[RESOLVED] Error (No image files match) for second level hcp_task_fmri_analysis

Issues
1

Hello everyone,
I am new to the community and I am trying to run a HCP-style task fMRI analysis on our pre-processed data. We have two runs and in the first level I specified has 6 contrasts.

Here is what I think happens: The first level runs through without a problem and the second level also has no issue until it tries to access cope7. Then it crashes because cope7 does not exist but this make sense because in the first level I only specified 6 contrasts.

Am I missing something? Are there additional contrasts that somehow implicit and which are not working? When I open my 2nd level .fsf file with feat I can’t even find anything related to that. Before that I had issues with write/read and file permissions but if this were still an issue that I’d expect none of it to run.

I am really banging my head against the keyboard here so I appreciate any even the smallest nudge in the right direction.

Here is an error log from a crash and the .fsf files. The only thing I modified is I removed all read scalar data that is float32 and similar rows like smoothing vertex XXX from the log.

Example error log

Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
mode = 11220.2
sig = 1195
Spatially smoothing auto corr estimates
.............................
Completed
Tukey M = 30
Tukey estimates... Completed
Completed
Prewhitening and Computing PEs...
Percentage done:
1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
Saving results... 
Completed
Thu Jun  8 22:11:39 CST 2023:TaskfMRILevel1.sh: MAIN: RUN_GLM: Run film_gls on cortical surface data
Thu Jun  8 22:11:39 CST 2023:TaskfMRILevel1.sh: MAIN: RUN_GLM: Prepare for film_gls
Thu Jun  8 22:12:58 CST 2023:TaskfMRILevel1.sh: MAIN: RUN_GLM: Run film_gls on surface data
Log directory is: /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results/tfMRI_OLMr_RUN1_AP/tfMRI_OLMr_RUN1_AP_hp200_s4_level1.feat/L_SurfaceStats
read gifti 

paradigm.getDesignMatrix().Nrows()=928
paradigm.getDesignMatrix().Ncols()=14
sizeTS=928
numTS=32492
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
read gifti 
Spatially smoothing auto corr estimates for surface
do smooth
done distances

