Hi all, I've been using the HCPpipelines scripts for preprocessing / task-analysis, but am having trouble with the level2 task analysis. I'm running the current latest (v3.27.0), and have modeled my files similar to the FSF templates <https://github.com/Washington-University/HCPpipelines/tree/v3.27.0/Examples/fsf_templates> on the repo.
I've attached a log of my output, as well as a level 2 design fsf from a particular task (made up of 4 runs). Any suggestions would be appreciated, thank you. Cheers, Mathias _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
/opt/HCP-Pipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.sh --path=/output
--subject=sub-BANDA001 --lvl1tasks=task-conflict_run-01_bold
--lvl1fsfs=task-conflict_run-01_bold --lvl2task=NONE --lvl2fsf=NONE
--lowresmesh=32 --grayordinatesres=2 --origsmoothingFWHM=2 --confound="NONE"
--finalsmoothingFWHM=4 --temporalfilter=200 --vba="NO" --regname="NONE"
--parcellation=MMP
--parcellationfile=/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Parsing Command
Line Options
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Path: /output
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Subject:
sub-BANDA001
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelOnefMRINames: task-conflict_run-01_bold
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelOnefsfNames: task-conflict_run-01_bold
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelTwofMRIName: NONE
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelTwofsfNames: NONE
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: LowResMesh: 32
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
GrayordinatesResolution: 2
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
OriginalSmoothingFWHM: 2
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Confound: NONE
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
FinalSmoothingFWHM: 4
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: TemporalFilter:
200
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
VolumeBasedProcessing: NO
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: RegName: NONE
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Parcellation: MMP
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
ParcellationFile: /opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: INFO: Determined that the
FSL version in use is 5.0.9
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: TEST_FSL_VERSION:
Beginning analyses with FSL version 5.0.9
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1: Running
Level 1 Analysis for Both Phase Encoding Directions
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1:
LevelOnefMRIName: task-conflict_run-01_bold
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1: Issuing
command: /opt/HCP-Pipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh
sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/ROIs
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-01_bold
task-conflict_run-01_bold 32 2 2 NONE 4 200 NO NONE MMP
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: TaskfMRILevel1.sh
arguments: sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/ROIs
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-01_bold
task-conflict_run-01_bold 32 2 2 NONE 4 200 NO NONE MMP
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Subject:
sub-BANDA001
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ResultsFolder:
/output/sub-BANDA001/MNINonLinear/Results
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ROIsFolder:
/output/sub-BANDA001/MNINonLinear/ROIs
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: DownSampleFolder:
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LevelOnefMRIName:
task-conflict_run-01_bold
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LevelOnefsfName:
task-conflict_run-01_bold
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LowResMesh: 32
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
GrayordinatesResolution: 2
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
OriginalSmoothingFWHM: 2
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Confound: NONE
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
FinalSmoothingFWHM: 4
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: TemporalFilter: 200
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
VolumeBasedProcessing: NO
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: RegName: NONE
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Parcellation: MMP
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ParcellationFile:
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: TOOL_VERSIONS: Showing HCP
Pipelines version
v3.27.0
Mon Jul 23 15:37:42 UTC 2018 - TaskfMRILevel1.sh: TOOL_VERSIONS: Showing
Connectome Workbench (wb_command) version
Connectome Workbench
Type: Command Line Application
Version: 1.3.0
Qt Compiled Version: 5.7.0
Qt Runtime Version: 5.7.0
Commit: 3a9c975177525cd409952466381533c4cf0683b7
Commit Date: 2018-05-07 15:08:22 -0500
Compiled with OpenMP: YES
Compiler: g++ (/home/caret/gcc/install/gcc-4.8.5/bin)
Compiler Version: 4.8.5
Compiled Debug: NO
Operating System: Linux
Mon Jul 23 15:37:43 UTC 2018 - TaskfMRILevel1.sh: INFO: Determined that the FSL
version in use is 5.0.9
Mon Jul 23 15:37:43 UTC 2018 - TaskfMRILevel1.sh: MAIN: DETERMINE_ANALYSES:
Parcellated Analysis requested
Mon Jul 23 15:37:43 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
SmoothingString: _s4
Mon Jul 23 15:37:43 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
TemporalFilterString: _hp200
Mon Jul 23 15:37:43 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
RegString:
Mon Jul 23 15:37:43 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
ParcellationString: _MMP
Mon Jul 23 15:37:43 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
Extension: ptseries.nii
Mon Jul 23 15:37:43 UTC 2018 - TaskfMRILevel1.sh: MAIN: IMAGE_INFO: TR_vol: 0.8
Mon Jul 23 15:37:44 UTC 2018 - TaskfMRILevel1.sh: MAIN: IMAGE_INFO: npts: 280
Mon Jul 23 15:37:44 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: FEATDir:
/output/sub-BANDA001/MNINonLinear/Results/task-conflict_run-01_bold/task-conflict_run-01_bold_hp200_s4_level1_MMP.feat
Mon Jul 23 15:37:44 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Copying
fsf file to .feat directory
Mon Jul 23 15:37:44 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Set highpass filter string to the desired highpass filter to 200
Mon Jul 23 15:37:44 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Set smoothing to be equal to final smoothing to 4
Mon Jul 23 15:37:44 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Change string in output directory name to _hp200_s4_level1_MMP
Mon Jul 23 15:37:44 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Scan length matches number of timepoints in template.fsf: 280
Mon Jul 23 15:37:44 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Create
design files, model confounds if desired
Mon Jul 23 15:37:45 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Parcellate data if a Parcellation was provided
Mon Jul 23 15:37:45 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Parcellating data
Mon Jul 23 15:37:45 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Notice: currently parcellated time series has _s4 in file name, but
no additional smoothing was applied!
