QSM DICOM files error

[quentinduche]

I have this error when downloading QSM DICOM files that prevents dicom files to be extracted.
Not too sure this has something to do with the warning (though the dcm2iix --version are the same).

WARNING!: Current dcm2niix path /home/qduche/Software/fsl/bin/dcm2niix is different from dcm2niix configured path /usr/bin/dcm2niix
**********************************
*  Downloading subject VHD_0158  *
**********************************
	- acq-B-qsm VHD_0158 [1/1]
studyName:cohorte?vhd AND datasetName:QSM_3DMULTIGRE_B AND subjectName:VHD_0158 AND examinationComment:VHD*M0 AND examinationDate:[* TO *]
Proxy configuration file not found. Proxy will be ignored.
get keycloak token... Downloading dataset 1321296
/home/qduche/data/vhd/tmp_archived_dicoms/VHD_0158/Dataset_VHD_0158_1321296_QSM_3DMULTIGRE_B_QSM_3DMULTIGRE_B_20250204152145.zip: 102MiB [00:00, 850MiB/s] 
Downloading dataset 1321300
/home/qduche/data/vhd/tmp_archived_dicoms/VHD_0158/Dataset_VHD_0158_1321300_QSM_3DMULTIGRE_B_QSM_3DMULTIGRE_B_20250204152204.zip: 80.0MiB [00:00, 863MiB/s]
Downloading dataset 1321302
/home/qduche/data/vhd/tmp_archived_dicoms/VHD_0158/Dataset_VHD_0158_1321302_QSM_3DMULTIGRE_B_QSM_3DMULTIGRE_B_20250204152226.zip: 76.5MiB [00:00, 1.10GiB/s]
2025-02-04 15:22:54,225 [ WARNING] 'VHD_0158' label contained non-alphanumeric character(s), it was cleaned to be 'VHD0158'
Traceback (most recent call last):
  File "/home/qduche/Projects/VHD/download_cohort/./vhd_dl_qsm_b.py", line 213, in <module>
    main()
  File "/home/qduche/Projects/VHD/download_cohort/./vhd_dl_qsm_b.py", line 210, in main
    s2b.download()
  File "/home/qduche/Dev/shanoir_downloader/shanoir2bids.py", line 787, in download
    self.download_subject(subject_to_search=subject_to_search)
  File "/home/qduche/Dev/shanoir_downloader/shanoir2bids.py", line 758, in download_subject
    workflow(**workflow_params)
  File "/home/qduche/Projects/VHD/env/lib/python3.12/site-packages/heudiconv/main.py", line 479, in workflow
    prep_conversion(
  File "/home/qduche/Projects/VHD/env/lib/python3.12/site-packages/heudiconv/convert.py", line 259, in prep_conversion
    convert(
  File "/home/qduche/Projects/VHD/env/lib/python3.12/site-packages/heudiconv/convert.py", line 606, in convert
    convert_dicom(
  File "/home/qduche/Projects/VHD/env/lib/python3.12/site-packages/heudiconv/convert.py", line 761, in convert_dicom
    compress_dicoms(
  File "/home/qduche/Projects/VHD/env/lib/python3.12/site-packages/heudiconv/dicoms.py", line 593, in compress_dicoms
    dcm_time = get_reproducible_int(dicom_list)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/qduche/Projects/VHD/env/lib/python3.12/site-packages/heudiconv/dicoms.py", line 506, in get_reproducible_int
    dicom = dcm.dcmread(dicom_list[0], stop_before_pixels=True, force=True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/qduche/Projects/VHD/env/lib/python3.12/site-packages/pydicom/filereader.py", line 1042, in dcmread
    fp = open(fp, "rb")
         ^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/qduche/data/vhd/tmp_dicoms/VHD_0158/1162821/VHD_0158_20240731_QSM_3DMULTIGRE_B_1.4.9.12.34.1.8527.1019430574810669775696083940960843371423.dcm'

[alexpron]

Hello @quentinduche , it smells like permission error spirit due tot either datalad or NAS. It might also be the not correctly imported QSM Dicom files