Completed
Thu Jun  8 23:55:03 CST 2023:TaskfMRILevel1.sh: MAIN: RUN_GLM: Merge Cortical Surface and Subcortical Volume into Grayordinates
Thu Jun  8 23:56:16 CST 2023:TaskfMRILevel1.sh: MAIN: Complete
Thu Jun  8 23:56:16 CST 2023:TaskfMRIAnalysis.sh: RUN_LEVEL2: Combine Data Across Phase Encoding Directions in the Level 2 Analysis
Thu Jun  8 23:56:16 CST 2023:TaskfMRIAnalysis.sh: RUN_LEVEL2: Issuing command: /opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh R0111_7TSESS1 /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/fsaverage_LR32k tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP tfMRI_OLMr tfMRI_OLMr 32 4 200 NO NONE NONE NONE NONE
Thu Jun  8 23:56:16 CST 2023:TaskfMRILevel2.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Thu Jun  8 23:56:16 CST 2023:TaskfMRILevel2.sh: FSLDIR: /opt/fsl/fsl
Thu Jun  8 23:56:16 CST 2023:TaskfMRILevel2.sh: CARET7DIR: /opt/workbench/workbench/bin_rh_linux64
Thu Jun  8 23:56:16 CST 2023:TaskfMRILevel2.sh: TOOL_VERSIONS: Showing HCP Pipelines version
v4.6.0-rc-30d3848
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: TOOL_VERSIONS: Showing Connectome Workbench (wb_command) version
Connectome Workbench
Type: Command Line Application
Version: 1.5.0
Qt Compiled Version: 5.7.0
Qt Runtime Version: 5.7.0
Commit: 76441605d20536d81034a64c9d34ec393aa528b9
Commit Date: 2021-02-16 13:46:47 -0600
Compiled with OpenMP: YES
Compiler: g++ (/export/gcc-4.8.5/bin)
Compiler Version: 4.8.5
Compiled Debug: NO
Operating System: Linux
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: INFO: Determined that the FSL version in use is 6.0.5.1:57b01774
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: TaskfMRILevel2.sh arguments: R0111_7TSESS1 /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/fsaverage_LR32k tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP tfMRI_OLMr tfMRI_OLMr 32 4 200 NO NONE NONE NONE NONE
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: Subject: R0111_7TSESS1
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: ResultsFolder: /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: DownSampleFolder: /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/fsaverage_LR32k
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: LevelOnefMRINames: tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: LevelOnefsfNames: tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: LevelTwofMRIName: tfMRI_OLMr
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: LevelTwofsfName: tfMRI_OLMr
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: LowResMesh: 32
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: FinalSmoothingFWHM: 4
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: TemporalFilter: 200
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: VolumeBasedProcessing: NO
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: RegName: NONE
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: Parcellation: NONE
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: ProcSTRING: NONE
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: READ_ARGS: TemporalSmoothing: NONE
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES: Dense Analysis requested
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES: Analyses: GrayordinatesStats 
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES: ParcellationString: 
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES: ExtensionList: dtseries.nii 
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES: ScalarExtensionList: dscalar.nii 
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: MAIN: SET_NAME_STRINGS: SmoothingString: _s4
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: MAIN: SET_NAME_STRINGS: TemporalFilterString: _hp200
Thu Jun  8 23:56:17 CST 2023:TaskfMRILevel2.sh: MAIN: SET_NAME_STRINGS: RegString: 
Thu Jun  8 23:56:19 CST 2023:TaskfMRILevel2.sh: CHECK INPUTS: Necessary input files exist
Thu Jun  8 23:56:19 CST 2023:TaskfMRILevel2.sh: Make design files
Thu Jun  8 23:56:20 CST 2023:TaskfMRILevel2.sh: Loop over Level 2 Analyses requested: GrayordinatesStats 
Thu Jun  8 23:56:20 CST 2023:TaskfMRILevel2.sh: Run Analysis: GrayordinatesStats
Thu Jun  8 23:56:20 CST 2023:TaskfMRILevel2.sh: Copy over Level 1 stats folders and convert CIFTI to NIFTI if required
Thu Jun  8 23:56:38 CST 2023:TaskfMRILevel2.sh: Convert CIFTI files to fakeNIFTI
Thu Jun  8 23:58:31 CST 2023:TaskfMRILevel2.sh: Create dof and Mask files for input to flameo (Level 2 analysis)
Thu Jun  8 23:58:42 CST 2023:TaskfMRILevel2.sh: Merge COPES and VARCOPES for 10 Contrasts
Thu Jun  8 23:58:42 CST 2023:TaskfMRILevel2.sh: Contrast Number: 1
Thu Jun  8 23:58:43 CST 2023:TaskfMRILevel2.sh: Contrast Number: 2
Thu Jun  8 23:58:43 CST 2023:TaskfMRILevel2.sh: Contrast Number: 3
Thu Jun  8 23:58:43 CST 2023:TaskfMRILevel2.sh: Contrast Number: 4
Thu Jun  8 23:58:44 CST 2023:TaskfMRILevel2.sh: Contrast Number: 5
Thu Jun  8 23:58:46 CST 2023:TaskfMRILevel2.sh: Contrast Number: 6
Thu Jun  8 23:58:47 CST 2023:TaskfMRILevel2.sh: Contrast Number: 7
Image Exception : #63 :: No image files match: /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results/tfMRI_OLMr/tfMRI_OLMr_hp200_s4_level2.feat/GrayordinatesStats/1/cope7
terminate called after throwing an instance of 'std::runtime_error'
  what():  No image files match: /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results/tfMRI_OLMr/tfMRI_OLMr_hp200_s4_level2.feat/GrayordinatesStats/1/cope7
/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh: line 294: 68933 Aborted                 fslmerge -t ${LevelTwoFEATDir}/${Analysis}/cope${copeCounter}.nii.gz $COPEMERGE
Thu Jun  8 23:58:47 CST 2023:TaskfMRILevel2.sh: While running '/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh R0111_7TSESS1 /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/fsaverage_LR32k tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP tfMRI_OLMr tfMRI_OLMr 32 4 200 NO NONE NONE NONE NONE':
Thu Jun  8 23:58:47 CST 2023:TaskfMRILevel2.sh: ERROR: 'fslmerge' command failed with return code: 134
Thu Jun  8 23:58:47 CST 2023:TaskfMRILevel2.sh: ERROR: 'fslmerge' command failed with return code: 134

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: TaskfMRILevel2.sh
stopped at line: 354
           call: fslmerge -t ${LevelTwoFEATDir}/${Analysis}/cope${copeCounter}.nii.gz $COPEMERGE
  expanded call: fslmerge -t /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results/tfMRI_OLMr/tfMRI_OLMr_hp200_s4_level2.feat/GrayordinatesStats/cope7.nii.gz /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results/tfMRI_OLMr/tfMRI_OLMr_hp200_s4_level2.feat/GrayordinatesStats/1/cope7.nii.gz /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results/tfMRI_OLMr/tfMRI_OLMr_hp200_s4_level2.feat/GrayordinatesStats/2/cope7.nii.gz
       hostname: bnode05
      exit code: 134
---------------------------------------------------

===> Aborting execution!