Mon Jul 23 15:37:46 UTC 2018 - TaskfMRILevel1.sh: MAIN: TEMPORAL_FILTER: Add
temporal filtering to CIFTI file
Mon Jul 23 15:37:46 UTC 2018 - TaskfMRILevel1.sh: MAIN: RUN_GLM: Parcellated
Analysis
Log directory is:
/output/sub-BANDA001/MNINonLinear/Results/task-conflict_run-01_bold/task-conflict_run-01_bold_hp200_s4_level1_MMP.feat/ParcellatedStats
paradigm.getDesignMatrix().Nrows()=280
paradigm.getDesignMatrix().Ncols()=8
sizeTS=280
numTS=54
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
Tukey M = 16
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,Completed
Saving results...
Completed
Mon Jul 23 15:37:49 UTC 2018 - TaskfMRILevel1.sh: MAIN: Complete
Mon Jul 23 15:37:49 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: Completed
/opt/HCP-Pipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.sh --path=/output
--subject=sub-BANDA001 --lvl1tasks=task-conflict_run-02_bold
--lvl1fsfs=task-conflict_run-02_bold --lvl2task=NONE --lvl2fsf=NONE
--lowresmesh=32 --grayordinatesres=2 --origsmoothingFWHM=2 --confound="NONE"
--finalsmoothingFWHM=4 --temporalfilter=200 --vba="NO" --regname="NONE"
--parcellation=MMP
--parcellationfile=/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Parsing Command
Line Options
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Path: /output
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Subject:
sub-BANDA001
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelOnefMRINames: task-conflict_run-02_bold
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelOnefsfNames: task-conflict_run-02_bold
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelTwofMRIName: NONE
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelTwofsfNames: NONE
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: LowResMesh: 32
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
GrayordinatesResolution: 2
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
OriginalSmoothingFWHM: 2
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Confound: NONE
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
FinalSmoothingFWHM: 4
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: TemporalFilter:
200
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
VolumeBasedProcessing: NO
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: RegName: NONE
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Parcellation: MMP
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
ParcellationFile: /opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: INFO: Determined that the
FSL version in use is 5.0.9
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: TEST_FSL_VERSION:
Beginning analyses with FSL version 5.0.9
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1: Running
Level 1 Analysis for Both Phase Encoding Directions
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1:
LevelOnefMRIName: task-conflict_run-02_bold
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1: Issuing
command: /opt/HCP-Pipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh
sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/ROIs
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-02_bold
task-conflict_run-02_bold 32 2 2 NONE 4 200 NO NONE MMP
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: TaskfMRILevel1.sh
arguments: sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/ROIs
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-02_bold
task-conflict_run-02_bold 32 2 2 NONE 4 200 NO NONE MMP
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Subject:
sub-BANDA001
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ResultsFolder:
/output/sub-BANDA001/MNINonLinear/Results
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ROIsFolder:
/output/sub-BANDA001/MNINonLinear/ROIs
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: DownSampleFolder:
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LevelOnefMRIName:
task-conflict_run-02_bold
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LevelOnefsfName:
task-conflict_run-02_bold
