heudiconv with ReproIn heuristic

Tutorial: How to create a BIDS dataset

Installation

Depending on your environment, paste the installation command here:

# < replace with installation command >

Download the data

Download the data by Nastase et al. (2020) from Zenodo. Note that the download make take a few minutes.

wget https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz

Code Output

--2026-02-05 18:30:21--  https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz
Resolving zenodo.org (zenodo.org)... 137.138.153.219, 137.138.52.235, 188.185.43.153, ...
Connecting to zenodo.org (zenodo.org)|137.138.153.219|:443... connected.
HTTP request sent, awaiting response... 301 MOVED PERMANENTLY
Location: /records/3677090/files/0219191_mystudy-0219-1114.tar.gz [following]
--2026-02-05 18:30:22--  https://zenodo.org/records/3677090/files/0219191_mystudy-0219-1114.tar.gz
Reusing existing connection to zenodo.org:443.
HTTP request sent, awaiting response... 200 OK
Length: 405671662 (387M) [application/octet-stream]
Saving to: ‘0219191_mystudy-0219-1114.tar.gz’

          0219191_m   0%[                    ]       0  --.-KB/s                        0219191_my   0%[                    ]  43.49K   181KB/s                       0219191_mys   0%[                    ] 209.66K   453KB/s                      0219191_myst   0%[                    ] 859.97K  1.23MB/s                     0219191_mystu   0%[                    ]   3.41M  3.76MB/s                    0219191_mystud   2%[                    ]   9.28M  8.21MB/s                   0219191_mystudy   3%[                    ]  15.44M  11.4MB/s                  0219191_mystudy-   5%[>                   ]  20.75M  13.2MB/s                 0219191_mystudy-0   7%[>                   ]  27.23M  15.2MB/s                0219191_mystudy-02   8%[>                   ]  34.70M  17.1MB/s               0219191_mystudy-021  10%[=>                  ]  41.68M  18.5MB/s               219191_mystudy-0219  12%[=>                  ]  49.14M  19.6MB/s               19191_mystudy-0219-  14%[=>                  ]  55.37M  20.3MB/s               9191_mystudy-0219-1  16%[==>                 ]  62.77M  21.2MB/s               191_mystudy-0219-11  18%[==>                 ]  69.71M  21.9MB/s    eta 14s    91_mystudy-0219-111  19%[==>                 ]  77.03M  22.6MB/s    eta 14s    1_mystudy-0219-1114  21%[===>                ]  83.94M  23.1MB/s    eta 14s    _mystudy-0219-1114.  23%[===>                ]  90.82M  23.5MB/s    eta 14s    mystudy-0219-1114.t  25%[====>               ]  96.96M  25.2MB/s    eta 14s    ystudy-0219-1114.ta  27%[====>               ] 104.68M  26.7MB/s    eta 12s    study-0219-1114.tar  28%[====>               ] 111.70M  28.1MB/s    eta 12s    tudy-0219-1114.tar.  30%[=====>              ] 119.31M  29.3MB/s    eta 12s    udy-0219-1114.tar.g  32%[=====>              ] 125.89M  30.1MB/s    eta 12s    dy-0219-1114.tar.gz  34%[=====>              ] 132.07M  30.1MB/s    eta 12s    y-0219-1114.tar.gz   35%[======>             ] 138.10M  30.0MB/s    eta 10s    -0219-1114.tar.gz    37%[======>             ] 143.98M  30.1MB/s    eta 10s    0219-1114.tar.gz     38%[======>             ] 150.45M  30.1MB/s    eta 10s    219-1114.tar.gz      40%[=======>            ] 156.63M  30.0MB/s    eta 10s    19-1114.tar.gz       42%[=======>            ] 163.54M  30.0MB/s    eta 10s    9-1114.tar.gz        44%[=======>            ] 170.90M  30.0MB/s    eta 8s     -1114.tar.gz         46%[========>           ] 178.37M  30.1MB/s    eta 8s     1114.tar.gz          47%[========>           ] 184.12M  30.0MB/s    eta 8s     114.tar.gz           49%[========>           ] 190.89M  29.9MB/s    eta 8s     14.tar.gz            51%[=========>          ] 198.06M  30.1MB/s    eta 8s     4.tar.gz             52%[=========>          ] 204.24M  29.9MB/s    eta 7s     .tar.gz              54%[=========>          ] 211.30M  29.9MB/s    eta 7s     tar.gz               56%[==========>         ] 217.39M  29.7MB/s    eta 7s     ar.gz                58%[==========>         ] 224.56M  29.7MB/s    eta 7s     r.gz                 59%[==========>         ] 231.73M  29.9MB/s    eta 7s     .gz                  61%[===========>        ] 238.92M  29.8MB/s    eta 5s     gz                   63%[===========>        ] 245.86M  29.8MB/s    eta 5s     z                    65%[============>       ] 252.82M  29.7MB/s    eta 5s                          67%[============>       ] 259.99M  29.7MB/s    eta 5s                       0  68%[============>       ] 265.76M  29.7MB/s    eta 5s                      02  70%[=============>      ] 272.33M  29.8MB/s    eta 4s                     021  72%[=============>      ] 278.59M  29.8MB/s    eta 4s                    0219  73%[=============>      ] 285.75M  30.0MB/s    eta 4s                   02191  75%[==============>     ] 292.91M  30.3MB/s    eta 4s                  021919  76%[==============>     ] 297.06M  29.7MB/s    eta 4s                 0219191  78%[==============>     ] 303.56M  29.6MB/s    eta 3s                0219191_  80%[===============>    ] 311.20M  29.7MB/s    eta 3s               0219191_m  82%[===============>    ] 318.55M  29.8MB/s    eta 3s              0219191_my  84%[===============>    ] 325.75M  30.1MB/s    eta 3s             0219191_mys  86%[================>   ] 333.43M  30.1MB/s    eta 3s            0219191_myst  87%[================>   ] 340.20M  30.1MB/s    eta 2s           0219191_mystu  89%[================>   ] 346.89M  30.2MB/s    eta 2s          0219191_mystud  91%[=================>  ] 354.54M  30.4MB/s    eta 2s         0219191_mystudy  93%[=================>  ] 361.59M  30.3MB/s    eta 2s        0219191_mystudy-  95%[==================> ] 368.85M  30.4MB/s    eta 2s       0219191_mystudy-0  96%[==================> ] 375.03M  30.1MB/s    eta 0s      0219191_mystudy-02  98%[==================> ] 382.71M  30.2MB/s    eta 0s     0219191_mystudy-021 100%[===================>] 386.88M  30.3MB/s    in 14s     

2026-02-05 18:30:36 (28.3 MB/s) - ‘0219191_mystudy-0219-1114.tar.gz’ saved [405671662/405671662]

Prepare the data

Now we need to extract the downloaded archive. The following command extracts the tar.gz archive (-x extract, -v verbose, -z gzip, -f file).