Thu Jun  8 23:58:47 CST 2023:TaskfMRIAnalysis.sh: While running '/opt/HCP/HCPpipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.sh --study-folder=/home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp --subject=R0111_7TSESS1 --lvl1tasks=tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP --lvl2task=tfMRI_OLMr --confound=Confound_Parameters.txt --origsmoothingFWHM=2 --finalsmoothingFWHM=4 --highpassfilter=200':
Thu Jun  8 23:58:47 CST 2023:TaskfMRIAnalysis.sh: ERROR: '/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh' command failed with return code: 134
Thu Jun  8 23:58:47 CST 2023:TaskfMRIAnalysis.sh: ERROR: '/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh' command failed with return code: 134

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: TaskfMRIAnalysis.sh
stopped at line: 259
           call: ${HCPPIPEDIR_tfMRIAnalysis}/TaskfMRILevel2.sh $Subject $ResultsFolder $DownSampleFolder $LevelOnefMRINames $LevelOnefsfNames $LevelTwofMRIName $LevelTwofsfName $LowResMesh $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing $RegName $Parcellation $ProcSTRING $TemporalSmoothing
  expanded call: /opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh R0111_7TSESS1 /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/Results /home1/Jaquent/VP00157_HCP/sessions/R0111_7TSESS1/hcp/R0111_7TSESS1/MNINonLinear/fsaverage_LR32k tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP tfMRI_OLMr tfMRI_OLMr 32 4 200 NO NONE NONE NONE NONE
       hostname: bnode05
      exit code: 134
---------------------------------------------------

===> Aborting execution!
2

Because of length limitations here is the rest:

First level .fsf from Run 1


# 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) 1

# Cleanup first-level standard-space images
set fmri(sscleanup_yn) 0

# Output directory
set fmri(outputdir) "tfMRI_OLMr_RUN2_AP_hp200_s4_level1"

# TR(s)
set fmri(tr) 1

# Total volumes
set fmri(npts) 123

# 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) 3.09

# Noise level
set fmri(noise) 0.412671

# Noise AR(1)
set fmri(noisear) 0.189

# 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

# GDC Test
set fmri(gdc) ""

# EPI dwell time (ms)
set fmri(dwell) 0.0

# EPI TE (ms)
set fmri(te) 0.0

# % 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) 0

# Spatial smoothing FWHM (mm)
set fmri(smooth) 4

# 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

# Higher-level permutations
set fmri(randomisePermutations) 5000

# Number of EVs
set fmri(evs_orig) 4
set fmri(evs_real) 8
set fmri(evs_vox) 0

# 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

# 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) 0

# P threshold
set fmri(prob_thresh) 0.05

# Z threshold
set fmri(z_thresh) 3.1

# 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) 0

# Registration to initial structural
set fmri(reginitial_highres_yn) 0

# Search space for registration to initial structural
# 0   : No search
# 90  : Normal search
# 180 : Full search
set fmri(reginitial_highres_search) 90

# Degrees of Freedom for registration to initial structural
set fmri(reginitial_highres_dof) 3

# Registration to main structural
set fmri(reghighres_yn) 0

# Search space for registration to main structural
# 0   : No search
# 90  : Normal search
# 180 : Full search
set fmri(reghighres_search) 90

# Degrees of Freedom for registration to main structural
set fmri(reghighres_dof) BBR

# Registration to standard image?
set fmri(regstandard_yn) 0

# Use alternate reference images?
set fmri(alternateReference_yn) 0

# Standard image
set fmri(regstandard) "/share/apps/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) 100

# Number of lower-level copes feeding into higher-level analysis
set fmri(ncopeinputs) 0

# 4D AVW data or FEAT directory (1)
set feat_files(1) "../tfMRI_OLMr_RUN2_AP"

# Add confound EVs text file
set fmri(confoundevs) 0

# EV 1 title
set fmri(evtitle1) "con"

# 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
# 8 : Alternate Double-Gamma
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) "../EVs/reg2_control.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

# Orthogonalise EV 1 wrt EV 3
set fmri(ortho1.3) 0

# Orthogonalise EV 1 wrt EV 4
set fmri(ortho1.4) 0

# EV 2 title
set fmri(evtitle2) "con_PM"

# 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
# 8 : Alternate Double-Gamma
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) "../EVs/reg2_control_PM.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