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LowResMesh: 32
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
GrayordinatesResolution: 2
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
OriginalSmoothingFWHM: 2
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Confound: NONE
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
FinalSmoothingFWHM: 4
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: TemporalFilter: 200
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
VolumeBasedProcessing: NO
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: RegName: NONE
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Parcellation: MMP
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ParcellationFile:
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: TOOL_VERSIONS: Showing HCP
Pipelines version
v3.27.0
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: TOOL_VERSIONS: Showing
Connectome Workbench (wb_command) version
Connectome Workbench
Type: Command Line Application
Version: 1.3.0
Qt Compiled Version: 5.7.0
Qt Runtime Version: 5.7.0
Commit: 3a9c975177525cd409952466381533c4cf0683b7
Commit Date: 2018-05-07 15:08:22 -0500
Compiled with OpenMP: YES
Compiler: g++ (/home/caret/gcc/install/gcc-4.8.5/bin)
Compiler Version: 4.8.5
Compiled Debug: NO
Operating System: Linux
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: INFO: Determined that the FSL
version in use is 5.0.9
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: MAIN: DETERMINE_ANALYSES:
Parcellated Analysis requested
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
SmoothingString: _s4
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
TemporalFilterString: _hp200
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
RegString:
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
ParcellationString: _MMP
Mon Jul 23 15:37:51 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
Extension: ptseries.nii
Mon Jul 23 15:37:52 UTC 2018 - TaskfMRILevel1.sh: MAIN: IMAGE_INFO: TR_vol: 0.8
Mon Jul 23 15:37:52 UTC 2018 - TaskfMRILevel1.sh: MAIN: IMAGE_INFO: npts: 280
Mon Jul 23 15:37:52 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: FEATDir:
/output/sub-BANDA001/MNINonLinear/Results/task-conflict_run-02_bold/task-conflict_run-02_bold_hp200_s4_level1_MMP.feat
Mon Jul 23 15:37:52 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Copying
fsf file to .feat directory
Mon Jul 23 15:37:52 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Set highpass filter string to the desired highpass filter to 200
Mon Jul 23 15:37:52 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Set smoothing to be equal to final smoothing to 4
Mon Jul 23 15:37:52 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Change string in output directory name to _hp200_s4_level1_MMP
Mon Jul 23 15:37:52 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Scan length matches number of timepoints in template.fsf: 280
Mon Jul 23 15:37:52 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Create
design files, model confounds if desired
Mon Jul 23 15:37:53 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Parcellate data if a Parcellation was provided
Mon Jul 23 15:37:53 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Parcellating data
Mon Jul 23 15:37:53 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Notice: currently parcellated time series has _s4 in file name, but
no additional smoothing was applied!
Mon Jul 23 15:37:54 UTC 2018 - TaskfMRILevel1.sh: MAIN: TEMPORAL_FILTER: Add
temporal filtering to CIFTI file
Mon Jul 23 15:37:54 UTC 2018 - TaskfMRILevel1.sh: MAIN: RUN_GLM: Parcellated
Analysis
Log directory is:
/output/sub-BANDA001/MNINonLinear/Results/task-conflict_run-02_bold/task-conflict_run-02_bold_hp200_s4_level1_MMP.feat/ParcellatedStats
paradigm.getDesignMatrix().Nrows()=280
paradigm.getDesignMatrix().Ncols()=8
sizeTS=280
numTS=54
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
Tukey M = 16
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,Completed
Saving results...
