 0000000..043c015
--- /dev/null
+++ b/design_tem_o.fsf
@@ -0,0 +1,505 @@
+
+# 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-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
+
+# Output directory
+set fmri(outputdir) ""
+
+# TR(s)
+set fmri(tr) 2.0000000000
+
+# Total volumes
+set fmri(npts) 120
+
+# 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) 1
+
+# Slice timings file
+set fmri(st_file) ""
+
+# BET brain extraction
+set fmri(bet_yn) 0
+
+# Spatial smoothing FWHM (mm)
+set fmri(smooth) 6.0
+
+# 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) 2
+set fmri(ncon_real) 2
+
+# 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
+
+# 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) 90
+
+# Degrees of Freedom for registration to main structural
+set fmri(reghighres_dof) BBR
+
+# Registration to standard image?
+set fmri(regstandard_yn) 1
+
+# Use alternate reference images?
+set fmri(alternateReference_yn) 0
+
+# Standard image
+set fmri(regstandard) "/usr/local/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) 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) 60
+
+# Total voxels
+set fmri(totalVoxels) 39321600
+
+
+# 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) pathf
+
+# Add confound EVs text file
+set fmri(confoundevs) 0
+
+# Subject's structural image for analysis 1
+set highres_files(1) paths
+
+# EV 1 title
+set fmri(evtitle1) "i"
+
+# 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) 0
+
+# 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) 2
+
+# 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
+
+# Skip (EV 1)
+set fmri(skip1) 0
+
+# Off (EV 1)
+set fmri(off1) 20
+
+# On (EV 1)
+set fmri(on1) 20
+
+# Phase (EV 1)
+set fmri(phase1) 0
+
+# Stop (EV 1)
+set fmri(stop1) -1
+
+# Gamma sigma (EV 1)
+set fmri(gammasigma1) 3
+
+# Gamma delay (EV 1)
+set fmri(gammadelay1) 6
+
+# 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) "d"
+
+# 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) 0
+
+# 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) 2
+
+# Convolve phase (EV 2)
+set fmri(convolve_phase2) 20
+
+# Apply temporal filtering (EV 2)
+set fmri(tempfilt_yn2) 1
+
+# Add temporal derivative (EV 2)
+set fmri(deriv_yn2) 1
+
+# Skip (EV 2)
+set fmri(skip2) 0
+
+# Off (EV 2)
+set fmri(off2) 20
+
+# On (EV 2)
+set fmri(on2) 20
+
+# Phase (EV 2)
+set fmri(phase2) 0
+
+# Stop (EV 2)
+set fmri(stop2) -1
+
+# Gamma sigma (EV 2)
+set fmri(gammasigma2) 3
+
+# Gamma delay (EV 2)
+set fmri(gammadelay2) 6
+
+# 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) "i"
+
+# 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) -1
+
+# Real contrast_real vector 1 element 4
+set fmri(con_real1.4) 0
+
+# Display images for contrast_real 2
+set fmri(conpic_real.2) 1
+
+# Title for contrast_real 2
+set fmri(conname_real.2) "d"
+
+# 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
+
+# Display images for contrast_orig 1
+set fmri(conpic_orig.1) 1
+
+# Title for contrast_orig 1
+set fmri(conname_orig.1) "i"
+
+# 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) -1
+
+# Display images for contrast_orig 2
+set fmri(conpic_orig.2) 1
+
+# Title for contrast_orig 2
+set fmri(conname_orig.2) "d"
+
+# 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
+
+# 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 2 with real contrast/F-test 1?
+set fmri(conmask2_1) 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
diff --git a/rubyfmri1.5.rb b/rubyfmri1.5.rb
new file mode 100755
index 0000000..5050f0f
--- /dev/null
+++ b/rubyfmri1.5.rb
@@ -0,0 +1,174 @@
+#!/usr/bin/env ruby
+# the Dicom folder has to have the number of volumes in the name ex: Hand_80
+# Modules required:
+require 'rubygems'
+require 'dcm2nii-ruby'
+require 'fsl-ruby'
+require 'narray'
+require 'nifti'
+require 'chunky_png'
+require 'optparse'
+require 'prawn'
+require 'find'
+require 'fileutils'
+
+options = {}
+option_parser = OptionParser.new do |opts|
+
+  opts.on("-f DICOMDIR", "The DICOM directory") do |dicomdir|
+    options[:dicomdir] = dicomdir
+  end
+
+  #opts.on("-o OUTPUTDIR", "The output directory") do |outputdir|
+   # options[:outputdir] = outputdir
+  #end
+  
+  #opts.on("-z ZTHRESHOLD", 'The Z threshold for run feat') do |zthreshold|
+   #       options[:zthreshold]=zthreshold
+  #end
+  
+  
+  opts.on("-b BETORMASK", 'SELECT BET OR BRAIN MASK') do |betormask|
+          options[:betormask]=betormask
+  end
+
+  #opts.on("-s", "--studyInfo patfName,patlName,patId,studyDate, accessionNo", Array, "The study information for the report") do |study|
+   #   options[:study] = study
+  #end
+
+end
+
+option_parser.parse!