# Orthogonalise EV 2 wrt EV 3
set fmri(ortho2.3) 0

# Orthogonalise EV 2 wrt EV 4
set fmri(ortho2.4) 0

# EV 3 title
set fmri(evtitle3) "ret"

# Basic waveform shape (EV 3)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
# 10 : Empty (all zeros)
set fmri(shape3) 3

# Convolution (EV 3)
# 0 : None
# 1 : Gaussian
# 2 : Gamma
# 3 : Double-Gamma HRF
# 4 : Gamma basis functions
# 5 : Sine basis functions
# 6 : FIR basis functions
# 8 : Alternate Double-Gamma
set fmri(convolve3) 3

# Convolve phase (EV 3)
set fmri(convolve_phase3) 0

# Apply temporal filtering (EV 3)
set fmri(tempfilt_yn3) 1

# Add temporal derivative (EV 3)
set fmri(deriv_yn3) 1

# Custom EV file (EV 3)
set fmri(custom3) "../EVs/reg2_retrieval.txt"

# Orthogonalise EV 3 wrt EV 0
set fmri(ortho3.0) 0

# Orthogonalise EV 3 wrt EV 1
set fmri(ortho3.1) 0

# Orthogonalise EV 3 wrt EV 2
set fmri(ortho3.2) 0

# Orthogonalise EV 3 wrt EV 3
set fmri(ortho3.3) 0

# Orthogonalise EV 3 wrt EV 4
set fmri(ortho3.4) 0

# EV 4 title
set fmri(evtitle4) "ret_PM"

# Basic waveform shape (EV 4)
# 0 : Square
# 1 : Sinusoid
# 2 : Custom (1 entry per volume)
# 3 : Custom (3 column format)
# 4 : Interaction
# 10 : Empty (all zeros)
set fmri(shape4) 3

# Convolution (EV 4)
# 0 : None
# 1 : Gaussian
# 2 : Gamma
# 3 : Double-Gamma HRF
# 4 : Gamma basis functions
# 5 : Sine basis functions
# 6 : FIR basis functions
# 8 : Alternate Double-Gamma
set fmri(convolve4) 3

# Convolve phase (EV 4)
set fmri(convolve_phase4) 0

# Apply temporal filtering (EV 4)
set fmri(tempfilt_yn4) 1

# Add temporal derivative (EV 4)
set fmri(deriv_yn4) 1

# Custom EV file (EV 4)
set fmri(custom4) "../EVs/reg2_retrieval_PM.txt"

# Orthogonalise EV 4 wrt EV 0
set fmri(ortho4.0) 0

# Orthogonalise EV 4 wrt EV 1
set fmri(ortho4.1) 0

# Orthogonalise EV 4 wrt EV 2
set fmri(ortho4.2) 0

# Orthogonalise EV 4 wrt EV 3
set fmri(ortho4.3) 0

# Orthogonalise EV 4 wrt EV 4
set fmri(ortho4.4) 0

# 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) "con"

# Real contrast_real vector 1 element 1
set fmri(con_real1.1) 1.0

# 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

# Display images for contrast_real 2
set fmri(conpic_real.2) 1

# Title for contrast_real 2
set fmri(conname_real.2) "con_PM"

# Real contrast_real vector 2 element 1
set fmri(con_real2.1) 0

# Real contrast_real vector 2 element 2
set fmri(con_real2.2) 0

# Real contrast_real vector 2 element 3
set fmri(con_real2.3) 1.0

# Real contrast_real vector 2 element 4
set fmri(con_real2.4) 0

# Real contrast_real vector 2 element 5
set fmri(con_real2.5) 0

# Real contrast_real vector 2 element 6
set fmri(con_real2.6) 0

# Real contrast_real vector 2 element 7
set fmri(con_real2.7) 0

# Real contrast_real vector 2 element 8
set fmri(con_real2.8) 0

# Display images for contrast_real 3
set fmri(conpic_real.3) 1

# Title for contrast_real 3
set fmri(conname_real.3) "ret"

# Real contrast_real vector 3 element 1
set fmri(con_real3.1) 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) 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) 1.0