Completed
Mon Jul 23 15:37:57 UTC 2018 - TaskfMRILevel1.sh: MAIN: Complete
Mon Jul 23 15:37:57 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: Completed
/opt/HCP-Pipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.sh --path=/output
--subject=sub-BANDA001 --lvl1tasks=task-conflict_run-03_bold
--lvl1fsfs=task-conflict_run-03_bold --lvl2task=NONE --lvl2fsf=NONE
--lowresmesh=32 --grayordinatesres=2 --origsmoothingFWHM=2 --confound="NONE"
--finalsmoothingFWHM=4 --temporalfilter=200 --vba="NO" --regname="NONE"
--parcellation=MMP
--parcellationfile=/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Parsing Command
Line Options
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Path: /output
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Subject:
sub-BANDA001
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelOnefMRINames: task-conflict_run-03_bold
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelOnefsfNames: task-conflict_run-03_bold
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelTwofMRIName: NONE
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelTwofsfNames: NONE
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: LowResMesh: 32
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
GrayordinatesResolution: 2
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
OriginalSmoothingFWHM: 2
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Confound: NONE
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
FinalSmoothingFWHM: 4
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: TemporalFilter:
200
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
VolumeBasedProcessing: NO
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: RegName: NONE
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Parcellation: MMP
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
ParcellationFile: /opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: INFO: Determined that the
FSL version in use is 5.0.9
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: TEST_FSL_VERSION:
Beginning analyses with FSL version 5.0.9
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1: Running
Level 1 Analysis for Both Phase Encoding Directions
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1:
LevelOnefMRIName: task-conflict_run-03_bold
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1: Issuing
command: /opt/HCP-Pipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh
sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/ROIs
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-03_bold
task-conflict_run-03_bold 32 2 2 NONE 4 200 NO NONE MMP
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: TaskfMRILevel1.sh
arguments: sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/ROIs
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-03_bold
task-conflict_run-03_bold 32 2 2 NONE 4 200 NO NONE MMP
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Subject:
sub-BANDA001
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ResultsFolder:
/output/sub-BANDA001/MNINonLinear/Results
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ROIsFolder:
/output/sub-BANDA001/MNINonLinear/ROIs
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: DownSampleFolder:
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LevelOnefMRIName:
task-conflict_run-03_bold
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LevelOnefsfName:
task-conflict_run-03_bold
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LowResMesh: 32
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
GrayordinatesResolution: 2
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
OriginalSmoothingFWHM: 2
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Confound: NONE
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
FinalSmoothingFWHM: 4
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: TemporalFilter: 200
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
VolumeBasedProcessing: NO
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: RegName: NONE
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Parcellation: MMP
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ParcellationFile:
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: TOOL_VERSIONS: Showing HCP
Pipelines version
v3.27.0
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: TOOL_VERSIONS: Showing
Connectome Workbench (wb_command) version
Connectome Workbench
Type: Command Line Application
Version: 1.3.0
Qt Compiled Version: 5.7.0
Qt Runtime Version: 5.7.0
Commit: 3a9c975177525cd409952466381533c4cf0683b7
Commit Date: 2018-05-07 15:08:22 -0500
Compiled with OpenMP: YES
Compiler: g++ (/home/caret/gcc/install/gcc-4.8.5/bin)
Compiler Version: 4.8.5
Compiled Debug: NO
Operating System: Linux
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: INFO: Determined that the FSL
version in use is 5.0.9
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: MAIN: DETERMINE_ANALYSES:
Parcellated Analysis requested
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
SmoothingString: _s4
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
TemporalFilterString: _hp200
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
RegString:
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
ParcellationString: _MMP
Mon Jul 23 15:37:59 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
Extension: ptseries.nii
Mon Jul 23 15:38:00 UTC 2018 - TaskfMRILevel1.sh: MAIN: IMAGE_INFO: TR_vol: 0.8
Mon Jul 23 15:38:00 UTC 2018 - TaskfMRILevel1.sh: MAIN: IMAGE_INFO: npts: 280
Mon Jul 23 15:38:00 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: FEATDir:
/output/sub-BANDA001/MNINonLinear/Results/task-conflict_run-03_bold/task-conflict_run-03_bold_hp200_s4_level1_MMP.feat
Mon Jul 23 15:38:00 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Copying
fsf file to .feat directory
Mon Jul 23 15:38:00 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Set highpass filter string to the desired highpass filter to 200
Mon Jul 23 15:38:00 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Set smoothing to be equal to final smoothing to 4
Mon Jul 23 15:38:00 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Change string in output directory name to _hp200_s4_level1_MMP
Mon Jul 23 15:38:00 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Scan length matches number of timepoints in template.fsf: 280
Mon Jul 23 15:38:00 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Create
design files, model confounds if desired
Mon Jul 23 15:38:01 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Parcellate data if a Parcellation was provided
Mon Jul 23 15:38:01 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Parcellating data
Mon Jul 23 15:38:01 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Notice: currently parcellated time series has _s4 in file name, but
no additional smoothing was applied!
Mon Jul 23 15:38:02 UTC 2018 - TaskfMRILevel1.sh: MAIN: TEMPORAL_FILTER: Add
temporal filtering to CIFTI file
Mon Jul 23 15:38:02 UTC 2018 - TaskfMRILevel1.sh: MAIN: RUN_GLM: Parcellated
Analysis
Log directory is:
/output/sub-BANDA001/MNINonLinear/Results/task-conflict_run-03_bold/task-conflict_run-03_bold_hp200_s4_level1_MMP.feat/ParcellatedStats
paradigm.getDesignMatrix().Nrows()=280
paradigm.getDesignMatrix().Ncols()=8
sizeTS=280
numTS=54
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
Tukey M = 16
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,Completed
Saving results...