tar -xvzf 0219191_mystudy-0219-1114.tar.gz

Code Output

0219191_mystudy-0219-1114/
0219191_mystudy-0219-1114/.DS_Store
0219191_mystudy-0219-1114/gzip-report.log
0219191_mystudy-0219-1114/TransferStatus.log
0219191_mystudy-0219-1114/dcm/
0219191_mystudy-0219-1114/dcm/12-320-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-118-1.dcm.gz
0219191_mystudy-0219-1114/dcm/7-5-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-32-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-188-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-393-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-10-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-189-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-34-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-86-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-178-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-84-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-262-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-129-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-256-1.dcm.gz
0219191_mystudy-0219-1114/dcm/7-3-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-113-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-139-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-169-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-222-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-209-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-69-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-115-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-97-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-481-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-306-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-349-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-197-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-437-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-113-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-338-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-17-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-386-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-71-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-216-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-300-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-202-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-66-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-86-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-363-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-353-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-48-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-88-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-380-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-442-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-162-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-85-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-319-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-138-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-284-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-46-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-14-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-4-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-104-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-19-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-181-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-429-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-306-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-158-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-245-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-58-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-80-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-410-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-349-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-85-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-191-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-169-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-437-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-177-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-173-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-67-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-172-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-134-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-414-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-326-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-175-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-172-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-291-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-334-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-470-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-8-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-50-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-41-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-318-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-465-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-333-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-14-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-344-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-331-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-117-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-74-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-59-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-293-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-9-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-196-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-93-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-14-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-269-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-60-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-247-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-119-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-345-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-395-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-72-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-191-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-76-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-452-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-403-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-95-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-183-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-223-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-137-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-184-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-192-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-96-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-47-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-178-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-223-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-146-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-86-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-400-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-41-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-321-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-130-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-141-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-290-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-407-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-361-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-65-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-145-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-37-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-335-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-198-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-82-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-471-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-120-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-111-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-391-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-433-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-161-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-161-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-422-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-98-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-267-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-154-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-322-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-392-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-169-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-448-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-49-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-165-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-268-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-191-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-232-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-451-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-229-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-242-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-146-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-20-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-263-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-104-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-173-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-391-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-321-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-238-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-243-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-27-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-18-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-179-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-21-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-81-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-473-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-96-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-64-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-22-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-145-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-38-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-340-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-51-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-6-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-149-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-456-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-126-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-54-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-293-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-17-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-144-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-290-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-364-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-79-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-116-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-227-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-167-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-28-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-114-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-128-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-10-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-256-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-101-1.dcm.gz
0219191_mystudy-0219-1114/dcm/2-1-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-394-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-88-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-219-1.dcm.gz
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0219191_mystudy-0219-1114/dcm/9-239-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-485-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-48-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-114-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-252-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-138-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-162-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-185-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-365-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-330-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-189-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-161-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-78-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-202-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-149-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-409-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-175-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-91-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-54-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-455-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-384-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-416-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-160-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-300-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-108-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-210-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-264-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-301-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-444-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-106-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-421-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-12-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-246-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-385-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-148-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-115-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-51-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-138-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-153-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-371-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-340-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-162-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-118-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-159-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-357-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-76-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-153-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-231-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-241-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-271-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-446-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-348-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-132-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-364-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-304-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-456-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-444-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-393-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-78-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-116-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-251-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-249-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-377-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-255-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-286-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-21-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-174-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-120-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-128-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-30-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-398-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-204-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-244-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-45-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-39-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-379-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-379-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-61-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-200-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-6-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-303-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-473-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-33-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-171-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-81-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-176-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-60-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-7-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-50-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-366-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-323-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-228-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-101-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-48-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-207-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-80-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-111-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-136-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-402-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-457-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-45-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-243-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-194-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-331-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-169-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-329-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-151-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-416-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-326-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-314-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-101-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-72-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-39-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-77-1.dcm.gz
0219191_mystudy-0219-1114/dcm/5-1-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-82-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-131-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-406-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-161-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-238-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-35-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-168-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-8-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-394-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-90-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-31-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-36-1.dcm.gz
0219191_mystudy-0219-1114/dcm/13-60-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-279-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-140-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-225-1.dcm.gz
0219191_mystudy-0219-1114/dcm/11-480-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-210-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-402-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-482-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-358-1.dcm.gz
0219191_mystudy-0219-1114/dcm/10-12-1.dcm.gz

Inspect the raw data

Let’s navigate into the directory and see what’s inside the dataset. Using tree -L 2 we show the directory structure with a maximum depth of 2 levels.