+
+inidicom=options[:dicomdir]
+betormask=options[:betormask]
+
+#zthreshold=options[:zthreshold]
+nvolumes=80
+zthreshold=2.3
+
+
+# CAMBIAR EL NOMBRE DE LA CARPETA QUE CONTIENE LOS DICOMS
+dirname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+completepath="#{inidicom}/#{dirname[0]}"
+newname="#{inidicom}/0DICOM"
+
+FileUtils.mv completepath, newname
+
+#CONVERT DICOM TO NIFTI
+#SE CORRE EL COMANDO DE MCVERTER
+
+`mcverter -f fsl -x -d -n -o #{inidicom} #{inidicom}`
+
+dirnewname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+dirniiname=dirnewname[1]
+
+dirniipath="#{inidicom}/#{dirniiname}"
+dirniilist=Dir.entries(dirniipath).select {|entry| File.directory? File.join(dirniipath,entry) and !(entry =='.' || entry == '..') }
+
+volaxfolder=1
+flair=1
+dirniilist.each do |name|
+  
+  isvol=name.scan("VOL_AX")
+  
+  if isvol.empty?
+    else
+      volaxfolder=name
+  end
+  
+  isflair=name.scan("FLAIR")
+  
+  if isflair.empty?
+  else
+    flair=name
+  end
+end
+
+puts volaxfolder
+dirniilist.delete(volaxfolder)
+dirniilist.delete(flair)
+
+volaxa=Dir["#{dirniipath}/#{volaxfolder}/*.nii"]
+volaxf="#{dirniipath}/#{volaxfolder}"
+volax=volaxa[0]
+newvolax="#{dirniipath}/#{volaxfolder}/volax.nii"
+FileUtils.mv volax, newvolax
+
+
+flair=Dir["#{dirniipath}/#{flair}/*.nii"]
+flairdir=Dir["#{dirniipath}/#{flair}"]
+flair_reg="#{flairdir}/flair_reg.nii"
+#### END METHODS ####
+
+beginning_time = Time.now
+
+
+
+if betormask=="1"
+  # PERFORM BRAIN EXTRACTION
+  puts "CON BET"
+  bet = FSL::BET.new(newvolax, volaxf, {fi_threshold: 0.45, v_gradient: 0})
+  bet.command
+  bet_image = bet.get_result
+
+else
+  puts "CON MASK"
+  mask_image="#{dirniipath}/#{volaxfolder}/maskedvol.nii.gz"
+  
+  `standard_space_roi #{newvolax} #{mask_image} -b`
+  bet_image="#{dirniipath}/#{volaxfolder}/maskbetvol.nii.gz"
+  puts bet_image
+   `bet  #{mask_image} #{bet_image} -f 0.15`
+end 
+
+
+#FEAT command line
+
+dirniilist.each do |dn|
+  puts  dn
+  
+nifftifiled= Dir.glob("#{dirniipath}/#{dn}/*.nii")
+nifftifile=nifftifiled[0];
+puts nifftifile
+
+isvol=nifftifile.scan("ORTOGONAL")
+
+
+if isvol.empty?
+  puts "no ortogonal"
+  `cp /Users/catalinabustamante/Documents/codigo/rubyfmri/design_tem_1.5.fsf #{dirniipath}/#{dn}/design_tem_1.5.fsf`
+  else
+    puts "ortogonal"
+  `cp /Users/catalinabustamante/Documents/codigo/rubyfmri/design_tem_1.5_o.fsf #{dirniipath}/#{dn}/design_tem_1.5.fsf`
+end
+
+
+path="#{dirniipath}/#{dn}/design_tem_1.5.fsf"
+puts path
+design = File.read(path) 
+replace=design.gsub(/set fmri\(([npts)]+)\) 80/,"set fmri(npts) #{nvolumes}")
+replace = replace.gsub(/set fmri\(([z_thresh)]+)\) 2.3/, "set fmri(z_thresh) #{zthreshold}")
+replace = replace.gsub(/set feat_files\(([1)]+)\) pathf/, "set feat_files(1) \"#{nifftifile}\"")
+replace = replace.gsub(/set highres_files\(([1)]+)\) paths/, "set highres_files(1) \"#{bet_image}\"")
+File.open(path, "w") {|file| file.puts replace}
+`feat #{path}`
+
+featpath=Dir.glob("#{dirniipath}/#{dn}/*.feat")
+featpath=featpath[0]
+    puts featpath
+
+`/usr/local/fsl/bin/renderhighres #{featpath} standard highres 1 1 15`
+ 
+if dn==dirniilist[0]
+  matriz=Dir.glob("#{featpath}/reg/highres2standard.mat")
+  `flirt -in #{flair} -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out #{flair_reg} -init #{matriz} -applyxfm`
+end
+
+
+end
+
+end_time = Time.now
+puts "Time elapsed #{(end_time - beginning_time)} seconds"
