diff --git a/bids/code/bidscoin/bidscoiner.errors b/bids/code/bidscoin/bidscoiner.errors index e69de29..f95671a 100644 --- a/bids/code/bidscoin/bidscoiner.errors +++ b/bids/code/bidscoin/bidscoiner.errors @@ -0,0 +1,30 @@ +2020-02-25 09:52:09 - bidscoin - WARNING Existing BIDS output-directory found, which may result in duplicate data (with increased run-index). Make sure /data/bids/sub-TD902TD/ was cleaned-up from old data before (re)running the bidscoiner +2020-02-25 09:52:14 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScout_dir-ROW_run-3_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/001-AAHead_Scout" (errorcode 0) +2020-02-25 09:52:14 - 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) +2020-02-25 09:52:14 - 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) +2020-02-25 09:52:15 - 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) +2020-02-25 09:52:21 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_run-3_T1w" -o "/data/bids/sub-TD902TD/anat" "/data/raw/sub-TD902TD/005-T1w" (errorcode 0) +2020-02-25 09:52:21 - 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-3_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/006-task-music_SBRef" (errorcode 0) +2020-02-25 09:52:53 - 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-3_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/007-task-music" (errorcode 0) +2020-02-25 09:52:53 - 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) +2020-02-25 09:52:53 - 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-5_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/009-task-prosody_SBRef" (errorcode 0) +2020-02-25 09:52:54 - 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-5_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/010-task-prosody" (errorcode 0) +2020-02-25 09:52:54 - 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) +2020-02-25 09:52:54 - 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-6_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/012-task-prosody_SBRef" (errorcode 0) +2020-02-25 09:53:34 - 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-6_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/013-task-prosody" (errorcode 0) +2020-02-25 09:53:34 - 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) +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/1 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/10 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/11 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/12 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/13 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/14 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/2 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/3 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/4 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/5 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/6 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/7 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/8 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 diff --git a/bids/code/bidscoin/bidscoiner.log b/bids/code/bidscoin/bidscoiner.log index 8cacc5e..9541ef3 100644 --- a/bids/code/bidscoin/bidscoiner.log +++ b/bids/code/bidscoin/bidscoiner.log @@ -4,3 +4,564 @@ 2020-02-23 11:31:26 - bidscoin - INFO Creating dataset description file: /data/bids/dataset_description.json 2020-02-23 11:31:26 - bidscoin - INFO Creating README file: /data/bids/README 2020-02-23 11:31:26 - bidscoin - INFO No bidsmap file found: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap.yaml +2020-02-24 14:32:35 - bidscoin - INFO +2020-02-24 14:32:35 - bidscoin - INFO -------------- START BIDScoiner 2.3: BIDS 1.2.1 ------------ +2020-02-24 14:32:35 - bidscoin - INFO >>> bidscoiner sourcefolder=/data/raw bidsfolder=/data/bids subjects=None force=True participants=False bidsmap=bidsmap.yaml subprefix=sub- sesprefix=ses- +2020-02-24 14:32:35 - bidscoin - INFO No bidsmap file found: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap.yaml +2020-02-24 17:04:07 - bidscoin - INFO +2020-02-24 17:04:07 - bidscoin - INFO -------------- START BIDScoiner 2.3: BIDS 1.2.1 ------------ +2020-02-24 17:04:07 - bidscoin - INFO >>> bidscoiner sourcefolder=/data/raw bidsfolder=/data/bids subjects=None force=True participants=False bidsmap=bidsmap.yaml subprefix=sub- sesprefix=ses- +2020-02-24 17:04:07 - bidscoin - INFO Reading: /data/bids/code/bidscoin/bidsmap.yaml +2020-02-24 17:04:08 - bidscoin - INFO Writing ['extra_data/'] entries to /data/bids.bidsignore +2020-02-24 17:04:08 - bidscoin - INFO Coining subject (1/1): /data/raw/sub-TD902TD +2020-02-24 17:04:08 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/001-AAHead_Scout +2020-02-24 17:04:08 - 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" +2020-02-24 17:04:12 - 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 4.105977 seconds (0.123729 for core code). + +2020-02-24 17:04:12 - 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) +2020-02-24 17:04:12 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag +2020-02-24 17:04:12 - 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" +2020-02-24 17:04:12 - 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 0.111881 seconds (0.009426 for core code). + +2020-02-24 17:04:12 - 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) +2020-02-24 17:04:12 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor +2020-02-24 17:04:12 - 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" +2020-02-24 17:04:12 - 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 0.094481 seconds (0.007063 for core code). + +2020-02-24 17:04:12 - 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) +2020-02-24 17:04:12 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra +2020-02-24 17:04:12 - 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" +2020-02-24 17:04:12 - 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 0.047906 seconds (0.006758 for core code). + +2020-02-24 17:04:12 - 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) +2020-02-24 17:04:12 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/005-T1w +2020-02-24 17:04:12 - 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" +2020-02-24 17:04:26 - 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 14.088181 seconds (0.266489 for core code). + +2020-02-24 17:04:26 - 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) +2020-02-24 17:04:26 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/006-task-music_SBRef +2020-02-24 17:04:26 - 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" +2020-02-24 17:04:26 - 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 0.052832 seconds (0.005792 for core code). + +2020-02-24 17:04:26 - 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) +2020-02-24 17:04:27 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/007-task-music +2020-02-24 17:04:27 - 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" +2020-02-24 17:05:10 - 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 43.950619 seconds (0.648386 for core code). + +2020-02-24 17:05:10 - 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) +2020-02-24 17:05:11 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/008-task-music_PhysioLog +2020-02-24 17:05:11 - 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" +2020-02-24 17:05:11 - 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 + +2020-02-24 17:05:11 - 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) +2020-02-24 17:05:11 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/009-task-prosody_SBRef +2020-02-24 17:05:11 - 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" +2020-02-24 17:05:11 - 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 0.052925 seconds (0.006540 for core code). + +2020-02-24 17:05:11 - 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) +2020-02-24 17:05:11 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/010-task-prosody +2020-02-24 17:05:11 - 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" +2020-02-24 17:05:12 - 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 1.233223 seconds (0.030843 for core code). + +2020-02-24 17:05:12 - 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) +2020-02-24 17:05:12 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/011-task-prosody_PhysioLog +2020-02-24 17:05:12 - 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" +2020-02-24 17:05:12 - 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 + +2020-02-24 17:05:12 - 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) +2020-02-24 17:05:12 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/012-task-prosody_SBRef +2020-02-24 17:05:12 - 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" +2020-02-24 17:05:12 - 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 0.054688 seconds (0.005812 for core code). + +2020-02-24 17:05:12 - 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) +2020-02-24 17:05:12 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/013-task-prosody +2020-02-24 17:05:12 - 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" +2020-02-24 17:06:01 - 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 49.270335 seconds (0.761777 for core code). + +2020-02-24 17:06:01 - 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) +2020-02-24 17:06:01 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/014-task-prosody_PhysioLog +2020-02-24 17:06:01 - 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" +2020-02-24 17:06:01 - 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 + +2020-02-24 17:06:01 - 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) +2020-02-24 17:06:01 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/1 +2020-02-24 17:06:01 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/10 +2020-02-24 17:06:01 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/11 +2020-02-24 17:06:01 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/12 +2020-02-24 17:06:01 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/13 +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/14 +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/2 +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/3 +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/4 +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/5 +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/6 +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/7 +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/8 +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 +2020-02-24 17:06:02 - bidscoin - INFO Writing acquisition time data to: /data/bids/sub-TD902TD/sub-TD902TD_scans.tsv +2020-02-24 17:06:02 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 +2020-02-25 05:11:46 - bidscoin - INFO +2020-02-25 05:11:46 - bidscoin - INFO -------------- START BIDScoiner 2.3: BIDS 1.2.1 ------------ +2020-02-25 05:11:46 - bidscoin - INFO >>> bidscoiner sourcefolder=/data/raw bidsfolder=/data/bids subjects=None force=True participants=False bidsmap=bidsmap.yaml subprefix=sub- sesprefix=ses- +2020-02-25 05:11:46 - bidscoin - INFO Reading: /data/bids/code/bidscoin/bidsmap.yaml +2020-02-25 05:11:46 - bidscoin - INFO Writing ['extra_data/'] entries to /data/bids.bidsignore +2020-02-25 05:11:46 - bidscoin - INFO Coining subject (1/1): /data/raw/sub-TD902TD +2020-02-25 05:11:46 - bidscoin - WARNING Existing BIDS output-directory found, which may result in duplicate data (with increased run-index). Make sure /data/bids/sub-TD902TD/ was cleaned-up from old data before (re)running the bidscoiner +2020-02-25 05:11:46 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/001-AAHead_Scout +2020-02-25 05:11:46 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScout_dir-ROW_run-2_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/001-AAHead_Scout" +2020-02-25 05:11:50 - 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-2_echo-1 (160x160x128x1) +compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScout_dir-ROW_run-2_echo-1.nii" +Conversion required 3.823778 seconds (0.136816 for core code). + +2020-02-25 05:11:50 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScout_dir-ROW_run-2_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/001-AAHead_Scout" (errorcode 0) +2020-02-25 05:11:50 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag +2020-02-25 05:11:50 - 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" +2020-02-25 05:11:51 - 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_i00001a (162x162x2x1) +compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001a.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003a (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_i00003a.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00004a (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_i00004a.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002a (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_i00002a.nii" +Conversion required 0.175529 seconds (0.012822 for core code). + +2020-02-25 05:11:51 - 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) +2020-02-25 05:11:51 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor +2020-02-25 05:11:51 - 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" +2020-02-25 05:11:51 - 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_i00002a (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_i00002a.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001a (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_i00001a.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003a (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_i00003a.nii" +Conversion required 0.121709 seconds (0.009398 for core code). + +2020-02-25 05:11:51 - 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) +2020-02-25 05:11:51 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra +2020-02-25 05:11:51 - 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" +2020-02-25 05:11:51 - 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_i00001a (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_i00001a.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003a (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_i00003a.