tree -L 2 0219191_mystudy-0219-1114

Code Output

0219191_mystudy-0219-1114
├── TransferStatus.log
├── dcm
│   ├── 1-1-1.dcm.gz
│   ├── 1-10-1.dcm.gz
│   ├── 1-100-1.dcm.gz
│   ├── 1-101-1.dcm.gz
│   ├── 1-102-1.dcm.gz
│   ├── 1-103-1.dcm.gz
│   ├── 1-104-1.dcm.gz
│   ├── 1-105-1.dcm.gz
│   ├── 1-106-1.dcm.gz
│   ├── 1-107-1.dcm.gz
│   ├── 1-108-1.dcm.gz
│   ├── 1-109-1.dcm.gz
│   ├── 1-11-1.dcm.gz
│   ├── 1-110-1.dcm.gz
│   ├── 1-111-1.dcm.gz
│   ├── 1-112-1.dcm.gz
│   ├── 1-113-1.dcm.gz
│   ├── 1-114-1.dcm.gz
│   ├── 1-115-1.dcm.gz
│   ├── 1-116-1.dcm.gz
│   ├── 1-117-1.dcm.gz
│   ├── 1-118-1.dcm.gz
│   ├── 1-119-1.dcm.gz
│   ├── 1-12-1.dcm.gz
│   ├── 1-120-1.dcm.gz
│   ├── 1-121-1.dcm.gz
│   ├── 1-122-1.dcm.gz
│   ├── 1-123-1.dcm.gz
│   ├── 1-124-1.dcm.gz
│   ├── 1-125-1.dcm.gz
│   ├── 1-126-1.dcm.gz
│   ├── 1-127-1.dcm.gz
│   ├── 1-128-1.dcm.gz
│   ├── 1-13-1.dcm.gz
│   ├── 1-14-1.dcm.gz
│   ├── 1-15-1.dcm.gz
│   ├── 1-16-1.dcm.gz
│   ├── 1-17-1.dcm.gz
│   ├── 1-18-1.dcm.gz
│   ├── 1-19-1.dcm.gz
│   ├── 1-2-1.dcm.gz
│   ├── 1-20-1.dcm.gz
│   ├── 1-21-1.dcm.gz
│   ├── 1-22-1.dcm.gz
│   ├── 1-23-1.dcm.gz
│   ├── 1-24-1.dcm.gz
│   ├── 1-25-1.dcm.gz
│   ├── 1-26-1.dcm.gz
│   ├── 1-27-1.dcm.gz
│   ├── 1-28-1.dcm.gz
│   ├── 1-29-1.dcm.gz
│   ├── 1-3-1.dcm.gz
│   ├── 1-30-1.dcm.gz
│   ├── 1-31-1.dcm.gz
│   ├── 1-32-1.dcm.gz
│   ├── 1-33-1.dcm.gz
│   ├── 1-34-1.dcm.gz
│   ├── 1-35-1.dcm.gz
│   ├── 1-36-1.dcm.gz
│   ├── 1-37-1.dcm.gz
│   ├── 1-38-1.dcm.gz
│   ├── 1-39-1.dcm.gz
│   ├── 1-4-1.dcm.gz
│   ├── 1-40-1.dcm.gz
│   ├── 1-41-1.dcm.gz
│   ├── 1-42-1.dcm.gz
│   ├── 1-43-1.dcm.gz
│   ├── 1-44-1.dcm.gz
│   ├── 1-45-1.dcm.gz
│   ├── 1-46-1.dcm.gz
│   ├── 1-47-1.dcm.gz
│   ├── 1-48-1.dcm.gz
│   ├── 1-49-1.dcm.gz
│   ├── 1-5-1.dcm.gz
│   ├── 1-50-1.dcm.gz
│   ├── 1-51-1.dcm.gz
│   ├── 1-52-1.dcm.gz
│   ├── 1-53-1.dcm.gz
│   ├── 1-54-1.dcm.gz
│   ├── 1-55-1.dcm.gz
│   ├── 1-56-1.dcm.gz
│   ├── 1-57-1.dcm.gz
│   ├── 1-58-1.dcm.gz
│   ├── 1-59-1.dcm.gz
│   ├── 1-6-1.dcm.gz
│   ├── 1-60-1.dcm.gz
│   ├── 1-61-1.dcm.gz
│   ├── 1-62-1.dcm.gz
│   ├── 1-63-1.dcm.gz
│   ├── 1-64-1.dcm.gz
│   ├── 1-65-1.dcm.gz
│   ├── 1-66-1.dcm.gz
│   ├── 1-67-1.dcm.gz
│   ├── 1-68-1.dcm.gz
│   ├── 1-69-1.dcm.gz
│   ├── 1-7-1.dcm.gz
│   ├── 1-70-1.dcm.gz
│   ├── 1-71-1.dcm.gz
│   ├── 1-72-1.dcm.gz
│   ├── 1-73-1.dcm.gz
│   ├── 1-74-1.dcm.gz
│   ├── 1-75-1.dcm.gz
│   ├── 1-76-1.dcm.gz
│   ├── 1-77-1.dcm.gz
│   ├── 1-78-1.dcm.gz
│   ├── 1-79-1.dcm.gz
│   ├── 1-8-1.dcm.gz
│   ├── 1-80-1.dcm.gz
│   ├── 1-81-1.dcm.gz
│   ├── 1-82-1.dcm.gz
│   ├── 1-83-1.dcm.gz
│   ├── 1-84-1.dcm.gz
│   ├── 1-85-1.dcm.gz
│   ├── 1-86-1.dcm.gz
│   ├── 1-87-1.dcm.gz
│   ├── 1-88-1.dcm.gz
│   ├── 1-89-1.dcm.gz
│   ├── 1-9-1.dcm.gz
│   ├── 1-90-1.dcm.gz
│   ├── 1-91-1.dcm.gz
│   ├── 1-92-1.dcm.gz
│   ├── 1-93-1.dcm.gz
│   ├── 1-94-1.dcm.gz
│   ├── 1-95-1.dcm.gz
│   ├── 1-96-1.dcm.gz
│   ├── 1-97-1.dcm.gz
│   ├── 1-98-1.dcm.gz
│   ├── 1-99-1.dcm.gz
│   ├── 10-1-1.dcm.gz
│   ├── 10-10-1.dcm.gz
│   ├── 10-100-1.dcm.gz
│   ├── 10-101-1.dcm.gz
│   ├── 10-102-1.dcm.gz
│   ├── 10-103-1.dcm.gz
│   ├── 10-104-1.dcm.gz
│   ├── 10-105-1.dcm.gz
│   ├── 10-106-1.dcm.gz
│   ├── 10-107-1.dcm.gz
│   ├── 10-108-1.dcm.gz
│   ├── 10-109-1.dcm.gz
│   ├── 10-11-1.dcm.gz
│   ├── 10-110-1.dcm.gz
│   ├── 10-111-1.dcm.gz
│   ├── 10-112-1.dcm.gz
│   ├── 10-113-1.dcm.gz
│   ├── 10-114-1.dcm.gz
│   ├── 10-115-1.dcm.gz
│   ├── 10-116-1.dcm.gz
│   ├── 10-117-1.dcm.gz
│   ├── 10-118-1.dcm.gz
│   ├── 10-119-1.dcm.gz
│   ├── 10-12-1.dcm.gz
│   ├── 10-120-1.dcm.gz
│   ├── 10-121-1.dcm.gz
│   ├── 10-122-1.dcm.gz
│   ├── 10-123-1.dcm.gz
│   ├── 10-124-1.dcm.gz
│   ├── 10-125-1.dcm.gz
│   ├── 10-126-1.dcm.gz
│   ├── 10-127-1.dcm.gz
│   ├── 10-128-1.dcm.gz
│   ├── 10-129-1.dcm.gz
│   ├── 10-13-1.dcm.gz
│   ├── 10-130-1.dcm.gz
│   ├── 10-131-1.dcm.gz
│   ├── 10-132-1.dcm.gz
│   ├── 10-133-1.dcm.gz
│   ├── 10-134-1.dcm.gz
│   ├── 10-135-1.dcm.gz
│   ├── 10-136-1.dcm.gz
│   ├── 10-137-1.dcm.gz
│   ├── 10-138-1.dcm.gz
│   ├── 10-139-1.dcm.gz
│   ├── 10-14-1.dcm.gz
│   ├── 10-140-1.dcm.gz
│   ├── 10-141-1.dcm.gz
│   ├── 10-142-1.dcm.gz
│   ├── 10-143-1.dcm.gz
│   ├── 10-144-1.dcm.gz
│   ├── 10-145-1.dcm.gz
│   ├── 10-146-1.dcm.gz
│   ├── 10-147-1.dcm.gz
│   ├── 10-148-1.dcm.gz
│   ├── 10-149-1.dcm.gz
│   ├── 10-15-1.dcm.gz
│   ├── 10-150-1.dcm.gz
│   ├── 10-151-1.dcm.gz
│   ├── 10-152-1.dcm.gz
│   ├── 10-153-1.dcm.gz
│   ├── 10-154-1.dcm.gz
│   ├── 10-155-1.dcm.gz
│   ├── 10-156-1.dcm.gz
│   ├── 10-157-1.dcm.gz
│   ├── 10-158-1.dcm.gz
│   ├── 10-159-1.dcm.gz
│   ├── 10-16-1.dcm.gz
│   ├── 10-160-1.dcm.gz
│   ├── 10-161-1.dcm.gz