\ No newline at end of file
diff --git a/rubyfmri1.5_120din.rb b/rubyfmri1.5_120din.rb
new file mode 100755
index 0000000..01783a4
--- /dev/null
+++ b/rubyfmri1.5_120din.rb
@@ -0,0 +1,191 @@
+#!/usr/bin/env ruby
+# the Dicom folder has to have the number of volumes in the name ex: Hand_80
+# Modules required:
+require 'rubygems'
+require 'dcm2nii-ruby'
+require 'fsl-ruby'
+require 'narray'
+require 'nifti'
+require 'optparse'
+require 'find'
+require 'fileutils'
+
+options = {}
+option_parser = OptionParser.new do |opts|
+
+  opts.on("-f DICOMDIR", "The DICOM directory") do |dicomdir|
+    options[:dicomdir] = dicomdir
+  end
+
+  #opts.on("-o OUTPUTDIR", "The output directory") do |outputdir|
+   # options[:outputdir] = outputdir
+  #end
+  
+  #opts.on("-z ZTHRESHOLD", 'The Z threshold for run feat') do |zthreshold|
+   #       options[:zthreshold]=zthreshold
+  #end
+  
+  
+  opts.on("-b BETORMASK", 'SELECT BET OR BRAIN MASK') do |betormask|
+          options[:betormask]=betormask
+  end
+
+  #opts.on("-s", "--studyInfo patfName,patlName,patId,studyDate, accessionNo", Array, "The study information for the report") do |study|
+   #   options[:study] = study
+  #end
+
+end
+
+option_parser.parse!
+
+inidicom=options[:dicomdir]
+betormask=options[:betormask]
+
+#zthreshold=options[:zthreshold]
+nvolumes=120
+zthreshold=2.3
+trvalue=3.0000000000
+
+
+# CAMBIAR EL NOMBRE DE LA CARPETA QUE CONTIENE LOS DICOMS
+dirname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+completepath="#{inidicom}/#{dirname[0]}"
+newname="#{inidicom}/0DICOM"
+niifile="#{inidicom}/NIFTI"
+
+FileUtils.mkdir niifile
+
+FileUtils.mv completepath, newname
+
+#CONVERT DICOM TO NIFTI
+#SE CORRE EL COMANDO DE MCVERTER
+
+`mcverter -f fsl -x -d -n -o #{niifile} #{inidicom}`
+
+dirnewname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+dirniiname=dirnewname[1]
+
+dirniipath="#{inidicom}/#{dirniiname}"
+
+puts dirniipath
+dirniilist=Dir.entries(dirniipath).select {|entry| File.directory? File.join(dirniipath,entry) and !(entry =='.' || entry == '..') }
+
+volaxfolder=1
+flair=1
+dirniilist.each do |name|
+  
+  isvol=name.scan("VOL_AX")
+  
+  if isvol.empty?
+    else
+      puts "el volumetrico"
+      volaxfolder=name
+  end
+  
+  isflair=name.scan("FLAIR")
+  
+  if isflair.empty?
+  else
+    flair=name
+  end
+end
+puts "volaxial"
+puts volaxfolder
+dirniilist.delete(volaxfolder)
+dirniilist.delete(flair)
+
+volaxa=Dir["#{dirniipath}/#{volaxfolder}/*.nii"]
+volaxf="#{dirniipath}/#{volaxfolder}"
+volax=volaxa[0]
+newvolax="#{dirniipath}/#{volaxfolder}/volax.nii"
+FileUtils.mv volax, newvolax
+
+
+
+flair=Dir["#{dirniipath}/#{flair}/*.nii"]
+flairdir=Dir["#{dirniipath}/#{flair}"]
+#### END METHODS ####
+
+beginning_time = Time.now
+
+
+
+if betormask=="1"
+  # PERFORM BRAIN EXTRACTION
+  puts "CON BET"
+  bet = FSL::BET.new(newvolax, volaxf, {fi_threshold: 0.45, v_gradient: 0})
+  bet.command
+  bet_image = bet.get_result
+
+else
+  puts "CON MASK"
+  mask_image="#{dirniipath}/#{volaxfolder}/maskedvol.nii.gz"
+  
+  `standard_space_roi #{newvolax} #{mask_image} -b`
+  bet_image="#{dirniipath}/#{volaxfolder}/maskbetvol.nii.gz"
+  puts bet_image
+   `bet  #{mask_image} #{bet_image} -f 0.15`
+end 
+
+
+#FEAT command line
+
+dirniilist.each do |dn|
+  puts  dn
+  
+nifftifiled= Dir.glob("#{dirniipath}/#{dn}/*.nii")
+nifftifile=nifftifiled[0];
+puts nifftifile
+
+isvol=nifftifile.scan("ORTO")
+
+
+if isvol.empty?