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002a (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_i00002a.nii" +Conversion required 0.095244 seconds (0.009804 for core code). + +2020-02-25 05:11:51 - 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) +2020-02-25 05:11:51 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/005-T1w +2020-02-25 05:11:51 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_run-2_T1w" -o "/data/bids/sub-TD902TD/anat" "/data/raw/sub-TD902TD/005-T1w" +2020-02-25 05:11:58 - 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-2_T1w (248x256x176x1) +compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/anat/sub-TD902TD_run-2_T1w.nii" +Conversion required 6.983188 seconds (0.253075 for core code). + +2020-02-25 05:11:58 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_run-2_T1w" -o "/data/bids/sub-TD902TD/anat" "/data/raw/sub-TD902TD/005-T1w" (errorcode 0) +2020-02-25 05:11:58 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/006-task-music_SBRef +2020-02-25 05:11:58 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-2_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/006-task-music_SBRef" +2020-02-25 05:11:58 - 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-2_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-2_echo-1_sbref.nii" +Conversion required 0.055006 seconds (0.007298 for core code). + +2020-02-25 05:11:58 - 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-2_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/006-task-music_SBRef" (errorcode 0) +2020-02-25 05:11:58 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/007-task-music +2020-02-25 05:11:58 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-2_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/007-task-music" +2020-02-25 05:12:32 - 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-2_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-2_echo-1_bold.nii" +Conversion required 34.280638 seconds (0.828551 for core code). + +2020-02-25 05:12:32 - 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-2_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/007-task-music" (errorcode 0) +2020-02-25 05:12:32 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/008-task-music_PhysioLog +2020-02-25 05:12:32 - 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" +2020-02-25 05:12:32 - 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 + +2020-02-25 05:12:32 - 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) +2020-02-25 05:12:32 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/009-task-prosody_SBRef +2020-02-25 05:12:32 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-3_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/009-task-prosody_SBRef" +2020-02-25 05:12:33 - 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-3_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-3_echo-1_sbref.nii" +Conversion required 0.056787 seconds (0.007427 for core code). + +2020-02-25 05:12:33 - 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-3_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/009-task-prosody_SBRef" (errorcode 0) +2020-02-25 05:12:33 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/010-task-prosody +2020-02-25 05:12:33 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-3_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/010-task-prosody" +2020-02-25 05:12:34 - 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-3_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-3_echo-1_bold.nii" +Conversion required 1.139228 seconds (0.037210 for core code). + +2020-02-25 05:12:34 - 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-3_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/010-task-prosody" (errorcode 0) +2020-02-25 05:12:34 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/011-task-prosody_PhysioLog +2020-02-25 05:12:34 - 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" +2020-02-25 05:12:34 - 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 + +2020-02-25 05:12:34 - 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) +2020-02-25 05:12:34 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/012-task-prosody_SBRef +2020-02-25 05:12:34 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-4_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/012-task-prosody_SBRef" +2020-02-25 05:12:34 - 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-4_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-4_echo-1_sbref.nii" +Conversion required 0.055530 seconds (0.007347 for core code). + +2020-02-25 05:12:34 - 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-4_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/012-task-prosody_SBRef" (errorcode 0) +2020-02-25 05:12:34 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/013-task-prosody +2020-02-25 05:12:34 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-4_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/013-task-prosody" +2020-02-25 05:13:11 - 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-4_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-4_echo-1_bold.nii" +Conversion required 37.191210 seconds (0.967785 for core code). + +2020-02-25 05:13:11 - 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-4_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/013-task-prosody" (errorcode 0) +2020-02-25 05:13:11 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/014-task-prosody_PhysioLog +2020-02-25 05:13:11 - 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" +2020-02-25 05:13:11 - 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 + +2020-02-25 05:13:11 - 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) +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/1 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/10 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/11 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/12 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/13 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/14 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/2 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/3 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/4 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/5 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/6 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/7 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/8 +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 +2020-02-25 05:13:11 - bidscoin - INFO Writing acquisition time data to: /data/bids/sub-TD902TD/sub-TD902TD_scans.tsv +2020-02-25 05:13:11 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 +2020-02-25 09:52:09 - bidscoin - INFO +2020-02-25 09:52:09 - bidscoin - INFO -------------- START BIDScoiner 2.3: BIDS 1.2.1 ------------ +2020-02-25 09:52:09 - bidscoin - INFO >>> bidscoiner sourcefolder=/data/raw bidsfolder=/data/bids subjects=None force=True participants=False bidsmap=bidsmap.yaml subprefix=sub- sesprefix=ses- +2020-02-25 09:52:09 - bidscoin - INFO Reading: /data/bids/code/bidscoin/bidsmap.yaml +2020-02-25 09:52:09 - bidscoin - INFO Writing ['extra_data/'] entries to /data/bids.bidsignore +2020-02-25 09:52:09 - bidscoin - INFO Coining subject (1/1): /data/raw/sub-TD902TD +2020-02-25 09:52:09 - bidscoin - WARNING Existing BIDS output-directory found, which may result in duplicate data (with increased run-index). Make sure /data/bids/sub-TD902TD/ was cleaned-up from old data before (re)running the bidscoiner +2020-02-25 09:52:09 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/001-AAHead_Scout +2020-02-25 09:52:09 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScout_dir-ROW_run-3_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/001-AAHead_Scout" +2020-02-25 09:52:14 - 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-3_echo-1 (160x160x128x1) +compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScout_dir-ROW_run-3_echo-1.nii" +Conversion required 4.472118 seconds (0.126952 for core code). + +2020-02-25 09:52:14 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_acq-AAHeadScout_dir-ROW_run-3_echo-1" -o "/data/bids/sub-TD902TD/extra_data" "/data/raw/sub-TD902TD/001-AAHead_Scout" (errorcode 0) +2020-02-25 09:52:14 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag +2020-02-25 09:52:14 - 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" +2020-02-25 09:52:14 - 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_i00001b (162x162x2x1) +compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001b.