│   ├── 10-162-1.dcm.gz
│   ├── 10-163-1.dcm.gz
│   ├── 10-164-1.dcm.gz
│   ├── 10-165-1.dcm.gz
│   ├── 10-166-1.dcm.gz
│   ├── 10-167-1.dcm.gz
│   ├── 10-168-1.dcm.gz
│   ├── 10-169-1.dcm.gz
│   ├── 10-17-1.dcm.gz
│   ├── 10-170-1.dcm.gz
│   ├── 10-171-1.dcm.gz
│   ├── 10-172-1.dcm.gz
│   ├── 10-173-1.dcm.gz
│   ├── 10-174-1.dcm.gz
│   ├── 10-175-1.dcm.gz
│   ├── 10-176-1.dcm.gz
│   ├── 10-177-1.dcm.gz
│   ├── 10-178-1.dcm.gz
│   ├── 10-179-1.dcm.gz
│   ├── 10-18-1.dcm.gz
│   ├── 10-180-1.dcm.gz
│   ├── 10-181-1.dcm.gz
│   ├── 10-182-1.dcm.gz
│   ├── 10-183-1.dcm.gz
│   ├── 10-184-1.dcm.gz
│   ├── 10-185-1.dcm.gz
│   ├── 10-186-1.dcm.gz
│   ├── 10-187-1.dcm.gz
│   ├── 10-188-1.dcm.gz
│   ├── 10-189-1.dcm.gz
│   ├── 10-19-1.dcm.gz
│   ├── 10-190-1.dcm.gz
│   ├── 10-191-1.dcm.gz
│   ├── 10-192-1.dcm.gz
│   ├── 10-193-1.dcm.gz
│   ├── 10-194-1.dcm.gz
│   ├── 10-195-1.dcm.gz
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│   ├── 9-39-1.dcm.gz
│   ├── 9-390-1.dcm.gz
│   ├── 9-391-1.dcm.gz
│   ├── 9-392-1.dcm.gz
│   ├── 9-393-1.dcm.gz
│   ├── 9-394-1.dcm.gz
│   ├── 9-395-1.dcm.gz
│   ├── 9-396-1.dcm.gz
│   ├── 9-397-1.dcm.gz
│   ├── 9-398-1.dcm.gz
│   ├── 9-399-1.dcm.gz
│   ├── 9-4-1.dcm.gz
│   ├── 9-40-1.dcm.gz
│   ├── 9-400-1.dcm.gz
│   ├── 9-401-1.dcm.gz
│   ├── 9-402-1.dcm.gz
│   ├── 9-403-1.dcm.gz
│   ├── 9-404-1.dcm.gz
│   ├── 9-405-1.dcm.gz
│   ├── 9-406-1.dcm.gz
│   ├── 9-407-1.dcm.gz
│   ├── 9-408-1.dcm.gz
│   ├── 9-409-1.dcm.gz
│   ├── 9-41-1.dcm.gz
│   ├── 9-410-1.dcm.gz
│   ├── 9-411-1.dcm.gz
│   ├── 9-412-1.dcm.gz
│   ├── 9-413-1.dcm.gz
│   ├── 9-414-1.dcm.gz
│   ├── 9-415-1.dcm.gz
│   ├── 9-416-1.dcm.gz
│   ├── 9-417-1.dcm.gz
│   ├── 9-418-1.dcm.gz
│   ├── 9-419-1.dcm.gz
│   ├── 9-42-1.dcm.gz
│   ├── 9-420-1.dcm.gz
│   ├── 9-421-1.dcm.gz
│   ├── 9-422-1.dcm.gz
│   ├── 9-423-1.dcm.gz
│   ├── 9-424-1.dcm.gz
│   ├── 9-425-1.dcm.gz
│   ├── 9-426-1.dcm.gz
│   ├── 9-427-1.dcm.gz
│   ├── 9-428-1.dcm.gz
│   ├── 9-429-1.dcm.gz
│   ├── 9-43-1.dcm.gz
│   ├── 9-430-1.dcm.gz
│   ├── 9-431-1.dcm.gz
│   ├── 9-432-1.dcm.gz
│   ├── 9-433-1.dcm.gz
│   ├── 9-434-1.dcm.gz
│   ├── 9-435-1.dcm.gz
│   ├── 9-436-1.dcm.gz
│   ├── 9-437-1.dcm.gz
│   ├── 9-438-1.dcm.gz
│   ├── 9-439-1.dcm.gz
│   ├── 9-44-1.dcm.gz
│   ├── 9-440-1.dcm.gz
│   ├── 9-441-1.dcm.gz
│   ├── 9-442-1.dcm.gz
│   ├── 9-443-1.dcm.gz
│   ├── 9-444-1.dcm.gz
│   ├── 9-445-1.dcm.gz
│   ├── 9-446-1.dcm.gz
│   ├── 9-447-1.dcm.gz
│   ├── 9-448-1.dcm.gz
│   ├── 9-449-1.dcm.gz
│   ├── 9-45-1.dcm.gz
│   ├── 9-450-1.dcm.gz
│   ├── 9-451-1.dcm.gz
│   ├── 9-452-1.dcm.gz
│   ├── 9-453-1.dcm.gz
│   ├── 9-454-1.dcm.gz
│   ├── 9-455-1.dcm.gz
│   ├── 9-456-1.dcm.gz
│   ├── 9-457-1.dcm.gz
│   ├── 9-458-1.dcm.gz
│   ├── 9-459-1.dcm.gz
│   ├── 9-46-1.dcm.gz
│   ├── 9-460-1.dcm.gz
│   ├── 9-461-1.dcm.gz
│   ├── 9-462-1.dcm.gz
│   ├── 9-463-1.dcm.gz
│   ├── 9-464-1.dcm.gz
│   ├── 9-465-1.dcm.gz
│   ├── 9-466-1.dcm.gz
│   ├── 9-467-1.dcm.gz
│   ├── 9-468-1.dcm.gz
│   ├── 9-469-1.dcm.gz
│   ├── 9-47-1.dcm.gz
│   ├── 9-470-1.dcm.gz
│   ├── 9-471-1.dcm.gz
│   ├── 9-472-1.dcm.gz
│   ├── 9-473-1.dcm.gz
│   ├── 9-474-1.dcm.gz
│   ├── 9-475-1.dcm.gz
│   ├── 9-476-1.dcm.gz
│   ├── 9-477-1.dcm.gz
│   ├── 9-478-1.dcm.gz
│   ├── 9-479-1.dcm.gz
│   ├── 9-48-1.dcm.gz
│   ├── 9-480-1.dcm.gz
│   ├── 9-481-1.dcm.gz
│   ├── 9-482-1.dcm.gz
│   ├── 9-483-1.dcm.gz
│   ├── 9-484-1.dcm.gz
│   ├── 9-485-1.dcm.gz
│   ├── 9-49-1.dcm.gz
│   ├── 9-5-1.dcm.gz
│   ├── 9-50-1.dcm.gz
│   ├── 9-51-1.dcm.gz
│   ├── 9-52-1.dcm.gz
│   ├── 9-53-1.dcm.gz
│   ├── 9-54-1.dcm.gz
│   ├── 9-55-1.dcm.gz
│   ├── 9-56-1.dcm.gz
│   ├── 9-57-1.dcm.gz
│   ├── 9-58-1.dcm.gz
│   ├── 9-59-1.dcm.gz
│   ├── 9-6-1.dcm.gz
│   ├── 9-60-1.dcm.gz
│   ├── 9-61-1.dcm.gz
│   ├── 9-62-1.dcm.gz
│   ├── 9-63-1.dcm.gz
│   ├── 9-64-1.dcm.gz
│   ├── 9-65-1.dcm.gz
│   ├── 9-66-1.dcm.gz
│   ├── 9-67-1.dcm.gz
│   ├── 9-68-1.dcm.gz
│   ├── 9-69-1.dcm.gz
│   ├── 9-7-1.dcm.gz
│   ├── 9-70-1.dcm.gz
│   ├── 9-71-1.dcm.gz
│   ├── 9-72-1.dcm.gz
│   ├── 9-73-1.dcm.gz
│   ├── 9-74-1.dcm.gz
│   ├── 9-75-1.dcm.gz
│   ├── 9-76-1.dcm.gz
│   ├── 9-77-1.dcm.gz
│   ├── 9-78-1.dcm.gz
│   ├── 9-79-1.dcm.gz
│   ├── 9-8-1.dcm.gz
│   ├── 9-80-1.dcm.gz
│   ├── 9-81-1.dcm.gz
│   ├── 9-82-1.dcm.gz
│   ├── 9-83-1.dcm.gz
│   ├── 9-84-1.dcm.gz
│   ├── 9-85-1.dcm.gz
│   ├── 9-86-1.dcm.gz
│   ├── 9-87-1.dcm.gz
│   ├── 9-88-1.dcm.gz
│   ├── 9-89-1.dcm.gz
│   ├── 9-9-1.dcm.gz
│   ├── 9-90-1.dcm.gz
│   ├── 9-91-1.dcm.gz
│   ├── 9-92-1.dcm.gz
│   ├── 9-93-1.dcm.gz
│   ├── 9-94-1.dcm.gz
│   ├── 9-95-1.dcm.gz
│   ├── 9-96-1.dcm.gz
│   ├── 9-97-1.dcm.gz
│   ├── 9-98-1.dcm.gz
│   └── 9-99-1.dcm.gz
└── gzip-report.log

