INFO: Running heudiconv version 0.13.1 latest 0.13.1 INFO: Analyzing 11997 dicoms WARNING: Ignoring /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/rawdata/SUB-20071-01_vc53043_20230412/scans/14-ABCD_T2w_SPC_vNav/resources/SNAPSHOTS/files/SUB-20071-01_vc53043_20230412_14_qc.gif since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING: Ignoring /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/rawdata/SUB-20071-01_vc53043_20230412/scans/14-ABCD_T2w_SPC_vNav/resources/SNAPSHOTS/files/SUB-20071-01_vc53043_20230412_14_qc_t.gif since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' INFO: Generated sequence info for 1 studies with 33 entries total WARNING: Heuristic is missing an `infotoids` method, assigning empty method and using provided subject id 20071. Provide `session` and `locator` fields for best results. INFO: Study session for StudySessionInfo(locator=None, session='53043', subject='20071') INFO: Need to process 1 study sessions INFO: PROCESSING STARTS: {'subject': '20071', 'outdir': '/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/', 'session': '53043'} INFO: Processing 33 pre-sorted seqinfo entries INFO: Reloading existing filegroup.json because /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/.heudiconv/20071/ses-53043/info/20071_ses-53043.edit.txt exists INFO: Doing conversion using dcm2niix INFO: Converting /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold (2200 DICOMs) -> /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func . Converter: dcm2niix . Output types: ('nii.gz',) INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixr8acbj2y/convert". INFO: [Node] Executing "convert" INFO: stdout 2023-06-26T12:16:29.510646:Chris Rorden's dcm2niiX version v1.0.20200331 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux) INFO: stdout 2023-06-26T12:16:29.510646:Found 2200 DICOM file(s) INFO: stdout 2023-06-26T12:16:29.510646:Slices not stacked: echo varies (TE 63.66, 38.94; echo 1, 1). Use 'merge 2D slices' option to force stacking INFO: stdout 2023-06-26T12:16:29.510646:Warning: Slice timing appears corrupted (range 26472.5..28070, TR=1761 ms) INFO: stdout 2023-06-26T12:16:29.510646:Convert 550 DICOM as /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv037_e1 (110x110x72x550) INFO: stdout 2023-06-26T12:17:07.981223:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv037_e1.nii" INFO: stdout 2023-06-26T12:17:07.981223:Warning: Slice timing appears corrupted (range 26450..28045, TR=1761 ms) INFO: stdout 2023-06-26T12:17:07.981223:Convert 550 DICOM as /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv037_e1a (110x110x72x550) INFO: stdout 2023-06-26T12:17:54.921656:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv037_e1a.nii" INFO: stdout 2023-06-26T12:17:54.921656:Warning: Slice timing appears corrupted (range 26415..28010, TR=1761 ms) INFO: stdout 2023-06-26T12:17:54.921656:Convert 550 DICOM as /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv037_e1b (110x110x72x550) INFO: stdout 2023-06-26T12:18:33.502001:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv037_e1b.nii" INFO: stdout 2023-06-26T12:18:33.502001:Warning: Slice timing appears corrupted (range 26497.5..28095, TR=1761 ms) INFO: stdout 2023-06-26T12:18:33.502001:Convert 550 DICOM as /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv037_e1c (110x110x72x550) INFO: stdout 2023-06-26T12:19:08.067031:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv037_e1c.nii" INFO: stdout 2023-06-26T12:19:08.067031:Conversion required 173.228975 seconds (12.976262 for core code). INFO: [Node] Finished "convert", elapsed time 173.801977s. Traceback (most recent call last): File "/home/usr/badenn/.local/bin/heudiconv", line 8, in sys.exit(main()) File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/cli/run.py", line 30, in main workflow(**kwargs) File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/main.py", line 463, in workflow prep_conversion( File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/convert.py", line 255, in prep_conversion convert( File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/convert.py", line 620, in convert bids_outfiles = save_converted_files( File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/convert.py", line 1018, in save_converted_files safe_movefile(fl, outfile, overwrite) File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/utils.py", line 444, in safe_movefile _safe_op_file(src, dest, "move", overwrite=overwrite) File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/utils.py", line 461, in _safe_op_file raise RuntimeError( RuntimeError: was asked to move /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv037_e1a.nii.gz but destination already exists: /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_echo-1_part-mag_bold.nii.gz   ~/GMT3/Noah/ASD_ADHD  16m 32s badenn@rocinante  