# Real contrast_real vector 3 element 6
set fmri(con_real3.6) 0

# Real contrast_real vector 3 element 7
set fmri(con_real3.7) 0

# Real contrast_real vector 3 element 8
set fmri(con_real3.8) 0

# Display images for contrast_real 4
set fmri(conpic_real.4) 1

# Title for contrast_real 4
set fmri(conname_real.4) "ret_PM"

# Real contrast_real vector 4 element 1
set fmri(con_real4.1) 0

# Real contrast_real vector 4 element 2
set fmri(con_real4.2) 0

# Real contrast_real vector 4 element 3
set fmri(con_real4.3) 0

# Real contrast_real vector 4 element 4
set fmri(con_real4.4) 0

# Real contrast_real vector 4 element 5
set fmri(con_real4.5) 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

# Display images for contrast_real 5
set fmri(conpic_real.5) 1

# Title for contrast_real 5
set fmri(conname_real.5) "ret - con"

# 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) 1

# 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

# Display images for contrast_real 6
set fmri(conpic_real.6) 1

# Title for contrast_real 6
set fmri(conname_real.6) "ret_PM - con_PM"

# 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) -1.0

# 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) 1.0

# Real contrast_real vector 6 element 8
set fmri(con_real6.8) 0

# Display images for contrast_orig 1
set fmri(conpic_orig.1) 1

# Title for contrast_orig 1
set fmri(conname_orig.1) "con"

# Real contrast_orig vector 1 element 1
set fmri(con_orig1.1) 1.0

# 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

# Display images for contrast_orig 2
set fmri(conpic_orig.2) 1

# Title for contrast_orig 2
set fmri(conname_orig.2) "con_PM"

# Real contrast_orig vector 2 element 1
set fmri(con_orig2.1) 0

# Real contrast_orig vector 2 element 2
set fmri(con_orig2.2) 1.0

# Real contrast_orig vector 2 element 3
set fmri(con_orig2.3) 0

# Real contrast_orig vector 2 element 4
set fmri(con_orig2.4) 0

# Display images for contrast_orig 3
set fmri(conpic_orig.3) 1

# Title for contrast_orig 3
set fmri(conname_orig.3) "ret"

# Real contrast_orig vector 3 element 1
set fmri(con_orig3.1) 0

# 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) 1.0

# Real contrast_orig vector 3 element 4
set fmri(con_orig3.4) 0

# Display images for contrast_orig 4
set fmri(conpic_orig.4) 1

# Title for contrast_orig 4
set fmri(conname_orig.4) "ret_PM"

# Real contrast_orig vector 4 element 1
set fmri(con_orig4.1) 0

# Real contrast_orig vector 4 element 2
set fmri(con_orig4.2) 0

# Real contrast_orig vector 4 element 3
set fmri(con_orig4.3) 0

# Real contrast_orig vector 4 element 4
set fmri(con_orig4.4) 1

# Display images for contrast_orig 5
set fmri(conpic_orig.5) 1

# Title for contrast_orig 5
set fmri(conname_orig.5) "ret - con"

# 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) 1

# Real contrast_orig vector 5 element 4
set fmri(con_orig5.4) 0

# Display images for contrast_orig 6
set fmri(conpic_orig.6) 1

# Title for contrast_orig 6
set fmri(conname_orig.6) "ret_PM - con_PM"

# 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) -1.0

# 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) 1.0

# Contrast masking - use >0 instead of thresholding?
set fmri(conmask_zerothresh_yn) 0

# Mask real contrast/F-test 1 with real contrast/F-test 2?
set fmri(conmask1_2) 0

# Mask real contrast/F-test 1 with real contrast/F-test 3?
set fmri(conmask1_3) 0

# Mask real contrast/F-test 1 with real contrast/F-test 4?
set fmri(conmask1_4) 0

# Mask real contrast/F-test 1 with real contrast/F-test 5?
set fmri(conmask1_5) 0

# Mask real contrast/F-test 1 with real contrast/F-test 6?
set fmri(conmask1_6) 0

# Mask real contrast/F-test 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

Second level .fsf


# 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) 2

# 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) 2

# 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) "tfMRI_OLMr_hp200_s4"

# TR(s)
set fmri(tr) 3

# Total volumes
set fmri(npts) 2

# Delete volumes
set fmri(ndelete) 0

# Perfusion tag/control order
set fmri(tagfirst) 1

# Number of first-level analyses
set fmri(multiple) 2

# 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) 0

# Brain/background threshold, %
set fmri(brain_thresh) 10

# Critical z for design efficiency calculation
set fmri(critical_z) 5.3

# Noise level
set fmri(noise) 0.66

# Noise AR(1)
set fmri(noisear) 0.34

# 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

# GDC Test
set fmri(gdc) ""

# EPI dwell time (ms)
set fmri(dwell) 0.0

# EPI TE (ms)
set fmri(te) 0.0

# % Signal loss threshold
set fmri(signallossthresh) 10

# Unwarp direction
set fmri(unwarp_dir) y-

# Slice timing correction
# 0 : None
# 1 : Regular up (0, 1, 2, 3, ...)
# 2 : Regular down
# 3 : Use slice order file
# 4 : Use slice timings file
# 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )
set fmri(st) 0