2 directories, 2663 files

Decompress the data

We need to decompress all gzipped DICOM files in the dcm directory:

gunzip 0219191_mystudy-0219-1114/dcm/*.dcm.gz

Run heudiconv

Finally, we can run heudiconv! The following command converts DICOM files to BIDS format using the ReproIn heuristic for subject 01 and session 01.

Here is an explanation for the flags and arguments:

• -f reproin specifies the converter file to use
• --subject 01 specifies the subject
• --ses 01 specifies the subject
• --bids is a flag for output into BIDS structure
• --files or directories containing files to process
• --overwrite overwrites existing converted files

heudiconv -f reproin --subject 01 --ses 01 --bids --files 0219191_mystudy-0219-1114/dcm --overwrite

Code Output

WARNING: Could not check for version updates: Connection to server could not be made
INFO: Running heudiconv version 1.3.4 latest Unknown
INFO: Analyzing 2661 dicoms
INFO: Filtering out 0 dicoms based on their filename
INFO: Generated sequence info for 1 studies with 13 entries total
INFO: Processing sequence infos to deduce study/session
INFO: Study session for StudySessionInfo(locator='Norman/Mennen/5516_greenEyes', session='01', subject='01')
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': '01', 'outdir': '/app/Norman/Mennen/5516_greenEyes', 'session': '01'}
INFO: Processing 13 pre-sorted seqinfo entries
INFO: Processing 13 seqinfo entries
WARNING: Previous run (4) was larger than explicitly specified 1
WARNING: Detected 3 duplicated run(s) for template {bids_subject_session_dir}/anat/{bids_subject_session_prefix}_scout: ['1-anat_ses-01_scout', '2-anat_ses-01_scout', '3-anat_ses-01_scout']
WARNING: Detected 2 duplicated run(s) for template {bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-sound_run-01_bold: ['6-func_ses-01_task-sound_run-01', '7-func_ses-01_task-sound_run-01']
INFO: Doing conversion using dcm2niix
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout (3 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:30:55,369 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niix9oi1mk2e/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix9oi1mk2e/convert".
260205-18:30:55,372 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:30:55,495 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.495920:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:30:55.495920:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:30:55,496 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.495920:Found 3 DICOM file(s)
INFO: stdout 2026-02-05T18:30:55.495920:Found 3 DICOM file(s)
260205-18:30:55,496 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.495920:Slices not stacked: orientation varies (vNav or localizer?) [0.996918 -0.0146115 0.077075 -0.00902414 0.954619 0.297693] != [0.999714 -0.00832137 0.0224079 0.00569606 0.993375 0.114773]
INFO: stdout 2026-02-05T18:30:55.495920:Slices not stacked: orientation varies (vNav or localizer?) [0.996918 -0.0146115 0.077075 -0.00902414 0.954619 0.297693] != [0.999714 -0.00832137 0.0224079 0.00569606 0.993375 0.114773]
260205-18:30:55,496 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.495920:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv789_i00001 (162x162x1x1)
INFO: stdout 2026-02-05T18:30:55.495920:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv789_i00001 (162x162x1x1)
260205-18:30:55,500 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.500025:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv789_i00002 (162x162x1x1)
INFO: stdout 2026-02-05T18:30:55.500025:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv789_i00002 (162x162x1x1)
260205-18:30:55,503 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.503566:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv789_i00003 (162x162x1x1)
INFO: stdout 2026-02-05T18:30:55.503566:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv789_i00003 (162x162x1x1)
260205-18:30:55,506 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.506502:Conversion required 0.016628 seconds (0.016608 for core code).
INFO: stdout 2026-02-05T18:30:55.506502:Conversion required 0.016628 seconds (0.016608 for core code).
260205-18:30:55,537 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.082982s.
INFO: [Node] Finished "convert", elapsed time 0.082982s.
WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_T1w (192 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:30:55,819 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixuzvryqhx/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixuzvryqhx/convert".
260205-18:30:55,858 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:30:55,958 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.958747:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:30:55.958747:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:30:55,958 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.958747:Found 192 DICOM file(s)
INFO: stdout 2026-02-05T18:30:55.958747:Found 192 DICOM file(s)
260205-18:30:55,958 nipype.interface INFO:
     stdout 2026-02-05T18:30:55.958747:Convert 192 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_T1w_heudiconv778 (256x256x192x1)
INFO: stdout 2026-02-05T18:30:55.958747:Convert 192 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_T1w_heudiconv778 (256x256x192x1)
260205-18:30:58,260 nipype.interface INFO:
     stdout 2026-02-05T18:30:58.260320:Conversion required 2.364249 seconds (2.364021 for core code).
INFO: stdout 2026-02-05T18:30:58.260320:Conversion required 2.364249 seconds (2.364021 for core code).
260205-18:30:58,287 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 2.428042s.
INFO: [Node] Finished "convert", elapsed time 2.428042s.
260205-18:31:03,909 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmeta5hs7vpqc/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmeta5hs7vpqc/embedder".
260205-18:31:03,921 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:31:07,196 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 3.2748559999999998s.
INFO: [Node] Finished "embedder", elapsed time 3.2748559999999998s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_T1w.json file
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold (179 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:31:07,222 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixo8yjm5r9/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixo8yjm5r9/convert".
260205-18:31:07,257 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:31:07,357 nipype.interface INFO:
     stdout 2026-02-05T18:31:07.357241:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:31:07.357241:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:31:07,357 nipype.interface INFO:
     stdout 2026-02-05T18:31:07.357241:Found 179 DICOM file(s)
INFO: stdout 2026-02-05T18:31:07.357241:Found 179 DICOM file(s)
260205-18:31:07,357 nipype.interface INFO:
     stdout 2026-02-05T18:31:07.357241:Convert 179 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold_heudiconv728 (64x64x27x179)
INFO: stdout 2026-02-05T18:31:07.357241:Convert 179 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold_heudiconv728 (64x64x27x179)
260205-18:31:10,354 nipype.interface INFO:
     stdout 2026-02-05T18:31:10.354214:Conversion required 3.059843 seconds (3.059605 for core code).
INFO: stdout 2026-02-05T18:31:10.354214:Conversion required 3.059843 seconds (3.059605 for core code).
260205-18:31:10,387 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 3.129354s.
INFO: [Node] Finished "convert", elapsed time 3.129354s.
260205-18:31:16,609 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmeta4vqimtpu/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmeta4vqimtpu/embedder".
260205-18:31:16,620 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:31:20,728 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 4.107611s.
INFO: [Node] Finished "embedder", elapsed time 4.107611s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json file
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_bold (485 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:31:20,760 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niix9hefpwve/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix9hefpwve/convert".
260205-18:31:20,855 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:31:21,46 nipype.interface INFO:
     stdout 2026-02-05T18:31:21.046234:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:31:21.046234:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:31:21,46 nipype.interface INFO:
     stdout 2026-02-05T18:31:21.046234:Found 485 DICOM file(s)
INFO: stdout 2026-02-05T18:31:21.046234:Found 485 DICOM file(s)
260205-18:31:21,46 nipype.interface INFO:
     stdout 2026-02-05T18:31:21.046234:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_bold_heudiconv743 (64x64x27x485)
INFO: stdout 2026-02-05T18:31:21.046234:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_bold_heudiconv743 (64x64x27x485)
260205-18:31:29,153 nipype.interface INFO:
     stdout 2026-02-05T18:31:29.153907:Conversion required 8.260883 seconds (8.259947 for core code).
INFO: stdout 2026-02-05T18:31:29.153907:Conversion required 8.260883 seconds (8.259947 for core code).
260205-18:31:29,183 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 8.326382s.
INFO: [Node] Finished "convert", elapsed time 8.326382s.