+  puts "no ortogonal"
+  `cp /Users/investigacioniatm/Documents/codigo/rubyfmri/design_tem_1_5_120.fsf #{dirniipath}/#{dn}/design_tem_1_5_120.fsf`
+  else
+    puts "ortogonal"
+  `cp /Users/investigacioniatm/Documents/codigo/rubyfmri/design_tem_1_5_120_o.fsf #{dirniipath}/#{dn}/design_tem_1_5_120.fsf`
+end
+
+
+path="#{dirniipath}/#{dn}/design_tem_1_5_120.fsf"
+puts path
+design = File.read(path) 
+replace = design.gsub(/set fmri\(([npts)]+)\) 120/,"set fmri(npts) #{nvolumes}")
+replace = replace.gsub(/set fmri\(([z_thresh)]+)\) 2.3/, "set fmri(z_thresh) #{zthreshold}")
+replace = replace.gsub(/set feat_files\(([1)]+)\) pathf/, "set feat_files(1) \"#{nifftifile}\"")
+replace = replace.gsub(/set highres_files\(([1)]+)\) paths/, "set highres_files(1) \"#{bet_image}\"")
+File.open(path, "w") {|file| file.puts replace}
+`feat #{path}`
+
+featpath=Dir.glob("#{dirniipath}/#{dn}/*.feat")
+featpath=featpath[0]
+    puts featpath
+
+`/usr/local/fsl/bin/renderhighres #{featpath} standard highres 1 1 15`
+
+matriz= "#{featpath}/hr/background_reg.mat" 
+
+`flirt -in #{featpath}/hr/background.nii.gz -ref #{bet_image} -out #{featpath}/hr/background_reg.nii.gz -omat #{matriz} -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12  -interp trilinear`
+
+thpath=Dir.glob("#{featpath}/hr/thresh_zstat*.nii.gz")
+
+
+thpath.each do |th|
+  puts th
+  threg=th.gsub('.nii.gz', '_reg.nii.gz')
+  puts threg
+  puts flairdir
+  puts matriz
+  `flirt -in #{th} -ref #{bet_image} -init #{matriz} -out #{threg} -applyxfm`
+end
+
+
+end
+
+
+end_time = Time.now
+puts "Time elapsed #{(end_time - beginning_time)} seconds"
\ No newline at end of file
diff --git a/rubyfmri1.5_lm.rb b/rubyfmri1.5_lm.rb
new file mode 100755
index 0000000..334af5c
--- /dev/null
+++ b/rubyfmri1.5_lm.rb
@@ -0,0 +1,177 @@
+#!/usr/bin/env ruby
+# the Dicom folder has to have the number of volumes in the name ex: Hand_80
+# Modules required:
+require 'rubygems'
+require 'dcm2nii-ruby'
+require 'fsl-ruby'
+require 'narray'
+require 'nifti'
+require 'chunky_png'
+require 'optparse'
+require 'prawn'
+require 'find'
+require 'fileutils'
+
+options = {}
+option_parser = OptionParser.new do |opts|
+
+  opts.on("-f DICOMDIR", "The DICOM directory") do |dicomdir|
+    options[:dicomdir] = dicomdir
+  end
+
+  #opts.on("-o OUTPUTDIR", "The output directory") do |outputdir|
+   # options[:outputdir] = outputdir
+  #end
+  
+  #opts.on("-z ZTHRESHOLD", 'The Z threshold for run feat') do |zthreshold|
+   #       options[:zthreshold]=zthreshold
+  #end
+  
+  
+  opts.on("-b BETORMASK", 'SELECT BET OR BRAIN MASK') do |betormask|
+          options[:betormask]=betormask
+  end
+
+  #opts.on("-s", "--studyInfo patfName,patlName,patId,studyDate, accessionNo", Array, "The study information for the report") do |study|
+   #   options[:study] = study
+  #end
+
+end
+
+option_parser.parse!
+
+inidicom=options[:dicomdir]
+betormask=options[:betormask]
+
+#zthreshold=options[:zthreshold]
+nvolumes=80
+zthreshold=2.3
+
+
+# CAMBIAR EL NOMBRE DE LA CARPETA QUE CONTIENE LOS DICOMS
+dirname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+completepath="#{inidicom}/#{dirname[0]}"
+newname="#{inidicom}/0DICOM"
+niifile="#{inidicom}/NIFTI"
+FileUtils.mkdir niifile
+
+FileUtils.mv completepath, newname
+
+#CONVERT DICOM TO NIFTI
+#SE CORRE EL COMANDO DE MCVERTER
+
+`mcverter -f fsl -x -d -n -o #{niifile} #{inidicom}`
+
+dirnewname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+dirniiname=dirnewname[1]
+
+dirniipath="#{inidicom}/#{dirniiname}"
+dirniilist=Dir.entries(dirniipath).select {|entry| File.directory? File.join(dirniipath,entry) and !(entry =='.' || entry == '..') }
+
+
+volaxfolder=1
+flair=1
+dirniilist.each do |name|
+  puts name
+  isvol=name.scan("VOL")
+  
+  if isvol.empty?
+    else
+      volaxfolder=name
+  end
+  
+  isflair=name.scan("FLAIR")
+  
+  if isflair.empty?
