Running on compute node: argon-itf-bx47-40.hpc. Job: 3239368 Task: 1 In directory: /Users/esorenson Starting on: Tue Feb 9 10:47:47 CST 2021 subjects: 01 02 04 05 06 07 08 09 11 12 13 14 15 total_subjects=13 dataset_dir: /Shared/lss_kahwang_hpc/data/IBC/ slots: 16 bids_directory: /Shared/lss_kahwang_hpc/data/IBC/BIDS/ singularity_path: /Shared/lss_kahwang_hpc/opt/fmriprep/fmriprep-20.1.1.simg working_directory: /localscratch/Users/esorenson/3239368_1/ working_dataset_dir: /localscratch/Users/esorenson/3239368_1/IBC/ working_fmriprep_dir: /localscratch/Users/esorenson/3239368_1/IBC/fmriprep/ working_freesurfer_dir: /localscratch/Users/esorenson/3239368_1/IBC/freesurfer/ freesurfer_license: /Shared/lss_kahwang_hpc/opt/freesurfer/license.txt Starting fmriprep on 01 Running on compute node: argon-itf-bx47-40.hpc. Job: 3239433 Task: 1 In directory: /Users/esorenson Starting on: Tue Feb 9 11:07:11 CST 2021 subjects: 01 02 04 05 06 07 08 09 11 12 13 14 15 total_subjects=13 dataset_dir: /Shared/lss_kahwang_hpc/data/IBC/ slots: 16 bids_directory: /Shared/lss_kahwang_hpc/data/IBC/BIDS/ singularity_path: /Shared/lss_kahwang_hpc/opt/fmriprep/fmriprep-20.1.1.simg working_directory: /localscratch/Users/esorenson/3239433_1/ working_dataset_dir: /localscratch/Users/esorenson/3239433_1/IBC/ working_fmriprep_dir: /localscratch/Users/esorenson/3239433_1/IBC/fmriprep/ working_freesurfer_dir: /localscratch/Users/esorenson/3239433_1/IBC/freesurfer/ freesurfer_license: /Shared/lss_kahwang_hpc/opt/freesurfer/license.txt Starting fmriprep on 01 bids-validator@1.4.0 1: [ERR] You have to define 'RepetitionTime' for this file. (code: 10 - REPETITION_TIME_MUST_DEFINE) ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiStandard_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiStandard_dir-pa_bold.nii.gz ./sub-01/ses-03/func/sub-01_ses-03_task-HcpEmotion_dir-ap_bold.nii.gz ./sub-01/ses-03/func/sub-01_ses-03_task-HcpEmotion_dir-pa_bold.nii.gz ./sub-01/ses-03/func/sub-01_ses-03_task-HcpGambling_dir-ap_bold.nii.gz ./sub-01/ses-03/func/sub-01_ses-03_task-HcpGambling_dir-pa_bold.nii.gz ... and 109 more files having this issue (Use --verbose to see them all).  Please visit https://neurostars.org/search?q=REPETITION_TIME_MUST_DEFINE for existing conversations about this issue. 2: [ERR] You have to define 'PhaseEncodingDirection' for this file. (code: 18 - PHASE_ENCODING_DIRECTION_MUST_DEFINE) ./sub-01/ses-03/fmap/sub-01_ses-03_dir-ap_epi.nii.gz ./sub-01/ses-03/fmap/sub-01_ses-03_dir-pa_epi.nii.gz ./sub-01/ses-04/fmap/sub-01_ses-04_dir-ap_epi.nii.gz ./sub-01/ses-04/fmap/sub-01_ses-04_dir-pa_epi.nii.gz ./sub-01/ses-05/fmap/sub-01_ses-05_dir-ap_epi.nii.gz ./sub-01/ses-05/fmap/sub-01_ses-05_dir-pa_epi.nii.gz ./sub-01/ses-06/fmap/sub-01_ses-06_dir-ap_epi.nii.gz ./sub-01/ses-06/fmap/sub-01_ses-06_dir-pa_epi.nii.gz ./sub-01/ses-07/fmap/sub-01_ses-07_dir-ap_epi.nii.gz ./sub-01/ses-07/fmap/sub-01_ses-07_dir-pa_epi.nii.gz ... and 28 more files having this issue (Use --verbose to see them all).  Please visit https://neurostars.org/search?q=PHASE_ENCODING_DIRECTION_MUST_DEFINE for existing conversations about this issue. 3: [ERR] You have to define 'TotalReadoutTime' for this file. (code: 19 - TOTAL_READOUT_TIME_MUST_DEFINE) ./sub-01/ses-03/fmap/sub-01_ses-03_dir-ap_epi.nii.gz ./sub-01/ses-03/fmap/sub-01_ses-03_dir-pa_epi.nii.gz ./sub-01/ses-04/fmap/sub-01_ses-04_dir-ap_epi.nii.gz ./sub-01/ses-04/fmap/sub-01_ses-04_dir-pa_epi.nii.gz ./sub-01/ses-05/fmap/sub-01_ses-05_dir-ap_epi.nii.gz ./sub-01/ses-05/fmap/sub-01_ses-05_dir-pa_epi.nii.gz ./sub-01/ses-06/fmap/sub-01_ses-06_dir-ap_epi.nii.gz ./sub-01/ses-06/fmap/sub-01_ses-06_dir-pa_epi.nii.gz ./sub-01/ses-07/fmap/sub-01_ses-07_dir-ap_epi.nii.gz ./sub-01/ses-07/fmap/sub-01_ses-07_dir-pa_epi.nii.gz ... and 28 more files having this issue (Use --verbose to see them all).  Please visit https://neurostars.org/search?q=TOTAL_READOUT_TIME_MUST_DEFINE for existing conversations about this issue. 