260205-18:31:46,144 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetaxsbo48in/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetaxsbo48in/embedder".
260205-18:31:46,168 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:31:57,491 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 11.322183s.
INFO: [Node] Finished "embedder", elapsed time 11.322183s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_bold.json file
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_bold (485 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:31:57,553 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixs67nm2mo/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixs67nm2mo/convert".
260205-18:31:57,648 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:31:57,843 nipype.interface INFO:
     stdout 2026-02-05T18:31:57.842981:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:31:57.842981:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:31:57,843 nipype.interface INFO:
     stdout 2026-02-05T18:31:57.842981:Found 485 DICOM file(s)
INFO: stdout 2026-02-05T18:31:57.842981:Found 485 DICOM file(s)
260205-18:31:57,843 nipype.interface INFO:
     stdout 2026-02-05T18:31:57.842981:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_bold_heudiconv516 (64x64x27x485)
INFO: stdout 2026-02-05T18:31:57.842981:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_bold_heudiconv516 (64x64x27x485)
260205-18:32:06,14 nipype.interface INFO:
     stdout 2026-02-05T18:32:06.014803:Conversion required 8.328845 seconds (8.328069 for core code).
INFO: stdout 2026-02-05T18:32:06.014803:Conversion required 8.328845 seconds (8.328069 for core code).
260205-18:32:06,49 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 8.400514s.
INFO: [Node] Finished "convert", elapsed time 8.400514s.
260205-18:32:22,574 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmeta9f3q4on8/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmeta9f3q4on8/embedder".
260205-18:32:22,598 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:32:33,774 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 11.176232s.
INFO: [Node] Finished "embedder", elapsed time 11.176232s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_bold.json file
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold (485 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:32:33,836 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixaakyvn0u/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixaakyvn0u/convert".
260205-18:32:33,930 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:32:34,123 nipype.interface INFO:
     stdout 2026-02-05T18:32:34.123659:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:32:34.123659:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:32:34,123 nipype.interface INFO:
     stdout 2026-02-05T18:32:34.123659:Found 485 DICOM file(s)
INFO: stdout 2026-02-05T18:32:34.123659:Found 485 DICOM file(s)
260205-18:32:34,123 nipype.interface INFO:
     stdout 2026-02-05T18:32:34.123659:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold_heudiconv344 (64x64x27x485)
INFO: stdout 2026-02-05T18:32:34.123659:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold_heudiconv344 (64x64x27x485)
260205-18:32:42,269 nipype.interface INFO:
     stdout 2026-02-05T18:32:42.268996:Conversion required 8.302907 seconds (8.302164 for core code).
INFO: stdout 2026-02-05T18:32:42.268996:Conversion required 8.302907 seconds (8.302164 for core code).
260205-18:32:42,299 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 8.36874s.
INFO: [Node] Finished "convert", elapsed time 8.36874s.
260205-18:32:58,611 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetah0sf1sbp/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetah0sf1sbp/embedder".
260205-18:32:58,635 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:33:09,717 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 11.081921s.
INFO: [Node] Finished "embedder", elapsed time 11.081921s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json file
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-04_bold (485 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:33:09,780 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixbrabgyfe/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixbrabgyfe/convert".
260205-18:33:09,873 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:33:10,69 nipype.interface INFO:
     stdout 2026-02-05T18:33:10.069148:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:33:10.069148:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:33:10,69 nipype.interface INFO:
     stdout 2026-02-05T18:33:10.069148:Found 485 DICOM file(s)
INFO: stdout 2026-02-05T18:33:10.069148:Found 485 DICOM file(s)
260205-18:33:10,69 nipype.interface INFO:
     stdout 2026-02-05T18:33:10.069148:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-04_bold_heudiconv382 (64x64x27x485)
INFO: stdout 2026-02-05T18:33:10.069148:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-04_bold_heudiconv382 (64x64x27x485)
260205-18:33:18,247 nipype.interface INFO:
     stdout 2026-02-05T18:33:18.247578:Conversion required 8.337986 seconds (8.337174 for core code).
INFO: stdout 2026-02-05T18:33:18.247578:Conversion required 8.337986 seconds (8.337174 for core code).
260205-18:33:18,276 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 8.402368s.
INFO: [Node] Finished "convert", elapsed time 8.402368s.
260205-18:33:35,864 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetapmb0omlh/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetapmb0omlh/embedder".
260205-18:33:35,887 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:33:46,923 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 11.035514s.
INFO: [Node] Finished "embedder", elapsed time 11.035514s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-04_bold.json file
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold (196 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:33:46,979 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixue3ldrzq/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixue3ldrzq/convert".
260205-18:33:47,16 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:33:47,120 nipype.interface INFO:
     stdout 2026-02-05T18:33:47.120926:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:33:47.120926:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:33:47,121 nipype.interface INFO:
     stdout 2026-02-05T18:33:47.120926:Found 196 DICOM file(s)
INFO: stdout 2026-02-05T18:33:47.120926:Found 196 DICOM file(s)
260205-18:33:47,121 nipype.interface INFO:
     stdout 2026-02-05T18:33:47.120926:Convert 196 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold_heudiconv217 (64x64x27x196)
INFO: stdout 2026-02-05T18:33:47.120926:Convert 196 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold_heudiconv217 (64x64x27x196)
260205-18:33:50,424 nipype.interface INFO:
     stdout 2026-02-05T18:33:50.424856:Conversion required 3.373261 seconds (3.372955 for core code).
INFO: stdout 2026-02-05T18:33:50.424856:Conversion required 3.373261 seconds (3.372955 for core code).
260205-18:33:50,451 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 3.434252s.
INFO: [Node] Finished "convert", elapsed time 3.434252s.
260205-18:33:57,189 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmeta2rltkjoo/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmeta2rltkjoo/embedder".
260205-18:33:57,200 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:34:01,488 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 4.287415s.
INFO: [Node] Finished "embedder", elapsed time 4.287415s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json file
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout__dup-01 (128 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:34:01,517 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niix7q4qx4ff/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix7q4qx4ff/convert".
260205-18:34:01,542 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:34:01,618 nipype.interface INFO:
     stdout 2026-02-05T18:34:01.618387:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:34:01.618387:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:34:01,618 nipype.interface INFO:
     stdout 2026-02-05T18:34:01.618387:Found 128 DICOM file(s)
INFO: stdout 2026-02-05T18:34:01.618387:Found 128 DICOM file(s)
260205-18:34:01,618 nipype.interface INFO:
     stdout 2026-02-05T18:34:01.618387:Convert 128 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-01_heudiconv718 (160x160x128x1)
INFO: stdout 2026-02-05T18:34:01.618387:Convert 128 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-01_heudiconv718 (160x160x128x1)
260205-18:34:02,192 nipype.interface INFO:
     stdout 2026-02-05T18:34:02.192821:Conversion required 0.613964 seconds (0.613926 for core code).
INFO: stdout 2026-02-05T18:34:02.192821:Conversion required 0.613964 seconds (0.613926 for core code).
260205-18:34:02,220 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.677199s.
INFO: [Node] Finished "convert", elapsed time 0.677199s.
260205-18:34:06,970 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetas1mpmh2x/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetas1mpmh2x/embedder".
260205-18:34:06,979 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:34:08,987 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 2.008053s.