+  else
+    flair=name
+  end
+end
+
+puts volaxfolder
+dirniilist.delete(volaxfolder)
+dirniilist.delete(flair)
+
+volaxa=Dir["#{dirniipath}/#{volaxfolder}/*.nii"]
+volaxf="#{dirniipath}/#{volaxfolder}"
+volax=volaxa[0]
+newvolax="#{dirniipath}/#{volaxfolder}/volax.nii"
+FileUtils.mv volax, newvolax
+
+
+flair=Dir["#{dirniipath}/#{flair}/*.nii"]
+flairdir=Dir["#{dirniipath}/#{flair}"]
+flair_reg="#{flairdir}/flair_reg.nii"
+#### END METHODS ####
+
+beginning_time = Time.now
+
+
+
+if betormask=="1"
+  # PERFORM BRAIN EXTRACTION
+  puts "CON BET"
+  bet = FSL::BET.new(newvolax, volaxf, {fi_threshold: 0.45, v_gradient: 0})
+  bet.command
+  bet_image = bet.get_result
+
+else
+  puts "CON MASK"
+  mask_image="#{dirniipath}/#{volaxfolder}/maskedvol.nii.gz"
+  
+  `standard_space_roi #{newvolax} #{mask_image} -b`
+  bet_image="#{dirniipath}/#{volaxfolder}/maskbetvol.nii.gz"
+  puts bet_image
+   `bet  #{mask_image} #{bet_image} -f 0.15`
+end 
+
+
+#FEAT command line
+
+dirniilist.each do |dn|
+  puts  dn
+  
+nifftifiled= Dir.glob("#{dirniipath}/#{dn}/*.nii")
+nifftifile=nifftifiled[0];
+puts nifftifile
+
+isvol=nifftifile.scan("ORTOGONAL")
+
+
+if isvol.empty?
+  puts "no ortogonal"
+  `cp /Users/investigacioniatm/Documents/codigo/rubyfmri/design_tem_1_5.fsf #{dirniipath}/#{dn}/design_tem_1.5.fsf`
+  else
+    puts "ortogonal"
+  `cp /Users/investigacioniatm/Documents/codigo/rubyfmri/design_tem_1_5_o.fsf #{dirniipath}/#{dn}/design_tem_1.5.fsf`
+end
+
+
+path="#{dirniipath}/#{dn}/design_tem_1.5.fsf"
+puts path
+design = File.read(path) 
+replace=design.gsub(/set fmri\(([npts)]+)\) 80/,"set fmri(npts) #{nvolumes}")
+replace = replace.gsub(/set fmri\(([z_thresh)]+)\) 2.3/, "set fmri(z_thresh) #{zthreshold}")
+replace = replace.gsub(/set feat_files\(([1)]+)\) pathf/, "set feat_files(1) \"#{nifftifile}\"")
+replace = replace.gsub(/set highres_files\(([1)]+)\) paths/, "set highres_files(1) \"#{bet_image}\"")
+File.open(path, "w") {|file| file.puts replace}
+`feat #{path}`
+
+featpath=Dir.glob("#{dirniipath}/#{dn}/*.feat")
+featpath=featpath[0]
+    puts featpath
+
+`/usr/local/fsl/bin/renderhighres #{featpath} standard highres 1 1 15`
+ 
+if dn==dirniilist[0]
+  matriz=Dir.glob("#{featpath}/reg/highres2standard.mat")
+  `flirt -in #{flair} -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out #{flair_reg} -init #{matriz} -applyxfm`
+end
+
+
+end
+
+end_time = Time.now
+puts "Time elapsed #{(end_time - beginning_time)} seconds"
\ No newline at end of file
diff --git a/rubyfmri3T.rb b/rubyfmri3T.rb
new file mode 100755
index 0000000..26ce3d6
--- /dev/null
+++ b/rubyfmri3T.rb
@@ -0,0 +1,191 @@
+#!/usr/bin/env ruby
+# the Dicom folder has to have the number of volumes in the name ex: Hand_80
+# Modules required:
+require 'rubygems'
+require 'dcm2nii-ruby'
+require 'fsl-ruby'
+require 'narray'
+require 'nifti'
+require 'optparse'
+require 'find'
+require 'fileutils'
+
+options = {}
+option_parser = OptionParser.new do |opts|
+
+  opts.on("-f DICOMDIR", "The DICOM directory") do |dicomdir|
+    options[:dicomdir] = dicomdir
+  end
+
+  #opts.on("-o OUTPUTDIR", "The output directory") do |outputdir|
+   # options[:outputdir] = outputdir
+  #end
+  
+  #opts.on("-z ZTHRESHOLD", 'The Z threshold for run feat') do |zthreshold|
+   #       options[:zthreshold]=zthreshold
+  #end
+  
+  
+  opts.on("-b BETORMASK", 'SELECT BET OR BRAIN MASK') do |betormask|
+          options[:betormask]=betormask
+  end
+
+  #opts.on("-s", "--studyInfo patfName,patlName,patId,studyDate, accessionNo", Array, "The study information for the report") do |study|
+   #   options[:study] = study
+  #end
+
+end
+
+option_parser.parse!