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003b (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_i00003b.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00004b (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_i00004b.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRsag_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002b (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_i00002b.nii" +Conversion required 0.174551 seconds (0.012474 for core code). + +2020-02-25 09:52:14 - 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) +2020-02-25 09:52:14 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor +2020-02-25 09:52:14 - 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" +2020-02-25 09:52:14 - 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_i00002b (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_i00002b.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00001b (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_i00001b.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRcor_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003b (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_i00003b.nii" +Conversion required 0.285633 seconds (0.008450 for core code). + +2020-02-25 09:52:14 - 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) +2020-02-25 09:52:14 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra +2020-02-25 09:52:14 - 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" +2020-02-25 09:52:15 - 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_i00001b (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_i00001b.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00003b (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_i00003b.nii" +Convert 1 DICOM as /data/bids/sub-TD902TD/extra_data/sub-TD902TD_acq-AAHeadScoutMPRtra_dir-InPlanePhaseEncodingDirection_run-1_echo-1_i00002b (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_i00002b.nii" +Conversion required 0.063812 seconds (0.008152 for core code). + +2020-02-25 09:52:15 - 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) +2020-02-25 09:52:15 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/005-T1w +2020-02-25 09:52:15 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_run-3_T1w" -o "/data/bids/sub-TD902TD/anat" "/data/raw/sub-TD902TD/005-T1w" +2020-02-25 09:52:21 - 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-3_T1w (248x256x176x1) +compress: "/usr/bin/pigz" -n -f -6 "/data/bids/sub-TD902TD/anat/sub-TD902TD_run-3_T1w.nii" +Conversion required 6.193973 seconds (0.240967 for core code). + +2020-02-25 09:52:21 - bidscoin - ERROR Failed to run /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_run-3_T1w" -o "/data/bids/sub-TD902TD/anat" "/data/raw/sub-TD902TD/005-T1w" (errorcode 0) +2020-02-25 09:52:21 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/006-task-music_SBRef +2020-02-25 09:52:21 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-3_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/006-task-music_SBRef" +2020-02-25 09:52:21 - 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-3_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-3_echo-1_sbref.nii" +Conversion required 0.056791 seconds (0.006711 for core code). + +2020-02-25 09:52:21 - 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-3_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/006-task-music_SBRef" (errorcode 0) +2020-02-25 09:52:21 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/007-task-music +2020-02-25 09:52:21 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskmusic_acq-epfid2d184_dir-COL_run-3_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/007-task-music" +2020-02-25 09:52:53 - 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-3_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-3_echo-1_bold.nii" +Conversion required 31.605688 seconds (0.751428 for core code). + +2020-02-25 09:52:53 - 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-3_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/007-task-music" (errorcode 0) +2020-02-25 09:52:53 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/008-task-music_PhysioLog +2020-02-25 09:52:53 - 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" +2020-02-25 09:52:53 - 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 + +2020-02-25 09:52:53 - 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) +2020-02-25 09:52:53 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/009-task-prosody_SBRef +2020-02-25 09:52:53 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-5_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/009-task-prosody_SBRef" +2020-02-25 09:52:53 - 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-5_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-5_echo-1_sbref.nii" +Conversion required 0.055340 seconds (0.006823 for core code). + +2020-02-25 09:52:53 - 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-5_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/009-task-prosody_SBRef" (errorcode 0) +2020-02-25 09:52:53 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/010-task-prosody +2020-02-25 09:52:53 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-5_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/010-task-prosody" +2020-02-25 09:52:54 - 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-5_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-5_echo-1_bold.nii" +Conversion required 1.167357 seconds (0.033557 for core code). + +2020-02-25 09:52:54 - 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-5_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/010-task-prosody" (errorcode 0) +2020-02-25 09:52:54 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/011-task-prosody_PhysioLog +2020-02-25 09:52:54 - 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" +2020-02-25 09:52:54 - 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 + +2020-02-25 09:52:54 - 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) +2020-02-25 09:52:54 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/012-task-prosody_SBRef +2020-02-25 09:52:54 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-6_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/012-task-prosody_SBRef" +2020-02-25 09:52:54 - 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-6_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-6_echo-1_sbref.nii" +Conversion required 0.053281 seconds (0.006632 for core code). + +2020-02-25 09:52:54 - 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-6_echo-1_sbref" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/012-task-prosody_SBRef" (errorcode 0) +2020-02-25 09:52:54 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/013-task-prosody +2020-02-25 09:52:54 - bidscoin - INFO Running: /usr/local/bin/dcm2niix -b y -z y -i n -f "sub-TD902TD_task-taskprosody_acq-epfid2d184_dir-COL_run-6_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/013-task-prosody" +2020-02-25 09:53:34 - 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-6_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-6_echo-1_bold.nii" +Conversion required 39.495045 seconds (0.927900 for core code). + +2020-02-25 09:53:34 - 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-6_echo-1_bold" -o "/data/bids/sub-TD902TD/func" "/data/raw/sub-TD902TD/013-task-prosody" (errorcode 0) +2020-02-25 09:53:34 - bidscoin - INFO Processing folder: /data/raw/sub-TD902TD/014-task-prosody_PhysioLog +2020-02-25 09:53:34 - 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" +2020-02-25 09:53:34 - 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 + +2020-02-25 09:53:34 - 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) +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/1 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/10 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/11 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/12 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/13 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/14 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/2 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/3 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/4 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/5 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/6 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/7 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/8 +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 +2020-02-25 09:53:34 - bidscoin - INFO Writing acquisition time data to: /data/bids/sub-TD902TD/sub-TD902TD_scans.tsv +2020-02-25 09:53:34 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 diff --git a/bids/code/bidscoin/bidsmap.yaml b/bids/code/bidscoin/bidsmap.yaml new file mode 100644 index 0000000..f591265 --- /dev/null +++ b/bids/code/bidscoin/bidsmap.yaml @@ -0,0 +1,368 @@ +# -------------------------------------------------------------------------------- +# This is a bidsmap YAML file with the key-value mappings for the different BIDS +# modalities (anat, func, dwi, etc). The modality attributes are the keys that map +# onto the BIDS labels. The bidsmap data-structure should be 5 levels deep: +# dict > dict > list > dict > dict +# +# NB: +# 1) Edit the bidsmap file to your needs before feeding it to bidscoiner.py +# 2) (Institute) users may create their own bidsmap_[template].yaml or +# bidsmap_[sample].yaml file +# +# For more information, see: +# https://github.com/Donders-Institute/bidscoin +# https://docs.ansible.com/ansible/latest/reference_appendices/YAMLSyntax.html +# -------------------------------------------------------------------------------- + + +Options: +# -------------------------------------------------------------------------------- +# General options +# -------------------------------------------------------------------------------- + bidscoin: + version: '2.3' # BIDScoin version (should correspond with the version in ../bidscoin/version.txt) + bidsignore: extra_data/ # Semicolon-separated list of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. extra_data/;pet/;myfile.txt;yourfile.csv + dcm2niix: # See dcm2niix -h and https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage for more info + path: /usr/local/bin/ # Command to set the path to dcm2niix (note the semi-colon), e.g. module add dcm2niix/1.0.20180622; or PATH=/opt/dcm2niix/bin:$PATH; or /opt/dcm2niix/bin/ or '"C:\Program Files\dcm2niix\"' (note the quotes to deal with the whitespace) + args: -b y -z y -i n # Argument string that is passed to dcm2niix. Tip: SPM users may want to use '-z n' (which produces unzipped nifti's, see dcm2niix -h for more information) + + +PlugIns: [] +# -------------------------------------------------------------------------------- +# List of plugins to edit the key-value heuristics / perform additional operations +# -------------------------------------------------------------------------------- +#- ~ # Either a fullpath name of the plugin or just the basename when it is in the default bidscoin/plugins folder + +PlugIn: +# -------------------------------------------------------------------------------- +# List of plugins to edit the key-value heuristics / perform additional operations +# -------------------------------------------------------------------------------- +#- ~ # Either a fullpath name of the plugin or just the basename when it is in the default bidscoin/plugins folder + + +DICOM: +# -------------------------------------------------------------------------------- +# DICOM key-value heuristics (DICOM fields that are mapped to the BIDS labels) +# -------------------------------------------------------------------------------- + subject: <> # <> extracts the subject label from the source directory during bidscoiner runtime. A DICOM attribute can also be used as subject-label instead, e.g. + session: <> # <> extracts the session label from the source directory during bidscoiner runtime. A DICOM attribute can also be used as session-label instead, e.g. + anat: # ----------------------- All anatomical series -------------------- + - provenance: /data/raw/sub-TD902TD/005-T1w/TD^TD902TD_005_T1w_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: T1w + SeriesDescription: T1w + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM']" + SequenceName: '*tfl3d1_16ns' + SequenceVariant: "['SK', 'SP', 'MP']" + ScanningSequence: "['GR', 'IR']" + MRAcquisitionType: 3D + SliceThickness: '1' + FlipAngle: '9' + EchoNumbers: 1 + EchoTime: '2.98' + RepetitionTime: '2300' + PhaseEncodingDirection: '' + bids: + acq: '' + ce: + rec: + run: <<1>> + mod: + suffix: T1w + func: # ----------------------- All functional series -------------------- + - provenance: /data/raw/sub-TD902TD/006-task-music_SBRef/TD^TD902TD_006_task-music_SBRef_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: task-music + SeriesDescription: task-music_SBRef + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC']" + SequenceName: epfid2d1_84 + SequenceVariant: "['SK', 'SS']" + ScanningSequence: EP + MRAcquisitionType: 2D + SliceThickness: '2.5' + FlipAngle: '45' + EchoNumbers: 1 + EchoTime: '30.2' + RepetitionTime: '1070' + PhaseEncodingDirection: '' + bids: + suffix: sbref + task: taskmusic + acq: epfid2d184 + ce: + dir: COL + rec: + run: <<1>> + echo: '1' + - provenance: /data/raw/sub-TD902TD/007-task-music/TD^TD902TD_007_task-music_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: task-music + SeriesDescription: task-music + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']" + SequenceName: epfid2d1_84 + SequenceVariant: "['SK', 'SS']" + ScanningSequence: EP + MRAcquisitionType: 2D + SliceThickness: '2.5' + FlipAngle: '45' + EchoNumbers: 1 + EchoTime: '30.2' + RepetitionTime: '1070' + PhaseEncodingDirection: '' + bids: + task: taskmusic + acq: epfid2d184 + ce: + dir: COL + rec: + run: <<1>> + echo: '1' + suffix: bold + - provenance: /data/raw/sub-TD902TD/009-task-prosody_SBRef/TD^TD902TD_009_task-prosody_SBRef_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: task-prosody + SeriesDescription: task-prosody_SBRef + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC']" + SequenceName: epfid2d1_84 + SequenceVariant: "['SK', 'SS']" + ScanningSequence: EP + MRAcquisitionType: 2D + SliceThickness: '2.5' + FlipAngle: '45' + EchoNumbers: 1 + EchoTime: '30.2' + RepetitionTime: '1070' + PhaseEncodingDirection: '' + bids: + suffix: sbref + task: taskprosody + acq: epfid2d184 + ce: + dir: COL + rec: + run: <<1>> + echo: '1' + - provenance: /data/raw/sub-TD902TD/010-task-prosody/TD^TD902TD_010_task-prosody_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: task-prosody + SeriesDescription: task-prosody + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']" + SequenceName: epfid2d1_84 + SequenceVariant: "['SK', 'SS']" + ScanningSequence: EP + MRAcquisitionType: 2D + SliceThickness: '2.5' + FlipAngle: '45' + EchoNumbers: 1 + EchoTime: '30.2' + RepetitionTime: '1070' + PhaseEncodingDirection: '' + bids: + task: taskprosody + acq: epfid2d184 + ce: + dir: COL + rec: + run: <<1>> + echo: '1' + suffix: bold + dwi: # ----------------------- All diffusion series --------------------- + fmap: # ----------------------- All fieldmap series ---------------------- + beh: # ----------------------- All behavioural data --------------------- + pet: # ----------------------- All PET series --------------------------- + extra_data: # ----------------------- All extra data --------------------------- + - provenance: /data/raw/sub-TD902TD/001-AAHead_Scout/TD^TD902TD_001_AAHead_Scout_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: AAHead_Scout + SeriesDescription: AAHead_Scout + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM']" + SequenceName: '*fl3d1_ns' + SequenceVariant: SP + ScanningSequence: GR + MRAcquisitionType: 3D + SliceThickness: '1.6000000238419' + FlipAngle: '8' + EchoNumbers: 1 + EchoTime: '1.37' + RepetitionTime: '3.15' + PhaseEncodingDirection: '' + bids: + acq: AAHeadScout + rec: + ce: + task: + echo: '1' + dir: ROW + run: <<1>> + mod: + suffix: + - provenance: /data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag/TD^TD902TD_002_AAHead_Scout_MPR_sag_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: AAHead_Scout + SeriesDescription: AAHead_Scout_MPR_sag + ImageType: "['DERIVED', 'PRIMARY', 'MPR', 'ND', 'NORM']" + SequenceName: '*fl3d1_ns' + SequenceVariant: SP + ScanningSequence: GR + MRAcquisitionType: 3D + SliceThickness: '1.6000000238419' + FlipAngle: '8' + EchoNumbers: 1 + EchoTime: '1.37' + RepetitionTime: '3.15' + PhaseEncodingDirection: '' + bids: + acq: AAHeadScoutMPRsag + rec: + ce: + task: + echo: '1' + dir: + run: <<1>> + mod: + suffix: + - provenance: /data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor/TD^TD902TD_003_AAHead_Scout_MPR_cor_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: AAHead_Scout + SeriesDescription: AAHead_Scout_MPR_cor + ImageType: "['DERIVED', 'PRIMARY', 'MPR', 'ND', 'NORM']" + SequenceName: '*fl3d1_ns' + SequenceVariant: SP + ScanningSequence: GR + MRAcquisitionType: 3D + SliceThickness: '1.6000000238419' + FlipAngle: '8' + EchoNumbers: 1 + EchoTime: '1.37' + RepetitionTime: '3.15' + PhaseEncodingDirection: '' + bids: + acq: AAHeadScoutMPRcor + rec: + ce: + task: + echo: '1' + dir: + run: <<1>> + mod: + suffix: + - provenance: /data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra/TD^TD902TD_004_AAHead_Scout_MPR_tra_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: AAHead_Scout + SeriesDescription: AAHead_Scout_MPR_tra + ImageType: "['DERIVED', 'PRIMARY', 'MPR', 'ND', 'NORM']" + SequenceName: '*fl3d1_ns' + SequenceVariant: SP + ScanningSequence: GR + MRAcquisitionType: 3D + SliceThickness: '1.6000000238419' + FlipAngle: '8' + EchoNumbers: 1 + EchoTime: '1.37' + RepetitionTime: '3.15' + PhaseEncodingDirection: '' + bids: + acq: AAHeadScoutMPRtra + rec: + ce: + task: + echo: '1' + dir: + run: <<1>> + mod: + suffix: + - provenance: /data/raw/sub-TD902TD/008-task-music_PhysioLog/TD^TD902TD_008_task-music_PhysioLog_00927_00001.dcm + attributes: + Modality: MR + ProtocolName: task-music + SeriesDescription: task-music_PhysioLog + ImageType: "['ORIGINAL', 'PRIMARY', 'RAWDATA', 'PHYSIO']" + SequenceName: '' + SequenceVariant: '' + ScanningSequence: '' + MRAcquisitionType: '' + SliceThickness: '' + FlipAngle: '' + EchoNumbers: '' + EchoTime: '' + RepetitionTime: '' + PhaseEncodingDirection: '' + bids: + acq: taskmusicPhysioLog + rec: + ce: + task: + echo: + dir: + run: <<1>> + mod: + suffix: + - provenance: /data/raw/sub-TD902TD/011-task-prosody_PhysioLog/TD^TD902TD_011_task-prosody_PhysioLog_00046_00001.dcm + attributes: + Modality: MR + ProtocolName: task-prosody + SeriesDescription: task-prosody_PhysioLog + ImageType: "['ORIGINAL', 'PRIMARY', 'RAWDATA', 'PHYSIO']" + SequenceName: '' + SequenceVariant: '' + ScanningSequence: '' + MRAcquisitionType: '' + SliceThickness: '' + FlipAngle: '' + EchoNumbers: '' + EchoTime: '' + RepetitionTime: '' + PhaseEncodingDirection: '' + bids: + acq: taskprosodyPhysioLog + rec: + ce: + task: + echo: + dir: + run: <<1>> + mod: + suffix: + leave_out: # ----------------------- Data that will be left out --------------- +PAR: +# -------------------------------------------------------------------------------- +# PAR key-value heuristics (Philips PAR fields that are mapped to the BIDS labels) +# -------------------------------------------------------------------------------- + + +P7: +# -------------------------------------------------------------------------------- +# P*.7 key-value heuristics (GE fields that are mapped to the BIDS labels) +# -------------------------------------------------------------------------------- + + +Nifti: +# -------------------------------------------------------------------------------- +# Nifti key-value heuristics (Nifti fields that are mapped to the BIDS labels) +# -------------------------------------------------------------------------------- + + +FileSystem: +# -------------------------------------------------------------------------------- +# File system key-value heuristics (these file- and foldernames will be mapped +# to the BIDS labels; Special substitutions can be performed using python's +# Format Specification Mini-Language) +# -------------------------------------------------------------------------------- + subject: <> # <> extracts the subject label from the source directory during bidscoiner runtime + session: <> # <> extracts the session label from the source directory during bidscoiner runtime + anat: # ----------------------- All anatomical series -------------------- + func: # ----------------------- All functional series -------------------- + dwi: # ----------------------- All diffusion series --------------------- + fmap: # ----------------------- All fieldmap series ---------------------- + beh: # ----------------------- All behavioural data --------------------- + extra_data: # ----------------------- All extra data --------------------------- + leave_out: # ----------------------- Data that will be left out --------------- diff --git a/bids/code/bidscoin/bidsmap_sample.yaml b/bids/code/bidscoin/bidsmap_sample.yaml new file mode 100644 index 0000000..f3dccfa --- /dev/null +++ b/bids/code/bidscoin/bidsmap_sample.yaml @@ -0,0 +1,296 @@ +# -------------------------------------------------------------------------------- +# This is a bidsmap YAML file with the key-value mappings for the different BIDS +# modalities (anat, func, dwi, etc). The modality attributes are the keys that map +# onto the BIDS labels. The bidsmap data-structure should be 5 levels deep: +# dict > dict > list > dict > dict +# +# NB: +# 1) Edit the bidsmap file to your needs before feeding it to bidscoiner.py +# 2) (Institute) users may create their own bidsmap_[template].yaml or +# bidsmap_[sample].yaml file +# +# For more information, see: +# https://github.com/Donders-Institute/bidscoin +# https://docs.ansible.com/ansible/latest/reference_appendices/YAMLSyntax.html +# -------------------------------------------------------------------------------- + + +Options: +# -------------------------------------------------------------------------------- +# General options +# -------------------------------------------------------------------------------- + bidscoin: + version: '2.3' # BIDScoin version (should correspond with the version in ../bidscoin/version.txt) + bidsignore: extra_data/ # Semicolon-separated list of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. extra_data/;pet/;myfile.txt;yourfile.csv + dcm2niix: # See