# Slice timings file
set fmri(st_file) ""

# BET brain extraction
set fmri(bet_yn) 1

# Spatial smoothing FWHM (mm)
set fmri(smooth) 5

# Intensity normalization
set fmri(norm_yn) 0

# Perfusion subtraction
set fmri(perfsub_yn) 0

# Highpass temporal filtering
set fmri(temphp_yn) 1

# Lowpass temporal filtering
set fmri(templp_yn) 0

# MELODIC ICA data exploration
set fmri(melodic_yn) 0

# Carry out main stats?
set fmri(stats_yn) 1

# Carry out prewhitening?
set fmri(prewhiten_yn) 1

# Add motion parameters to model
# 0 : No
# 1 : Yes
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) 3

# Higher-level permutations
set fmri(randomisePermutations) 5000

# Number of EVs
set fmri(evs_orig) 1
set fmri(evs_real) 1
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) 0

# 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) 3.1

# 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) 0

# Search space for registration to main structural
# 0   : No search
# 90  : Normal search
# 180 : Full search
set fmri(reghighres_search) 90

# Degrees of Freedom for registration to main structural
set fmri(reghighres_dof) BBR

# Registration to standard image?
set fmri(regstandard_yn) 1

# Use alternate reference images?
set fmri(alternateReference_yn) 0

# Standard image
set fmri(regstandard) "/public/software/apps/FSL/6.0.6.4/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) 100

# Number of lower-level copes feeding into higher-level analysis
set fmri(ncopeinputs) 0

# 4D AVW data or FEAT directory (1)
set feat_files(1) "../../tfMRI_OLMr_RUN1_AP/tfMRI_OLMr_RUN1_AP_hp200_s4.feat"

# 4D AVW data or FEAT directory (2)
set feat_files(2) "../../tfMRI_OLMr_RUN2_AP/tfMRI_OLMr_RUN2_AP_hp200_s4.feat"

# Add confound EVs text file
set fmri(confoundevs) 0

# 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) 2

# 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
# 8 : Alternate Double-Gamma
set fmri(convolve1) 0

# Convolve phase (EV 1)
set fmri(convolve_phase1) 0

# Apply temporal filtering (EV 1)
set fmri(tempfilt_yn1) 0

# Add temporal derivative (EV 1)
set fmri(deriv_yn1) 0

# Custom EV file (EV 1)
set fmri(custom1) "dummy"

# Orthogonalise EV 1 wrt EV 0
set fmri(ortho1.0) 0

# Orthogonalise EV 1 wrt EV 1
set fmri(ortho1.1) 0

# Higher-level EV value for EV 1 and input 1
set fmri(evg1.1) 1

# Higher-level EV value for EV 1 and input 2
set fmri(evg2.1) 1.0

# Group membership for input 1
set fmri(groupmem.1) 1

# Group membership for input 2
set fmri(groupmem.2) 1

# Contrast & F-tests mode
# real : control real EVs
# orig : control original EVs
set fmri(con_mode_old) real
set fmri(con_mode) real

# Display images for contrast_real 1
set fmri(conpic_real.1) 1

# Title for contrast_real 1
set fmri(conname_real.1) "group mean"

# Real contrast_real vector 1 element 1
set fmri(con_real1.1) 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

Qunex command

python3 qunex_container hcp_task_fmri_analysis \
--sessionsfolder="/home1/Jaquent/VP00157_HCP/sessions/" \
--sessions="/home1/Jaquent/VP00157_HCP/processing/sessions_hcp_batch.txt" \
--sessionids="R0076_7TSESS1" \
--overwrite="yes" \
--bash_pre="module load singularity" \
--hcp_task_lvl1tasks="tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP" \
--hcp_task_lvl2task="tfMRI_OLMr" \
--hcp_task_highpass="200" \
--hcp_bold_final_smoothFWHM="4" \
--hcp_task_confound="Confound_Parameters.txt" \
--container="/home1/Jaquent/Toolboxes/my_images/qunex_suite-0.95.2.sif" \
--scheduler="SLURM,time=2-00:00:00, mem-per-cpu=10GB, jobname=gridAdapt"
3

Hi,

Welcome to QuNex forums! Could you also provide the top of the error log, the portion where the HCP command call is specified. Just to confirm that QuNex properly maps all parameters to HCP parameters. At a glance I do not see any issues with that, so the issue must be either in the .fsf file or there is a bug in HCP Pipelines.