+
+inidicom=options[:dicomdir]
+betormask=options[:betormask]
+
+#zthreshold=options[:zthreshold]
+nvolumes=120
+zthreshold=2.3
+trvalue=2.0000000000
+
+
+# CAMBIAR EL NOMBRE DE LA CARPETA QUE CONTIENE LOS DICOMS
+dirname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+completepath="#{inidicom}/#{dirname[0]}"
+newname="#{inidicom}/0DICOM"
+niifile="#{inidicom}/NIFTI"
+
+FileUtils.mkdir niifile
+
+FileUtils.mv completepath, newname
+
+#CONVERT DICOM TO NIFTI
+#SE CORRE EL COMANDO DE MCVERTER
+
+`mcverter -f fsl -x -d -n -o #{niifile} #{inidicom}`
+
+dirnewname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+dirniiname=dirnewname[1]
+
+dirniipath="#{inidicom}/#{dirniiname}"
+
+puts dirniipath
+dirniilist=Dir.entries(dirniipath).select {|entry| File.directory? File.join(dirniipath,entry) and !(entry =='.' || entry == '..') }
+
+volaxfolder=1
+flair=1
+dirniilist.each do |name|
+  
+  isvol=name.scan("VOL_AX")
+  
+  if isvol.empty?
+    else
+      puts "el volumetrico"
+      volaxfolder=name
+  end
+  
+  isflair=name.scan("VISTA")
+  
+  if isflair.empty?
+  else
+    flair=name
+  end
+end
+puts "volaxial"
+puts volaxfolder
+dirniilist.delete(volaxfolder)
+dirniilist.delete(flair)
+
+volaxa=Dir["#{dirniipath}/#{volaxfolder}/*.nii"]
+volaxf="#{dirniipath}/#{volaxfolder}"
+volax=volaxa[0]
+newvolax="#{dirniipath}/#{volaxfolder}/volax.nii"
+FileUtils.mv volax, newvolax
+
+
+
+flair=Dir["#{dirniipath}/#{flair}/*.nii"]
+flairdir=Dir["#{dirniipath}/#{flair}"]
+#### END METHODS ####
+
+beginning_time = Time.now
+
+
+
+if betormask=="1"
+  # PERFORM BRAIN EXTRACTION
+  puts "CON BET"
+  bet = FSL::BET.new(newvolax, volaxf, {fi_threshold: 0.45, v_gradient: 0})
+  bet.command
+  bet_image = bet.get_result
+
+else
+  puts "CON MASK"
+  mask_image="#{dirniipath}/#{volaxfolder}/maskedvol.nii.gz"
+  
+  `standard_space_roi #{newvolax} #{mask_image} -b`
+  bet_image="#{dirniipath}/#{volaxfolder}/maskbetvol.nii.gz"
+  puts bet_image
+   `bet  #{mask_image} #{bet_image} -f 0.15`
+end 
+
+
+#FEAT command line
+
+dirniilist.each do |dn|
+  puts  dn
+  
+nifftifiled= Dir.glob("#{dirniipath}/#{dn}/*.nii")
+nifftifile=nifftifiled[0];
+puts nifftifile
+
+isvol=nifftifile.scan("ORTO")
+
+
+if isvol.empty?
+  puts "no ortogonal"
+  `cp /Users/investigacioniatm/Documents/codigo/rubyfmri/design_tem.fsf #{dirniipath}/#{dn}/design_tem.fsf`
+  else
+    puts "ortogonal"
+  `cp /Users/investigacioniatm/Documents/codigo/rubyfmri/design_tem_o.fsf #{dirniipath}/#{dn}/design_tem.fsf`
+end
+
+
+path="#{dirniipath}/#{dn}/design_tem.fsf"
+puts path
+design = File.read(path) 
+replace = design.gsub(/set fmri\(([npts)]+)\) 80/,"set fmri(npts) #{nvolumes}")
+replace = replace.gsub(/set fmri\(([z_thresh)]+)\) 2.3/, "set fmri(z_thresh) #{zthreshold}")
+replace = replace.gsub(/set feat_files\(([1)]+)\) pathf/, "set feat_files(1) \"#{nifftifile}\"")
+replace = replace.gsub(/set highres_files\(([1)]+)\) paths/, "set highres_files(1) \"#{bet_image}\"")
+File.open(path, "w") {|file| file.puts replace}
+`feat #{path}`
+
+featpath=Dir.glob("#{dirniipath}/#{dn}/*.feat")
+featpath=featpath[0]
+    puts featpath
+
+`/usr/local/fsl/bin/renderhighres #{featpath} standard highres 1 1 15`
+
+matriz= "#{featpath}/hr/background_reg.mat" 
+
+`flirt -in #{featpath}/hr/background.nii.gz -ref #{bet_image} -out #{featpath}/hr/background_reg.nii.gz -omat #{matriz} -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12  -interp trilinear`
+
+thpath=Dir.glob("#{featpath}/hr/thresh_zstat*.nii.gz")
+
+
+thpath.each do |th|
+  puts th
+  threg=th.gsub('.nii.gz', '_reg.nii.gz')