Completed
Mon Jul 23 15:38:05 UTC 2018 - TaskfMRILevel1.sh: MAIN: Complete
Mon Jul 23 15:38:05 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: Completed
/opt/HCP-Pipelines/TaskfMRIAnalysis/TaskfMRIAnalysis.sh --path=/output
--subject=sub-BANDA001 --lvl1tasks=task-conflict_run-04_bold
--lvl1fsfs=task-conflict_run-04_bold --lvl2task=task-conflict
--lvl2fsf=task-conflict --lowresmesh=32 --grayordinatesres=2
--origsmoothingFWHM=2 --confound="NONE" --finalsmoothingFWHM=4
--temporalfilter=200 --vba="NO" --regname="NONE" --parcellation=MMP
--parcellationfile=/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Parsing Command
Line Options
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Path: /output
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Subject:
sub-BANDA001
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelOnefMRINames: task-conflict_run-04_bold
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelOnefsfNames: task-conflict_run-04_bold
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelTwofMRIName: task-conflict
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
LevelTwofsfNames: task-conflict
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: LowResMesh: 32
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
GrayordinatesResolution: 2
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
OriginalSmoothingFWHM: 2
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Confound: NONE
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
FinalSmoothingFWHM: 4
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: TemporalFilter:
200
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
VolumeBasedProcessing: NO
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: RegName: NONE
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS: Parcellation: MMP
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: READ_ARGS:
ParcellationFile: /opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: INFO: Determined that the
FSL version in use is 5.0.9
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: TEST_FSL_VERSION:
Beginning analyses with FSL version 5.0.9
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1: Running
Level 1 Analysis for Both Phase Encoding Directions
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1:
LevelOnefMRIName: task-conflict_run-04_bold
Mon Jul 23 15:38:07 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL1: Issuing
command: /opt/HCP-Pipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh
sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/ROIs
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-04_bold
task-conflict_run-04_bold 32 2 2 NONE 4 200 NO NONE MMP
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: TaskfMRILevel1.sh
arguments: sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/ROIs
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-04_bold
task-conflict_run-04_bold 32 2 2 NONE 4 200 NO NONE MMP
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Subject:
sub-BANDA001
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ResultsFolder:
/output/sub-BANDA001/MNINonLinear/Results
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ROIsFolder:
/output/sub-BANDA001/MNINonLinear/ROIs
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: DownSampleFolder:
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LevelOnefMRIName:
task-conflict_run-04_bold
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LevelOnefsfName:
task-conflict_run-04_bold
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: LowResMesh: 32
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
GrayordinatesResolution: 2
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
OriginalSmoothingFWHM: 2
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Confound: NONE
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
FinalSmoothingFWHM: 4
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: TemporalFilter: 200
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS:
VolumeBasedProcessing: NO
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: RegName: NONE
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: Parcellation: MMP
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: READ_ARGS: ParcellationFile:
/opt/HCP-Pipelines/global/templates/hcp_mmp_v1_32k.dlabel.nii
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: TOOL_VERSIONS: Showing HCP
Pipelines version
v3.27.0
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: TOOL_VERSIONS: Showing
Connectome Workbench (wb_command) version
Connectome Workbench
Type: Command Line Application
Version: 1.3.0
Qt Compiled Version: 5.7.0
Qt Runtime Version: 5.7.0
Commit: 3a9c975177525cd409952466381533c4cf0683b7
Commit Date: 2018-05-07 15:08:22 -0500
Compiled with OpenMP: YES
Compiler: g++ (/home/caret/gcc/install/gcc-4.8.5/bin)
Compiler Version: 4.8.5
Compiled Debug: NO
Operating System: Linux
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: INFO: Determined that the FSL
version in use is 5.0.9
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: DETERMINE_ANALYSES:
Parcellated Analysis requested
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
SmoothingString: _s4
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
TemporalFilterString: _hp200
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
RegString:
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
ParcellationString: _MMP
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: SET_NAME_STRINGS:
Extension: ptseries.nii
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: IMAGE_INFO: TR_vol: 0.8
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: IMAGE_INFO: npts: 280
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: FEATDir:
/output/sub-BANDA001/MNINonLinear/Results/task-conflict_run-04_bold/task-conflict_run-04_bold_hp200_s4_level1_MMP.feat
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Copying
fsf file to .feat directory
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Set highpass filter string to the desired highpass filter to 200
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Set smoothing to be equal to final smoothing to 4
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Change string in output directory name to _hp200_s4_level1_MMP
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Change
design.fsf: Scan length matches number of timepoints in template.fsf: 280
Mon Jul 23 15:38:08 UTC 2018 - TaskfMRILevel1.sh: MAIN: MAKE_DESIGNS: Create
design files, model confounds if desired
Mon Jul 23 15:38:09 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Parcellate data if a Parcellation was provided
Mon Jul 23 15:38:09 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Parcellating data
Mon Jul 23 15:38:09 UTC 2018 - TaskfMRILevel1.sh: MAIN: SMOOTH_OR_PARCELLATE:
PARCELLATE: Notice: currently parcellated time series has _s4 in file name, but
no additional smoothing was applied!