As we mainly use other QuNex commands for task analyses, I won’t be able to be much help here unfortunately. I suggest you try asking on HCP users group (https://groups.google.com/a/humanconnectome.org/g/hcp-users), provide them the HCP command call (the call at the top of the log file) and fsf files.

Sorry, I could not help you out more here. I will ask my colleagues if someone has more experience with fsf files to jump in.

Jure

4

Do you mean this file:

Singularity 3.7.1 loaded
--> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXLIBRARY QUNEXLIBRARYETC TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR ANTSDIR PYLIBDIR FSLDIR FSLGPUDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder FSL_GPU_SCRIPTS FSLGPUBinary EDDYCUDADIR USEOCTAVE QUNEXENV CONDADIR MSMBINDIR MSMCONFIGDIR R_LIBS FSL_FIX_CIFTIRW FSFAST_HOME SUBJECTS_DIR MINC_BIN_DIR MNI_DIR MINC_LIB_DIR MNI_DATAPATH FSF_OUTPUT_FORMAT
[32m [0m
[32mGenerated by QuNex [0m
[32m------------------------------------------------------------------------ [0m
[32mVersion: 0.95.2 [0m
[32mUser: Jaquent [0m
[32mSystem: bnode16 [0m
[32mOS: RedHat Linux #1 SMP Fri Apr 20 16:44:24 UTC 2018 [0m
[32m------------------------------------------------------------------------ [0m
[32m [0m
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[32m [0m
[32m                       DEVELOPED & MAINTAINED BY: [0m
[32m [0m
[32m                    Anticevic Lab, Yale University [0m
[32m               Mind & Brain Lab, University of Ljubljana [0m
[32m                     Murray Lab, Yale University [0m
[32m [0m
[32m                      COPYRIGHT & LICENSE NOTICE: [0m
[32m [0m
[32mUse of this software is subject to the terms and conditions defined in [0m
[32m'LICENSES' which is a part of the QuNex Suite source code package: [0m
[32mhttps://gitlab.qunex.yale.edu/qunex/qunex/-/tree/master/LICENSES [0m
[32m [0m
[36m ---> Setting up Octave  [0m


[32m ........................ Running QuNex v0.95.2 ........................ [0m


[36m--- Full QuNex call for command: hcp_task_fmri_analysis [0m

[36mgmri hcp_task_fmri_analysis --sessionsfolder="/home1/Jaquent/VP00157_HCP/sessions/" --overwrite="yes" --hcp_task_lvl1tasks="tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP" --hcp_task_lvl2task="tfMRI_OLMr" --hcp_task_highpass="200" --hcp_bold_final_smoothFWHM="4" --hcp_task_confound="Confound_Parameters.txt" --sessions="/home1/Jaquent/VP00157_HCP/processing/sessions_hcp_batch.txt" --sessionids="R0093_7TSESS1" [0m

[36m--------------------------------------------------------- [0m


WARNING: passing the batchfile through the sessions parameter will be deprecated, please use the batchfile parameter!
WARNING: the sessionids parameter will be deprecated, please use the sessions parameter!
WARNING: Parameter qx_cifti_tail was not specified. Its value was imputed from parameter hcp_cifti_tail and set to '_Atlas'!
WARNING: Parameter qx_nifti_tail was not specified. Its value was imputed from parameter hcp_nifti_tail and set to ''!
WARNING: Parameter cifti_tail was not specified. Its value was imputed from parameter qx_cifti_tail and set to '_Atlas'!
WARNING: Parameter nifti_tail was not specified. Its value was imputed from parameter qx_nifti_tail and set to ''!