1: [WARN] You should define 'EchoTime' for this file. If you don't provide this information field map correction will not be possible. (code: 6 - ECHO_TIME_NOT_DEFINED) ./sub-01/ses-00/dwi/sub-01_ses-00_dwi.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-ap_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-pa_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-ap_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-pa_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiStandard_dir-ap_bold.nii.gz ... and 229 more files having this issue (Use --verbose to see them all).  Please visit https://neurostars.org/search?q=ECHO_TIME_NOT_DEFINED for existing conversations about this issue. 2: [WARN] You should define 'PhaseEncodingDirection' for this file. If you don't provide this information field map correction will not be possible. (code: 7 - PHASE_ENCODING_DIRECTION_NOT_DEFINED) ./sub-01/ses-00/dwi/sub-01_ses-00_dwi.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-ap_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-pa_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-ap_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-pa_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiStandard_dir-ap_bold.nii.gz ... and 229 more files having this issue (Use --verbose to see them all).  Please visit https://neurostars.org/search?q=PHASE_ENCODING_DIRECTION_NOT_DEFINED for existing conversations about this issue. 3: [WARN] You should define 'EffectiveEchoSpacing' for this file. If you don't provide this information field map correction will not be possible. (code: 8 - EFFECTIVE_ECHO_SPACING_NOT_DEFINED) ./sub-01/ses-00/dwi/sub-01_ses-00_dwi.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-ap_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-pa_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-ap_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-pa_sbref.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiStandard_dir-ap_bold.nii.gz ... and 229 more files having this issue (Use --verbose to see them all).  Please visit https://neurostars.org/search?q=EFFECTIVE_ECHO_SPACING_NOT_DEFINED for existing conversations about this issue. 4: [WARN] You should define 'TotalReadoutTime' for this file. If you don't provide this information field map correction using TOPUP might not be possible. (code: 9 - TOTAL_READOUT_TIME_NOT_DEFINED) ./sub-01/ses-00/dwi/sub-01_ses-00_dwi.nii.gz  Please visit https://neurostars.org/search?q=TOTAL_READOUT_TIME_NOT_DEFINED for existing conversations about this issue. 5: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED) ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSocial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiSpatial_dir-pa_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiStandard_dir-ap_bold.nii.gz ./sub-01/ses-00/func/sub-01_ses-00_task-ArchiStandard_dir-pa_bold.nii.gz ./sub-01/ses-03/func/sub-01_ses-03_task-HcpEmotion_dir-ap_bold.nii.gz ./sub-01/ses-03/func/sub-01_ses-03_task-HcpEmotion_dir-pa_bold.nii.gz ./sub-01/ses-03/func/sub-01_ses-03_task-HcpGambling_dir-ap_bold.nii.gz ./sub-01/ses-03/func/sub-01_ses-03_task-HcpGambling_dir-pa_bold.nii.gz ... and 109 more files having this issue (Use --verbose to see them all).  Please visit https://neurostars.org/search?q=SLICE_TIMING_NOT_DEFINED for existing conversations about this issue. 6: [WARN] NIfTI file's header field for unit information for x, y, z, and t dimensions empty or too short (code: 41 - NIFTI_UNIT) ./sub-01/ses-00/anat/sub-01_ses-00_FLAIR.nii.gz ./sub-01/ses-00/anat/sub-01_ses-00_acq-spc_T2w.nii.gz ./sub-01/ses-00/anat/sub-01_ses-00_acq-tse_T2w.nii.gz  Please visit https://neurostars.org/search?q=NIFTI_UNIT for existing conversations about this issue. 7: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)  Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue. Summary: Available Tasks: Available Modalities: 368 Files, 98.64GB FLAIR 1 - Subject T1w 18 - Sessions T2w dwi bold events sbref fieldmap  If you have any questions, please post on https://neurostars.org/tags/bids. Finished on: Tue Feb 9 11:22:34 CST 2021