INFO: [Node] Finished "embedder", elapsed time 2.008053s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout__dup-01.json file
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout__dup-02 (5 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:34:09,3 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixg3z5x4vh/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixg3z5x4vh/convert".
260205-18:34:09,6 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:34:09,46 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.046896:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:34:09.046896:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:34:09,47 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.046896:Found 5 DICOM file(s)
INFO: stdout 2026-02-05T18:34:09.046896:Found 5 DICOM file(s)
260205-18:34:09,47 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.046896:Slices not stacked: orientation varies (vNav or localizer?) [0.0012676 0.954584 0.29794 0.0238695 0.297826 -0.954322] != [0.515908 0.788925 0.333821 0.0413103 0.366319 -0.929572]
INFO: stdout 2026-02-05T18:34:09.046896:Slices not stacked: orientation varies (vNav or localizer?) [0.0012676 0.954584 0.29794 0.0238695 0.297826 -0.954322] != [0.515908 0.788925 0.333821 0.0413103 0.366319 -0.929572]
260205-18:34:09,47 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.046896:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv191_i00003 (162x162x1x1)
INFO: stdout 2026-02-05T18:34:09.046896:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv191_i00003 (162x162x1x1)
260205-18:34:09,50 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.050698:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv191_i00002 (162x162x1x1)
INFO: stdout 2026-02-05T18:34:09.050698:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv191_i00002 (162x162x1x1)
260205-18:34:09,54 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.054464:Convert 2 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv191_i00001 (162x162x2x1)
INFO: stdout 2026-02-05T18:34:09.054464:Convert 2 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv191_i00001 (162x162x2x1)
260205-18:34:09,61 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.061610:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv191_i00004 (162x162x1x1)
INFO: stdout 2026-02-05T18:34:09.061610:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv191_i00004 (162x162x1x1)
260205-18:34:09,64 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.064803:Conversion required 0.023320 seconds (0.023317 for core code).
INFO: stdout 2026-02-05T18:34:09.064803:Conversion required 0.023320 seconds (0.023317 for core code).
260205-18:34:09,94 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.087944s.
INFO: [Node] Finished "convert", elapsed time 0.087944s.
WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout__dup-03 (3 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:34:09,197 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixki7a6vyq/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixki7a6vyq/convert".
260205-18:34:09,200 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:34:09,240 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.240854:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:34:09.240854:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:34:09,241 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.240854:Found 3 DICOM file(s)
INFO: stdout 2026-02-05T18:34:09.240854:Found 3 DICOM file(s)
260205-18:34:09,241 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.240854:Slices not stacked: orientation varies (vNav or localizer?) [0.999714 -0.00832137 0.0224079 0.0238695 0.297826 -0.954322] != [0.99919 -0.00351184 0.040093 0.0399268 0.211814 -0.976494]
INFO: stdout 2026-02-05T18:34:09.240854:Slices not stacked: orientation varies (vNav or localizer?) [0.999714 -0.00832137 0.0224079 0.0238695 0.297826 -0.954322] != [0.99919 -0.00351184 0.040093 0.0399268 0.211814 -0.976494]
260205-18:34:09,241 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.240854:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv074_i00002 (162x162x1x1)
INFO: stdout 2026-02-05T18:34:09.240854:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv074_i00002 (162x162x1x1)
260205-18:34:09,244 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.244556:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv074_i00001 (162x162x1x1)
INFO: stdout 2026-02-05T18:34:09.244556:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv074_i00001 (162x162x1x1)
260205-18:34:09,247 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.247810:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv074_i00003 (162x162x1x1)
INFO: stdout 2026-02-05T18:34:09.247810:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv074_i00003 (162x162x1x1)
260205-18:34:09,250 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.250206:Conversion required 0.013914 seconds (0.013911 for core code).
INFO: stdout 2026-02-05T18:34:09.250206:Conversion required 0.013914 seconds (0.013911 for core code).
260205-18:34:09,275 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.073903s.
INFO: [Node] Finished "convert", elapsed time 0.073903s.
WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold__dup-01 (3 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:34:09,325 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixjd99evcf/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixjd99evcf/convert".
260205-18:34:09,328 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:34:09,370 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.370344:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:34:09.370344:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:34:09,370 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.370344:Found 3 DICOM file(s)
INFO: stdout 2026-02-05T18:34:09.370344:Found 3 DICOM file(s)
260205-18:34:09,370 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.370344:Convert 3 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold_dup-01_heudiconv600 (64x64x27x3)
INFO: stdout 2026-02-05T18:34:09.370344:Convert 3 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold_dup-01_heudiconv600 (64x64x27x3)
260205-18:34:09,422 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.422095:Conversion required 0.058988 seconds (0.058982 for core code).
INFO: stdout 2026-02-05T18:34:09.422095:Conversion required 0.058988 seconds (0.058982 for core code).
260205-18:34:09,444 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.11569s.
INFO: [Node] Finished "convert", elapsed time 0.11569s.
260205-18:34:09,556 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetaqx8nw7si/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetaqx8nw7si/embedder".
260205-18:34:09,559 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:34:09,632 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 0.072558s.
INFO: [Node] Finished "embedder", elapsed time 0.072558s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold__dup-01.json file
INFO: Converting /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold__dup-02 (12 DICOMs) -> /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func . Converter: dcm2niix . Output types: ('nii.gz', 'dicom')
260205-18:34:09,639 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixa8wrrgq3/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixa8wrrgq3/convert".
260205-18:34:09,644 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260205-18:34:09,689 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.688965:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-02-05T18:34:09.688965:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260205-18:34:09,689 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.688965:Found 12 DICOM file(s)
INFO: stdout 2026-02-05T18:34:09.688965:Found 12 DICOM file(s)
260205-18:34:09,689 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.688965:Convert 12 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold_dup-02_heudiconv922 (64x64x27x12)
INFO: stdout 2026-02-05T18:34:09.688965:Convert 12 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold_dup-02_heudiconv922 (64x64x27x12)
260205-18:34:09,890 nipype.interface INFO:
     stdout 2026-02-05T18:34:09.890120:Conversion required 0.210791 seconds (0.210774 for core code).
INFO: stdout 2026-02-05T18:34:09.890120:Conversion required 0.210791 seconds (0.210774 for core code).
260205-18:34:09,914 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.270101s.
INFO: [Node] Finished "convert", elapsed time 0.270101s.
260205-18:34:10,345 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmeta8y8aen99/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmeta8y8aen99/embedder".
260205-18:34:10,349 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260205-18:34:10,620 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 0.270086s.
INFO: [Node] Finished "embedder", elapsed time 0.270086s.
INFO: Post-treating /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold__dup-02.json file
INFO: Adding "IntendedFor" to the fieldmaps in /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01.
WARNING: We cannot add the IntendedFor field: no fmap/ in /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01
INFO: Populating template files under /app/Norman/Mennen/5516_greenEyes
INFO: PROCESSING DONE: {'subject': '01', 'outdir': '/app/Norman/Mennen/5516_greenEyes', 'session': '01'}

