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hw2/bids/code/bidscoin/bidscoiner.log

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2020-02-21 13:10:49 - bidscoin - INFO
2020-02-21 13:10:49 - bidscoin - INFO -------------- START BIDScoiner 2.3: BIDS 1.2.1 ------------
2020-02-21 13:10:49 - bidscoin - INFO >>> bidscoiner sourcefolder=/data/raw bidsfolder=/data/bids subjects=None force=True participants=False bidsmap=bidsmap.yaml subprefix=sub- sesprefix=ses-
2020-02-21 13:10:49 - bidscoin - INFO Creating dataset description file: /data/bids/dataset_description.json
2020-02-21 13:10:49 - bidscoin - INFO Creating README file: /data/bids/README
2020-02-21 13:10:49 - bidscoin - INFO Reading: /data/bids/code/bidscoin/bidsmap.yaml
2020-02-21 13:10:49 - bidscoin - INFO Writing ['extra_data/'] entries to /data/bids.bidsignore
2020-02-21 13:10:49 - bidscoin - INFO Coining subject (1/1): /data/raw/sub-TD902TD
2020-02-21 13:10:49 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/001-AAHead_Scout
2020-02-21 13:10:49 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScout_dir-ROW_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/001-AAHead_Scout"
2020-02-21 13:10:51 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 128 DICOM file(s)
Convert 128 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScout_dir-ROW_run-1_echo-1 (160x160x128x1)
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScout_dir-ROW_run-1_echo-1.nii"
Conversion required 2.806171 seconds (0.091399 for core code).
2020-02-21 13:10:51 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScout_dir-ROW_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/001-AAHead_Scout" (errorcode 0)
2020-02-21 13:10:52 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag
2020-02-21 13:10:52 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag"
2020-02-21 13:10:52 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 5 DICOM file(s)
slices not stacked: orientation varies (vNav or localizer?) [-0.0178669 0.945253 0.325848 0.0599034 0.326326 -0.943357] != [-0.00403708 0.994258 0.106932 0.0623806 0.106975 -0.992303]
Convert 2 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001 (162x162x2x1)
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001.nii"
Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003 (162x162x1x1)
Warning: Check that 2D images are not mirrored.
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003.nii"
Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00004 (162x162x1x1)
Warning: Check that 2D images are not mirrored.
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00004.nii"
Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002 (162x162x1x1)
Warning: Check that 2D images are not mirrored.
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002.nii"
Conversion required 0.117767 seconds (0.009945 for core code).
2020-02-21 13:10:52 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag" (errorcode 0)
2020-02-21 13:10:52 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor
2020-02-21 13:10:52 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor"
2020-02-21 13:10:52 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 3 DICOM file(s)
slices not stacked: orientation varies (vNav or localizer?) [0.998044 -0.00266448 0.0624543 0.0623806 0.106975 -0.992303] != [0.996946 -0.000148119 0.0780949 0.0779968 0.0520362 -0.995595]
Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002 (162x162x1x1)
Warning: Check that 2D images are not mirrored.
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002.nii"
Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001 (162x162x1x1)
Warning: Check that 2D images are not mirrored.
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001.nii"
Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003 (162x162x1x1)
Warning: Check that 2D images are not mirrored.
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003.nii"
Conversion required 0.058199 seconds (0.006681 for core code).
2020-02-21 13:10:52 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor" (errorcode 0)
2020-02-21 13:10:52 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra
2020-02-21 13:10:52 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra"
2020-02-21 13:10:52 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 3 DICOM file(s)
slices not stacked: orientation varies (vNav or localizer?) [0.996112 0.00834584 0.0877026 -0.0176687 0.994202 0.106069] != [0.997106 -0.00620212 0.0757702 -0.0134301 0.966621 0.255857]
Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001 (162x162x1x1)
Warning: Check that 2D images are not mirrored.
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001.nii"
Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003 (162x162x1x1)
Warning: Check that 2D images are not mirrored.
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003.nii"
Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002 (162x162x1x1)
Warning: Check that 2D images are not mirrored.
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002.nii"
Conversion required 0.054135 seconds (0.007007 for core code).
2020-02-21 13:10:52 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra" (errorcode 0)
2020-02-21 13:10:52 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/005-T1w
2020-02-21 13:10:52 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_run-1_T1w" -o "/data/bids/sub-TD902TD/anat" "/data/raw/sub-TD902TD/005-T1w"
2020-02-21 13:10:58 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 176 DICOM file(s)
Convert 176 DICOM as /data/bids/sub-TD902TD/anat/sub-TD902TD_run-1_T1w (248x256x176x1)
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/anat/sub-TD902TD_run-1_T1w.nii"
Conversion required 5.905438 seconds (0.178780 for core code).
2020-02-21 13:10:58 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_run-1_T1w" -o "/data/bids/sub-TD902TD/anat" "/data/raw/sub-TD902TD/005-T1w" (errorcode 0)
2020-02-21 13:10:58 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/006-task-music_SBRef
2020-02-21 13:10:58 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/006-task-music_SBRef"
2020-02-21 13:10:58 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 1 DICOM file(s)
Convert 1 DICOM as /data/bids/sub-TD902TD/func/sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_sbref (84x84x60x1)
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/func/sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_sbref.nii"
Conversion required 0.049736 seconds (0.006863 for core code).
2020-02-21 13:10:58 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/006-task-music_SBRef" (errorcode 0)
2020-02-21 13:10:58 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/007-task-music
2020-02-21 13:10:58 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/007-task-music"
2020-02-21 13:11:31 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 287 DICOM file(s)
slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')
Convert 287 DICOM as /data/bids/sub-TD902TD/func/sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_bold (84x84x60x287)
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/func/sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_bold.nii"
Conversion required 33.056733 seconds (0.698965 for core code).