dcm2niix -h and https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#General_Usage for more info + path: /usr/local/bin/ # Command to set the path to dcm2niix (note the semi-colon), e.g. module add dcm2niix/1.0.20180622; or PATH=/opt/dcm2niix/bin:$PATH; or /opt/dcm2niix/bin/ or '"C:\Program Files\dcm2niix\"' (note the quotes to deal with the whitespace) + args: -b y -z y -i n # Argument string that is passed to dcm2niix. Tip: SPM users may want to use '-z n' (which produces unzipped nifti's, see dcm2niix -h for more information) + + +PlugIns: [] +# -------------------------------------------------------------------------------- +# List of plugins to edit the key-value heuristics / perform additional operations +# -------------------------------------------------------------------------------- +#- ~ # Either a fullpath name of the plugin or just the basename when it is in the default bidscoin/plugins folder + +PlugIn: +# -------------------------------------------------------------------------------- +# List of plugins to edit the key-value heuristics / perform additional operations +# -------------------------------------------------------------------------------- +#- ~ # Either a fullpath name of the plugin or just the basename when it is in the default bidscoin/plugins folder + + +DICOM: +# -------------------------------------------------------------------------------- +# DICOM key-value heuristics (DICOM fields that are mapped to the BIDS labels) +# -------------------------------------------------------------------------------- + subject: <> # <> extracts the subject label from the source directory during bidscoiner runtime. A DICOM attribute can also be used as subject-label instead, e.g. + session: <> # <> extracts the session label from the source directory during bidscoiner runtime. A DICOM attribute can also be used as session-label instead, e.g. + anat: # ----------------------- All anatomical series -------------------- + - provenance: /data/bids/code/bidscoin/samples/anat/T1w/TD^TD902TD_005_T1w_00001_00124.dcm + attributes: + Modality: MR + ProtocolName: T1w + SeriesDescription: T1w + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM']" + SequenceName: '*tfl3d1_16ns' + SequenceVariant: "['SK', 'SP', 'MP']" + ScanningSequence: "['GR', 'IR']" + MRAcquisitionType: 3D + SliceThickness: '1' + FlipAngle: '9' + EchoNumbers: 1 + EchoTime: '2.98' + RepetitionTime: '2300' + PhaseEncodingDirection: '' + bids: + acq: T1w + ce: + rec: + run: <<1>> + mod: + suffix: T1w + func: # ----------------------- All functional series -------------------- + - provenance: /data/bids/code/bidscoin/samples/func/sbref/TD^TD902TD_006_task-music_SBRef_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: task-music + SeriesDescription: task-music_SBRef + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC']" + SequenceName: epfid2d1_84 + SequenceVariant: "['SK', 'SS']" + ScanningSequence: EP + MRAcquisitionType: 2D + SliceThickness: '2.5' + FlipAngle: '45' + EchoNumbers: 1 + EchoTime: '30.2' + RepetitionTime: '1070' + PhaseEncodingDirection: '' + bids: + suffix: sbref + task: taskmusicSBRef + acq: epfid2d184 + ce: + dir: COL + rec: + run: <<1>> + echo: '1' + - provenance: /data/bids/code/bidscoin/samples/func/sbref/TD^TD902TD_009_task-prosody_SBRef_00001_00001.dcm + attributes: + Modality: MR + ProtocolName: task-prosody + SeriesDescription: task-prosody_SBRef + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC']" + SequenceName: epfid2d1_84 + SequenceVariant: "['SK', 'SS']" + ScanningSequence: EP + MRAcquisitionType: 2D + SliceThickness: '2.5' + FlipAngle: '45' + EchoNumbers: 1 + EchoTime: '30.2' + RepetitionTime: '1070' + PhaseEncodingDirection: '' + bids: + suffix: sbref + task: taskprosodySBRef + acq: epfid2d184 + ce: + dir: COL + rec: + run: <<1>> + echo: '1' + - provenance: /data/bids/code/bidscoin/samples/func/bold/TD^TD902TD_013_task-prosody_00287_00287.dcm + attributes: + Modality: MR + ProtocolName: task-prosody + SeriesDescription: task-prosody + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']" + SequenceName: epfid2d1_84 + SequenceVariant: "['SK', 'SS']" + ScanningSequence: EP + MRAcquisitionType: 2D + SliceThickness: '2.5' + FlipAngle: '45' + EchoNumbers: 1 + EchoTime: '30.2' + RepetitionTime: '1070' + PhaseEncodingDirection: '' + bids: + task: taskprosody + acq: epfid2d184 + ce: + dir: COL + rec: + run: <<1>> + echo: '1' + suffix: bold + - provenance: /data/bids/code/bidscoin/samples/func/bold/TD^TD902TD_007_task-music_00131_00131.dcm + attributes: + Modality: MR + ProtocolName: task-music + SeriesDescription: task-music + ImageType: "['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']" + SequenceName: epfid2d1_84 + SequenceVariant: "['SK', 'SS']" + ScanningSequence: EP + MRAcquisitionType: 2D + SliceThickness: '2.5' + FlipAngle: '45' + EchoNumbers: 1 + EchoTime: '30.2' + RepetitionTime: '1070' + PhaseEncodingDirection: '' + bids: + task: taskmusic + acq: epfid2d184 + ce: + dir: COL + rec: + run: <<1>> + echo: '1' + suffix: bold + dwi: # ----------------------- All diffusion series --------------------- + fmap: # ----------------------- All fieldmap series ---------------------- + beh: # ----------------------- All behavioural data --------------------- + pet: # ----------------------- All PET series --------------------------- + extra_data: # ----------------------- All extra data --------------------------- + - provenance: + attributes: + Modality: + ProtocolName: + SeriesDescription: + ImageType: + SequenceName: + SequenceVariant: + ScanningSequence: + MRAcquisitionType: + SliceThickness: + FlipAngle: + EchoNumbers: + EchoTime: + RepetitionTime: + PhaseEncodingDirection: + bids: + acq: + rec: + ce: + task: + echo: + dir: + run: <<1>> + mod: + suffix: + + leave_out: # ----------------------- Data that will be left out --------------- + - provenance: + attributes: + Modality: + ProtocolName: + SeriesDescription: + ImageType: + SequenceName: + SequenceVariant: + ScanningSequence: + MRAcquisitionType: + SliceThickness: + FlipAngle: + EchoNumbers: + EchoTime: + RepetitionTime: + PhaseEncodingDirection: + bids: + acq: + rec: + ce: + task: + echo: + dir: + run: <<1>> + mod: + suffix: + + +PAR: +# -------------------------------------------------------------------------------- +# PAR key-value heuristics (Philips PAR fields that are mapped to the BIDS labels) +# -------------------------------------------------------------------------------- + + +P7: +# -------------------------------------------------------------------------------- +# P*.7 key-value heuristics (GE fields that are mapped to the BIDS labels) +# -------------------------------------------------------------------------------- + + +Nifti: +# -------------------------------------------------------------------------------- +# Nifti key-value heuristics (Nifti fields that are mapped to the BIDS labels) +# -------------------------------------------------------------------------------- + + +FileSystem: +# -------------------------------------------------------------------------------- +# File system key-value heuristics (these file- and foldernames will be mapped +# to the BIDS labels; Special substitutions can be performed using python's +# Format Specification Mini-Language) +# -------------------------------------------------------------------------------- + subject: <> # <> extracts the subject label from the source directory during bidscoiner runtime + session: <> # <> extracts the session label from the source directory during bidscoiner runtime + anat: # ----------------------- All anatomical series -------------------- + func: # ----------------------- All functional series -------------------- + dwi: # ----------------------- All diffusion series --------------------- + fmap: # ----------------------- All fieldmap series ---------------------- + beh: # ----------------------- All behavioural data --------------------- + extra_data: # ----------------------- All extra data --------------------------- + - attributes: + FolderName: + FileName: + FileExt: + bids: + acq: + rec: + ce: + task: + echo: + dir: + run: <<1>> + suffix: + mod: + + leave_out: # ----------------------- Data that will be left out --------------- + - attributes: + FolderName: + FileName: + FileExt: + bids: + acq: + rec: + ce: + task: + echo: + dir: + run: <<1>> + suffix: + mod: diff --git a/bids/code/bidscoin/bidsmapper.errors b/bids/code/bidscoin/bidsmapper.errors new file mode 100644 index 0000000..e1a8752 --- /dev/null +++ b/bids/code/bidscoin/bidsmapper.errors @@ -0,0 +1,14 @@ +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/1 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/10 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/11 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/12 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/13 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/14 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/2 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/3 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/4 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/5 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/6 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/7 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/8 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 diff --git a/bids/code/bidscoin/bidsmapper.log b/bids/code/bidscoin/bidsmapper.log new file mode 100644 index 0000000..2b0049b --- /dev/null +++ b/bids/code/bidscoin/bidsmapper.log @@ -0,0 +1,68 @@ +2020-02-24 16:28:52 - bidscoin - INFO +2020-02-24 16:28:52 - bidscoin - INFO -------------- START BIDSmapper ------------ +2020-02-24 16:28:52 - bidscoin - INFO No bidsmap file found: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap.yaml +2020-02-24 16:28:52 - bidscoin - INFO Reading: /data/bids/code/bidscoin/bidsmap_sample.yaml +2020-02-24 16:28:52 - bidscoin - INFO Parsing: /data/raw/sub-TD902TD (subject 1/1) +2020-02-24 16:28:52 - bidscoin - INFO New 'extra_data' sample found: /data/raw/sub-TD902TD/001-AAHead_Scout/TD^TD902TD_001_AAHead_Scout_00001_00001.dcm +2020-02-24 16:28:52 - bidscoin - INFO New 'extra_data' sample found: /data/raw/sub-TD902TD/002-AAHead_Scout_MPR_sag/TD^TD902TD_002_AAHead_Scout_MPR_sag_00001_00001.dcm +2020-02-24 16:28:52 - bidscoin - INFO New 'extra_data' sample found: /data/raw/sub-TD902TD/003-AAHead_Scout_MPR_cor/TD^TD902TD_003_AAHead_Scout_MPR_cor_00001_00001.dcm +2020-02-24 16:28:53 - bidscoin - INFO New 'extra_data' sample found: /data/raw/sub-TD902TD/004-AAHead_Scout_MPR_tra/TD^TD902TD_004_AAHead_Scout_MPR_tra_00001_00001.dcm +2020-02-24 16:28:53 - bidscoin - INFO New 'anat' sample found: /data/raw/sub-TD902TD/005-T1w/TD^TD902TD_005_T1w_00001_00001.dcm +2020-02-24 16:28:53 - bidscoin - INFO New 'func' sample found: /data/raw/sub-TD902TD/006-task-music_SBRef/TD^TD902TD_006_task-music_SBRef_00001_00001.dcm +2020-02-24 16:28:53 - bidscoin - INFO New 'func' sample found: /data/raw/sub-TD902TD/007-task-music/TD^TD902TD_007_task-music_00001_00001.dcm +2020-02-24 16:28:53 - bidscoin - INFO New 'extra_data' sample found: /data/raw/sub-TD902TD/008-task-music_PhysioLog/TD^TD902TD_008_task-music_PhysioLog_00927_00001.dcm +2020-02-24 16:28:53 - bidscoin - INFO New 'func' sample found: /data/raw/sub-TD902TD/009-task-prosody_SBRef/TD^TD902TD_009_task-prosody_SBRef_00001_00001.dcm +2020-02-24 16:28:53 - bidscoin - INFO New 'func' sample found: /data/raw/sub-TD902TD/010-task-prosody/TD^TD902TD_010_task-prosody_00001_00001.dcm +2020-02-24 16:28:53 - bidscoin - INFO New 'extra_data' sample found: /data/raw/sub-TD902TD/011-task-prosody_PhysioLog/TD^TD902TD_011_task-prosody_PhysioLog_00046_00001.dcm +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/1 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/10 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/11 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/12 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/13 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/14 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/2 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/3 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/4 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/5 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/6 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/7 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/8 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 +2020-02-24 16:28:53 - bidscoin - INFO No DICOM information found in the bidsmap and template +2020-02-24 16:28:53 - bidscoin - INFO Writing bidsmap to: /data/bids/code/bidscoin/bidsmap.yaml +2020-02-24 16:28:53 - bidscoin - INFO -------------- FINISHED! ------------------- +2020-02-24 16:28:53 - bidscoin - INFO +2020-02-24 16:28:53 - bidscoin - INFO The following BIDScoin errors and warnings were reported: + +>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/1 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/10 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/11 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/12 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/13 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/14 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/2 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/3 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/4 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/5 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/6 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/7 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/8 +2020-02-24 16:28:53 - bidscoin - WARNING Cannot find dicom files in:/data/raw/sub-TD902TD/9 +<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +2020-02-24 16:28:53 - bidscoin - INFO For the complete log see: /data/bids/code/bidscoin/bidsmapper.log +2020-02-24 16:28:53 - bidscoin - INFO NB: logfiles may contain identifiable information, e.g. from pathnames diff --git a/bids/code/bidscoin/bidstrainer.errors b/bids/code/bidscoin/bidstrainer.errors new file mode 100644 index 0000000..e69de29 diff --git a/bids/code/bidscoin/bidstrainer.log b/bids/code/bidscoin/bidstrainer.log new file mode 100644 index 0000000..db192e3 --- /dev/null +++ b/bids/code/bidscoin/bidstrainer.log @@ -0,0 +1,8 @@ +2020-02-24 13:18:38 - bidscoin - INFO ------------ START BIDStrainer ------------ +2020-02-24 13:18:38 - bidscoin - INFO Reading: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap_template.yaml +2020-02-24 13:19:10 - bidscoin - INFO Writing bidsmap to: /data/bids/code/bidscoin/bidsmap_sample.yaml +2020-02-24 13:19:10 - bidscoin - INFO ------------ FINISHED! ------------ +2020-02-24 16:28:09 - bidscoin - INFO ------------ START BIDStrainer ------------ +2020-02-24 16:28:09 - bidscoin - INFO Reading: /usr/local/miniconda/lib/python3.7/site-packages/bidscoin-2.3-py3.7.egg/heuristics/bidsmap_template.yaml +2020-02-24 16:28:51 - bidscoin - INFO Writing bidsmap to: /data/bids/code/bidscoin/bidsmap_sample.yaml +2020-02-24 16:28:51 - bidscoin - INFO ------------ FINISHED! ------------