+  puts threg
+  puts flairdir
+  puts matriz
+  `flirt -in #{th} -ref #{bet_image} -init #{matriz} -out #{threg} -applyxfm`
+end
+
+
+end
+
+
+end_time = Time.now
+puts "Time elapsed #{(end_time - beginning_time)} seconds"
\ No newline at end of file
diff --git a/rubyfmri3T80.rb b/rubyfmri3T80.rb
new file mode 100755
index 0000000..9ce70e9
--- /dev/null
+++ b/rubyfmri3T80.rb
@@ -0,0 +1,178 @@
+#!/usr/bin/env ruby
+# the Dicom folder has to have the number of volumes in the name ex: Hand_80
+# Modules required:
+require 'rubygems'
+require 'dcm2nii-ruby'
+require 'fsl-ruby'
+require 'nifti'
+require 'optparse'
+require 'find'
+require 'fileutils'
+
+options = {}
+option_parser = OptionParser.new do |opts|
+
+  opts.on("-f DICOMDIR", "The DICOM directory") do |dicomdir|
+    options[:dicomdir] = dicomdir
+  end
+
+  #opts.on("-o OUTPUTDIR", "The output directory") do |outputdir|
+   # options[:outputdir] = outputdir
+  #end
+  
+  #opts.on("-z ZTHRESHOLD", 'The Z threshold for run feat') do |zthreshold|
+   #       options[:zthreshold]=zthreshold
+  #end
+  
+  
+  opts.on("-b BETORMASK", 'SELECT BET OR BRAIN MASK') do |betormask|
+          options[:betormask]=betormask
+  end
+
+  #opts.on("-s", "--studyInfo patfName,patlName,patId,studyDate, accessionNo", Array, "The study information for the report") do |study|
+   #   options[:study] = study
+  #end
+
+end
+
+option_parser.parse!
+
+inidicom=options[:dicomdir]
+betormask=options[:betormask]
+
+#zthreshold=options[:zthreshold]
+nvolumes=120
+zthreshold=2.3
+
+
+# CAMBIAR EL NOMBRE DE LA CARPETA QUE CONTIENE LOS DICOMS
+dirname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+completepath="#{inidicom}/#{dirname[0]}"
+newname="#{inidicom}/0DICOM"
+
+FileUtils.mv completepath, newname
+
+#CONVERT DICOM TO NIFTI
+#SE CORRE EL COMANDO DE MCVERTER
+
+`mcverter -f fsl -x -d -n -o #{inidicom} #{inidicom}`
+
+dirnewname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+
+dirniiname=dirnewname[1]
+
+dirniipath="#{inidicom}/#{dirniiname}"
+
+puts dirniipath
+dirniilist=Dir.entries(dirniipath).select {|entry| File.directory? File.join(dirniipath,entry) and !(entry =='.' || entry == '..') }
+
+volaxfolder=1
+flair=1
+dirniilist.each do |name|
+  
+  isvol=name.scan("MPRAGE")
+  
+  if isvol.empty?
+    else
+      volaxfolder=name
+  end
+  
+  isflair=name.scan("FL")
+  
+  if isflair.empty?
+  else
+    flair=name
+  end
+end
+
+puts volaxfolder
+dirniilist.delete(volaxfolder)
+dirniilist.delete(flair)
+
+volaxa=Dir["#{dirniipath}/#{volaxfolder}/*.nii"]
+volaxf="#{dirniipath}/#{volaxfolder}"
+volax=volaxa[0]
+newvolax="#{dirniipath}/#{volaxfolder}/volax.nii"
+FileUtils.mv volax, newvolax
+
+puts "por aqui pase"
+
+flair=Dir["#{dirniipath}/#{flair}/*.nii"]
+flairdir=Dir["#{dirniipath}/#{flair}"]
+flair_reg="#{flairdir}/flair_reg.nii"
+#### END METHODS ####
+
+beginning_time = Time.now
+
+
+
+if betormask=="1"
+  # PERFORM BRAIN EXTRACTION
+  puts "CON BET"
+  bet = FSL::BET.new(newvolax, volaxf, {fi_threshold: 0.45, v_gradient: 0})
+  bet.command
+  bet_image = bet.get_result
+
+else
+  puts "CON MASK"
+  mask_image="#{dirniipath}/#{volaxfolder}/maskedvol.nii.gz"
+  
+  `standard_space_roi #{newvolax} #{mask_image} -b`
+  bet_image="#{dirniipath}/#{volaxfolder}/maskbetvol.nii.gz"
+  puts bet_image
+   `bet  #{mask_image} #{bet_image} -f 0.15`
+end 
+
+
+#FEAT command line
+
+dirniilist.each do |dn|
+  puts  dn
+  
+nifftifiled= Dir.glob("#{dirniipath}/#{dn}/*.nii")
+nifftifile=nifftifiled[0];
+puts nifftifile
+
+isvol=nifftifile.scan("ORTO")
+
+
+if isvol.empty?