2020-02-21 13:11:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/007-task-music" (errorcode 0)
2020-02-21 13:11:31 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/008-task-music_PhysioLog
2020-02-21 13:11:31 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskmusicPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/008-task-music_PhysioLog"
2020-02-21 13:11:31 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 1 DICOM file(s)
No valid DICOM images were found
2020-02-21 13:11:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskmusicPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/008-task-music_PhysioLog" (errorcode 2)
2020-02-21 13:11:31 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/009-task-prosody_SBRef
2020-02-21 13:11:31 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/009-task-prosody_SBRef"
2020-02-21 13:11:31 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 1 DICOM file(s)
Convert 1 DICOM as /data/bids/sub-TD902TD/func/sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_sbref (84x84x60x1)
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/func/sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_sbref.nii"
Conversion required 0.050585 seconds (0.007176 for core code).
2020-02-21 13:11:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/009-task-prosody_SBRef" (errorcode 0)
2020-02-21 13:11:31 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/010-task-prosody
2020-02-21 13:11:31 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/010-task-prosody"
2020-02-21 13:11:32 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 13 DICOM file(s)
slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')
Convert 13 DICOM as /data/bids/sub-TD902TD/func/sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_bold (84x84x60x13)
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/func/sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_bold.nii"
Conversion required 1.115222 seconds (0.036063 for core code).
2020-02-21 13:11:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/010-task-prosody" (errorcode 0)
2020-02-21 13:11:32 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/011-task-prosody_PhysioLog
2020-02-21 13:11:32 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskprosodyPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/011-task-prosody_PhysioLog"
2020-02-21 13:11:32 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 1 DICOM file(s)
No valid DICOM images were found
2020-02-21 13:11:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskprosodyPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/011-task-prosody_PhysioLog" (errorcode 2)
2020-02-21 13:11:32 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/012-task-prosody_SBRef
2020-02-21 13:11:32 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/012-task-prosody_SBRef"
2020-02-21 13:11:32 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 1 DICOM file(s)
Convert 1 DICOM as /data/bids/sub-TD902TD/func/sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_sbref (84x84x60x1)
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/func/sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_sbref.nii"
Conversion required 0.050570 seconds (0.006955 for core code).
2020-02-21 13:11:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/012-task-prosody_SBRef" (errorcode 0)
2020-02-21 13:11:32 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/013-task-prosody
2020-02-21 13:11:32 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/013-task-prosody"
2020-02-21 13:12:09 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 336 DICOM file(s)
slices stacked despite varying acquisition numbers (if this is not desired recompile with 'mySegmentByAcq')
Convert 336 DICOM as /data/bids/sub-TD902TD/func/sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_bold (84x84x60x336)
compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/func/sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_bold.nii"
Conversion required 36.509422 seconds (0.861163 for core code).
2020-02-21 13:12:09 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/013-task-prosody" (errorcode 0)
2020-02-21 13:12:09 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/014-task-prosody_PhysioLog
2020-02-21 13:12:09 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskprosodyPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/014-task-prosody_PhysioLog"
2020-02-21 13:12:09 - bidscoin - INFO Output:
Chris Rorden's dcm2niiX version v1.0.20181125 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux)
Found 1 DICOM file(s)
No valid DICOM images were found
2020-02-21 13:12:09 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskprosodyPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/014-task-prosody_PhysioLog" (errorcode 2)
2020-02-21 13:12:09 - bidscoin - INFO Writing acquisition time data to: /data/bids/sub-TD902TD/sub-TD902TD_scans.tsv
2020-02-21 13:12:09 - bidscoin - INFO Writing subject data to: /data/bids/participants.tsv
2020-02-21 13:12:09 - bidscoin - INFO Writing subject data dictionary to: /data/bids/participants.json
2020-02-21 13:12:09 - bidscoin - INFO -------------- FINISHED! ------------
2020-02-21 13:12:09 - bidscoin - INFO
2020-02-21 13:12:09 - bidscoin - INFO The following BIDScoin errors and warnings were reported:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
2020-02-21 13:10:51 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScout_dir-ROW_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/001-AAHead_Scout" (errorcode 0)
2020-02-21 13:10:52 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag" (errorcode 0)
2020-02-21 13:10:52 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor" (errorcode 0)
2020-02-21 13:10:52 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra" (errorcode 0)
2020-02-21 13:10:58 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_run-1_T1w" -o "/data/bids/sub-TD902TD/anat" "/data/raw/sub-TD902TD/005-T1w" (errorcode 0)
2020-02-21 13:10:58 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/006-task-music_SBRef" (errorcode 0)
2020-02-21 13:11:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-1_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/007-task-music" (errorcode 0)
2020-02-21 13:11:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskmusicPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/008-task-music_PhysioLog" (errorcode 2)
2020-02-21 13:11:31 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/009-task-prosody_SBRef" (errorcode 0)
2020-02-21 13:11:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-1_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/010-task-prosody" (errorcode 0)
2020-02-21 13:11:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskprosodyPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/011-task-prosody_PhysioLog" (errorcode 2)
2020-02-21 13:11:32 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/012-task-prosody_SBRef" (errorcode 0)
2020-02-21 13:12:09 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-2_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/013-task-prosody" (errorcode 0)
2020-02-21 13:12:09 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-taskprosodyPhysioLog_dir-InPlanePhaseEncodingDirection_run-1_echo-EchoNumbers" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/014-task-prosody_PhysioLog" (errorcode 2)
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2020-02-21 13:12:09 - bidscoin - INFO For the complete log see: /data/bids/code/bidscoin/bidscoiner.log
2020-02-21 13:12:09 - bidscoin - INFO NB: logfiles may contain identifiable information, e.g. from pathnames