12:20:43 PM ❯ heudiconv --files /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/rawdata/SUB-20071-01_vc53043_20230412/ -c dcm2niix -o /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD -b notop -s 20071 -ss 53043 -f /net/10.20.145.45/DOSENBACH03/GMT3/Noah/MSC/heuristics.py --overwrite >>heuristics_output_with_overwrite.txt INFO: Running heudiconv version 0.13.1 latest 0.13.1 INFO: Analyzing 11997 dicoms WARNING: Ignoring /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/rawdata/SUB-20071-01_vc53043_20230412/scans/14-ABCD_T2w_SPC_vNav/resources/SNAPSHOTS/files/SUB-20071-01_vc53043_20230412_14_qc.gif since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' WARNING: Ignoring /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/rawdata/SUB-20071-01_vc53043_20230412/scans/14-ABCD_T2w_SPC_vNav/resources/SNAPSHOTS/files/SUB-20071-01_vc53043_20230412_14_qc_t.gif since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber' INFO: Generated sequence info for 1 studies with 33 entries total WARNING: Heuristic is missing an `infotoids` method, assigning empty method and using provided subject id 20071. Provide `session` and `locator` fields for best results. INFO: Study session for StudySessionInfo(locator=None, session='53043', subject='20071') INFO: Need to process 1 study sessions INFO: PROCESSING STARTS: {'subject': '20071', 'outdir': '/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/', 'session': '53043'} INFO: Processing 33 pre-sorted seqinfo entries INFO: Reloading existing filegroup.json because /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/.heudiconv/20071/ses-53043/info/20071_ses-53043.edit.txt exists INFO: Doing conversion using dcm2niix INFO: Converting /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold (2200 DICOMs) -> /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func . Converter: dcm2niix . Output types: ('nii.gz',) INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix9dkekhre/convert". INFO: [Node] Executing "convert" INFO: stdout 2023-06-26T12:35:27.592798:Chris Rorden's dcm2niiX version v1.0.20200331 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0 (64-bit Linux) INFO: stdout 2023-06-26T12:35:27.592798:Found 2200 DICOM file(s) INFO: stdout 2023-06-26T12:35:27.592798:Slices not stacked: echo varies (TE 63.66, 38.94; echo 1, 1). Use 'merge 2D slices' option to force stacking INFO: stdout 2023-06-26T12:35:27.592798:Warning: Slice timing appears corrupted (range 26472.5..28070, TR=1761 ms) INFO: stdout 2023-06-26T12:35:27.592798:Convert 550 DICOM as /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv693_e1 (110x110x72x550) INFO: stdout 2023-06-26T12:36:03.039009:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv693_e1.nii" INFO: stdout 2023-06-26T12:36:03.039009:Warning: Slice timing appears corrupted (range 26450..28045, TR=1761 ms) INFO: stdout 2023-06-26T12:36:03.039009:Convert 550 DICOM as /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv693_e1a (110x110x72x550) INFO: stdout 2023-06-26T12:36:38.481006:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv693_e1a.nii" INFO: stdout 2023-06-26T12:36:38.481006:Warning: Slice timing appears corrupted (range 26415..28010, TR=1761 ms) INFO: stdout 2023-06-26T12:36:38.481006:Convert 550 DICOM as /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv693_e1b (110x110x72x550) INFO: stdout 2023-06-26T12:37:15.592549:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv693_e1b.nii" INFO: stdout 2023-06-26T12:37:15.592549:Warning: Slice timing appears corrupted (range 26497.5..28095, TR=1761 ms) INFO: stdout 2023-06-26T12:37:15.592549:Convert 550 DICOM as /net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv693_e1c (110x110x72x550) INFO: stdout 2023-06-26T12:38:02.250891:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/net/10.20.145.45/DOSENBACH03/GMT3/Noah/ASD_ADHD/sub-20071/ses-53043/func/sub-20071_ses-53043_task-rest_run-01_part-mag_bold_heudiconv693_e1c.nii" INFO: stdout 2023-06-26T12:38:02.250891:Conversion required 160.948591 seconds (12.709419 for core code). INFO: [Node] Finished "convert", elapsed time 164.316873s. Traceback (most recent call last): File "/home/usr/badenn/.local/bin/heudiconv", line 8, in sys.exit(main()) File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/cli/run.py", line 30, in main workflow(**kwargs) File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/main.py", line 463, in workflow prep_conversion( File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/convert.py", line 255, in prep_conversion convert( File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/convert.py", line 635, in convert tuneup_bids_json_files(bids_outfiles) File "/home/usr/badenn/.local/lib/python3.9/site-packages/heudiconv/bids.py", line 334, in tuneup_bids_json_files assert HEUDICONV_VERSION_JSON_KEY not in json_ AssertionError