# Generated by QuNex 0.95.2 on 2023-06-09_11.14.51.531346
#
=================================================================
gmri hcp_task_fmri_analysis \
  --sessionsfolder="/home1/Jaquent/VP00157_HCP/sessions/" \
  --overwrite="yes" \
  --hcp_task_lvl1tasks="tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP" \
  --hcp_task_lvl2task="tfMRI_OLMr" \
  --hcp_task_highpass="200" \
  --hcp_bold_final_smoothFWHM="4" \
  --hcp_task_confound="Confound_Parameters.txt" \
  --sessions="/home1/Jaquent/VP00157_HCP/processing/sessions_hcp_batch.txt" \
  --sessionids="R0093_7TSESS1" \
=================================================================

Starting multiprocessing sessions in /home1/Jaquent/VP00157_HCP/processing/sessions_hcp_batch.txt with a pool of 1 concurrent processes

---- Running local

Starting processing of sessions R0093_7TSESS1 at Friday, 09. June 2023 11:14:51
Running external command: /opt/HCP/HCPpipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.sh                 --study-folder="/home1/Jaquent/VP00157_HCP/sessions/R0093_7TSESS1/hcp"                 --subject="R0093_7TSESS1"                 --lvl1tasks="tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP"                 --lvl2task="tfMRI_OLMr"                --confound="Confound_Parameters.txt"                --origsmoothingFWHM="2"                --finalsmoothingFWHM="4"                --highpassfilter="200"

You can follow command's progress in:
/home1/Jaquent/VP00157_HCP/processing/logs/comlogs/tmp_hcp_task_fmri_analysis_R0093_7TSESS1_2023-06-09_11.14.51.535472.log
------------------------------------------------------------

------------------------------------------------------------
Session id: R0093_7TSESS1 
[started on Friday, 09. June 2023 11:14:51]
Running HCP fMRI task analysis pipeline [HCPStyleData] ...

------------------------------------------------------------
Running HCP Pipelines command via QuNex:

/opt/HCP/HCPpipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.sh 
    --study-folder="/home1/Jaquent/VP00157_HCP/sessions/R0093_7TSESS1/hcp" 
    --subject="R0093_7TSESS1" 
    --lvl1tasks="tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP" 
    --lvl2task="tfMRI_OLMr"
    --confound="Confound_Parameters.txt"
    --origsmoothingFWHM="2"
    --finalsmoothingFWHM="4"
    --highpassfilter="200"
------------------------------------------------------------


Running HCP fMRI task analysis

ERROR: Running HCP fMRI task analysis failed with error 134
... 
command executed:
/opt/HCP/HCPpipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.sh                 --study-folder="/home1/Jaquent/VP00157_HCP/sessions/R0093_7TSESS1/hcp"                 --subject="R0093_7TSESS1"                 --lvl1tasks="tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP"                 --lvl2task="tfMRI_OLMr"                --confound="Confound_Parameters.txt"                --origsmoothingFWHM="2"                --finalsmoothingFWHM="4"                --highpassfilter="200"

---> logfile: /home1/Jaquent/VP00157_HCP/processing/logs/comlogs/error_hcp_task_fmri_analysis_R0093_7TSESS1_2023-06-09_11.14.51.535472.log

HCP fMRI task analysis Preprocessing completed on Friday, 09. June 2023 13:01:58
------------------------------------------------------------


===> Final report for command hcp_task_fmri_analysis
... R0093_7TSESS1 ---> Error
===> Not all tasks completed fully!
rm: cannot remove \u2018/home1/Jaquent/tmp3k4xidjw\u2019: No such file or directory
5

Yes, the outgoing call can be found as:

/opt/HCP/HCPpipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.sh \
    --study-folder="/home1/Jaquent/VP00157_HCP/sessions/R0093_7TSESS1/hcp" \
    --subject="R0093_7TSESS1" \
    --lvl1tasks="tfMRI_OLMr_RUN1_AP@tfMRI_OLMr_RUN2_AP" \
    --lvl2task="tfMRI_OLMr" \
    --confound="Confound_Parameters.txt" \
    --origsmoothingFWHM="2" \
    --finalsmoothingFWHM="4" \
    --highpassfilter="200"

Above call looks perfectly fine. Did you maybe as a test try specifying less than 6 contrasts. Say, if you specify 4 contrasts, will it crash looking for the cope5 then?

Jure

6

No but that’s a great idea. I will try this.

Update: It’s working now but I don’t know why. Maybe the contrast names were the issue but I will have to investigate this.

7

Hi,

are there any updates regarding this issue? Did you manage to resolve it?

Jure

8

Hey Jure,
thanks for checking in. Yes, it seems to work now without an issue. The only thing that I can see that was different was that when I choose a name with space (" ") in it that it works for the copes that exists but somehow seem to add more than they are and then crash.

Best,
Alex

9

Spaces should be avoided in names and paths if possible. Spaces are often used as delimiters in various pipelines and tools, e.g. SESSION 1 might be split at the space and interpreted as a list of two values (SESSION and 1). We try to be robust regarding this in QuNex, but we often have no control about how the tools that we use interpret this.