Mon Jul 23 15:38:10 UTC 2018 - TaskfMRILevel1.sh: MAIN: TEMPORAL_FILTER: Add
temporal filtering to CIFTI file
Mon Jul 23 15:38:10 UTC 2018 - TaskfMRILevel1.sh: MAIN: RUN_GLM: Parcellated
Analysis
Log directory is:
/output/sub-BANDA001/MNINonLinear/Results/task-conflict_run-04_bold/task-conflict_run-04_bold_hp200_s4_level1_MMP.feat/ParcellatedStats
paradigm.getDesignMatrix().Nrows()=280
paradigm.getDesignMatrix().Ncols()=8
sizeTS=280
numTS=54
Calculating residuals...
Completed
Estimating residual autocorrelation...
Calculating raw AutoCorrs... Completed
Tukey M = 16
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,Completed
Saving results...
Completed
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel1.sh: MAIN: Complete
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL2: Combine
Data Across Phase Encoding Directions in the Level 2 Analysis
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRIAnalysis.sh: MAIN: RUN_LEVEL2: Issuing
command: /opt/HCP-Pipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh
sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-04_bold
task-conflict_run-04_bold task-conflict task-conflict 32 4 200 NO NONE MMP
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: TaskfMRILevel2.sh
arguments: sub-BANDA001 /output/sub-BANDA001/MNINonLinear/Results
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k task-conflict_run-04_bold
task-conflict_run-04_bold task-conflict task-conflict 32 4 200 NO NONE MMP
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: Subject:
sub-BANDA001
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: ResultsFolder:
/output/sub-BANDA001/MNINonLinear/Results
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: DownSampleFolder:
/output/sub-BANDA001/MNINonLinear/fsaverage_LR32k
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: LevelOnefMRINames:
task-conflict_run-04_bold
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: LevelOnefsfNames:
task-conflict_run-04_bold
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: LevelTwofMRIName:
task-conflict
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: LevelTwofsfName:
task-conflict
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: LowResMesh: 32
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS:
FinalSmoothingFWHM: 4
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: TemporalFilter: 200
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS:
VolumeBasedProcessing: NO
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: RegName: NONE
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: READ_ARGS: Parcellation: MMP
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: TOOL_VERSIONS: Showing HCP
Pipelines version
v3.27.0
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: TOOL_VERSIONS: Showing
Connectome Workbench (wb_command) version
Connectome Workbench
Type: Command Line Application
Version: 1.3.0
Qt Compiled Version: 5.7.0
Qt Runtime Version: 5.7.0
Commit: 3a9c975177525cd409952466381533c4cf0683b7
Commit Date: 2018-05-07 15:08:22 -0500
Compiled with OpenMP: YES
Compiler: g++ (/home/caret/gcc/install/gcc-4.8.5/bin)
Compiler Version: 4.8.5
Compiled Debug: NO
Operating System: Linux
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: INFO: Determined that the FSL
version in use is 5.0.9
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES:
Parcellated Analysis requested
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES:
Analyses: ParcellatedStats
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES:
ParcellationString: _MMP
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES:
ExtensionList: ptseries.nii
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: MAIN: DETERMINE_ANALYSES:
ScalarExtensionList: pscalar.nii
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: MAIN: SET_NAME_STRINGS:
SmoothingString: _s4
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: MAIN: SET_NAME_STRINGS:
TemporalFilterString: _hp200
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: MAIN: SET_NAME_STRINGS:
RegString:
Mon Jul 23 15:38:13 UTC 2018 - TaskfMRILevel2.sh: Make design files
terminate called after throwing an instance of 'NEWMAT::ProgramException'
/opt/HCP-Pipelines/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh: line 162: 58868
Aborted (core dumped) feat_model ${LevelTwoFEATDir}/design
design.fsf
Description: Binary data