+  puts "no ortogonal"
+  `cp /Users/investigacioniatm/Documents/codigo/rubyfmri/design_tem.fsf #{dirniipath}/#{dn}/design_tem.fsf`
+  else
+    puts "ortogonal"
+  `cp cp /Users/investigacioniatm/Documents/codigo/rubyfmri/design_tem_o.fsf #{dirniipath}/#{dn}/design_tem.fsf`
+end
+
+
+path="#{dirniipath}/#{dn}/design_tem.fsf"
+puts path
+design = File.read(path) 
+replace=design.gsub(/set fmri\(([npts)]+)\) 80/,"set fmri(npts) #{nvolumes}")
+replace = replace.gsub(/set fmri\(([z_thresh)]+)\) 2.3/, "set fmri(z_thresh) #{zthreshold}")
+replace = replace.gsub(/set feat_files\(([1)]+)\) pathf/, "set feat_files(1) \"#{nifftifile}\"")
+replace = replace.gsub(/set highres_files\(([1)]+)\) paths/, "set highres_files(1) \"#{bet_image}\"")
+File.open(path, "w") {|file| file.puts replace}
+`feat #{path}`
+
+featpath=Dir.glob("#{dirniipath}/#{dn}/*.feat")
+featpath=featpath[0]
+    puts featpath
+
+`/usr/local/fsl/bin/renderhighres #{featpath} standard highres 1 1 15`
+thpath=Dir.glob("#{featpath}/hr/thresh_zstat1.nii.gz")
+puts flair
+puts thpath
+thpath_reg=Dir.glob("#{featpath}/hr/thresh_zstat1_reg.nii.gz")
+puts thpath_reg
+matriz=Dir.glob("#{featpath}/reg/standard2highres.mat")
+puts matriz
+  `flirt -in #{thpath} -ref #{flair} -out #{thpath_reg} -init #{matriz} -applyxfm`
+
+
+
+end
+
+end_time = Time.now
+puts "Time elapsed #{(end_time - beginning_time)} seconds"
\ No newline at end of file
diff --git a/surfer.log b/surfer.log
deleted file mode 100755
index 849d270..0000000
--- a/surfer.log
+++ /dev/null
@@ -1,7 +0,0 @@
-
-
-############################
-Wed Jan  9 09:27:03 COT 2013
-/Users/catalinabustamante/codigo/rubycampus
-/Applications/freesurfer//tktools/tksurfer.bin P2 lh inflated 
-############################
diff --git a/threg.rb b/threg.rb
new file mode 100644
index 0000000..10bb010
--- /dev/null
+++ b/threg.rb
@@ -0,0 +1,42 @@
+require 'rubygems'
+require 'dcm2nii-ruby'
+require 'fsl-ruby'
+require 'narray'
+require 'nifti'
+require 'chunky_png'
+require 'optparse'
+require 'prawn'
+require 'find'
+require 'fileutils'
+
+options = {}
+option_parser = OptionParser.new do |opts|
+
+  opts.on("-f DICOMDIR", "The DICOM directory") do |dicomdir|
+    options[:dicomdir] = dicomdir
+  end
+end  
+	
+	option_parser.parse!
+
+	inidicom=options[:dicomdir]
+	
+	dirname= Dir.entries(inidicom).select {|entry| File.directory? File.join(inidicom,entry) and !(entry =='.' || entry == '..') }
+	
+  
+dirname.each do |dn|
+  thpathg= Dir.glob("#{inidicom}/#{dn}/*.feat/hr")
+  puts thpathg
+  thpath="#{thpathg[0]}/thresh_zstat1.nii.gz"
+	puts thpath
+ 
+  thpath_reg="#{thpathg[0]}/thresh_zstat1_reg.nii.gz"
+  puts thpath_reg
+	matriz="/Users/catalinabustamante/Documents/PACIENTES/fMRI/Leshaw_Nicholas_Daniel/LESHAW_NICHOLAS_DANIEL/00040004926_1_1101_PIE_DER_20140515/LESHAW_NICHOLAS_DANIEL_20140515_00040004926_1_1101_PIE_DER_SENSE_PIE_DER.feat/hr/background_reg.mat"
+  puts matriz
+	
+	flair="/Users/catalinabustamante/Documents/PACIENTES/fMRI/Leshaw_Nicholas_Daniel/LESHAW_NICHOLAS_DANIEL/00040004926_1_401_FL_VISTA_20140515/LESHAW_NICHOLAS_DANIEL_20140515_00040004926_1_401_FL_VISTA_SENSE_FL_VISTA.nii"
+	
+	puts flair
+	`flirt -in #{thpath} -ref #{flair} -out #{thpath_reg} -init #{matriz} -applyxfm`
+end
\ No newline at end of file