Inspecting the BIDS dataset

Let’s inspect the new folder in more detail:

tree -L 7 Norman

Code Output

Norman
└── Mennen
    └── 5516_greenEyes
        ├── CHANGES
        ├── README
        ├── dataset_description.json
        ├── participants.json
        ├── participants.tsv
        ├── scans.json
        ├── sourcedata
        │   ├── README
        │   └── sub-01
        │       └── ses-01
        │           ├── anat
        │           │   ├── sub-01_ses-01_T1w.dicom.tgz
        │           │   ├── sub-01_ses-01_scout.dicom.tgz
        │           │   ├── sub-01_ses-01_scout__dup-01.dicom.tgz
        │           │   ├── sub-01_ses-01_scout__dup-02.dicom.tgz
        │           │   └── sub-01_ses-01_scout__dup-03.dicom.tgz
        │           └── func
        │               ├── sub-01_ses-01_task-faces_run-01_bold.dicom.tgz
        │               ├── sub-01_ses-01_task-sound_run-01_bold.dicom.tgz
        │               ├── sub-01_ses-01_task-sound_run-01_bold__dup-01.dicom.tgz
        │               ├── sub-01_ses-01_task-sound_run-01_bold__dup-02.dicom.tgz
        │               ├── sub-01_ses-01_task-story_run-01_bold.dicom.tgz
        │               ├── sub-01_ses-01_task-story_run-02_bold.dicom.tgz
        │               ├── sub-01_ses-01_task-story_run-03_bold.dicom.tgz
        │               └── sub-01_ses-01_task-story_run-04_bold.dicom.tgz
        ├── sub-01
        │   └── ses-01
        │       ├── anat
        │       │   ├── sub-01_ses-01_T1w.json
        │       │   ├── sub-01_ses-01_T1w.nii.gz
        │       │   ├── sub-01_ses-01_scout1.json
        │       │   ├── sub-01_ses-01_scout1.nii.gz
        │       │   ├── sub-01_ses-01_scout2.json
        │       │   ├── sub-01_ses-01_scout2.nii.gz
        │       │   ├── sub-01_ses-01_scout3.json
        │       │   ├── sub-01_ses-01_scout3.nii.gz
        │       │   ├── sub-01_ses-01_scout__dup-01.json
        │       │   ├── sub-01_ses-01_scout__dup-01.nii.gz
        │       │   ├── sub-01_ses-01_scout__dup-021.json
        │       │   ├── sub-01_ses-01_scout__dup-021.nii.gz
        │       │   ├── sub-01_ses-01_scout__dup-022.json
        │       │   ├── sub-01_ses-01_scout__dup-022.nii.gz
        │       │   ├── sub-01_ses-01_scout__dup-023.json
        │       │   ├── sub-01_ses-01_scout__dup-023.nii.gz
        │       │   ├── sub-01_ses-01_scout__dup-024.json
        │       │   ├── sub-01_ses-01_scout__dup-024.nii.gz
        │       │   ├── sub-01_ses-01_scout__dup-031.json
        │       │   ├── sub-01_ses-01_scout__dup-031.nii.gz
        │       │   ├── sub-01_ses-01_scout__dup-032.json
        │       │   ├── sub-01_ses-01_scout__dup-032.nii.gz
        │       │   ├── sub-01_ses-01_scout__dup-033.json
        │       │   └── sub-01_ses-01_scout__dup-033.nii.gz
        │       ├── func
        │       │   ├── sub-01_ses-01_task-faces_run-01_bold.json
        │       │   ├── sub-01_ses-01_task-faces_run-01_bold.nii.gz
        │       │   ├── sub-01_ses-01_task-faces_run-01_events.tsv
        │       │   ├── sub-01_ses-01_task-sound_run-01_bold.json
        │       │   ├── sub-01_ses-01_task-sound_run-01_bold.nii.gz
        │       │   ├── sub-01_ses-01_task-sound_run-01_bold__dup-01.json
        │       │   ├── sub-01_ses-01_task-sound_run-01_bold__dup-01.nii.gz
        │       │   ├── sub-01_ses-01_task-sound_run-01_bold__dup-02.json
        │       │   ├── sub-01_ses-01_task-sound_run-01_bold__dup-02.nii.gz
        │       │   ├── sub-01_ses-01_task-sound_run-01_events.tsv
        │       │   ├── sub-01_ses-01_task-story_run-01_bold.json
        │       │   ├── sub-01_ses-01_task-story_run-01_bold.nii.gz
        │       │   ├── sub-01_ses-01_task-story_run-01_events.tsv
        │       │   ├── sub-01_ses-01_task-story_run-02_bold.json
        │       │   ├── sub-01_ses-01_task-story_run-02_bold.nii.gz
        │       │   ├── sub-01_ses-01_task-story_run-02_events.tsv
        │       │   ├── sub-01_ses-01_task-story_run-03_bold.json
        │       │   ├── sub-01_ses-01_task-story_run-03_bold.nii.gz
        │       │   ├── sub-01_ses-01_task-story_run-03_events.tsv
        │       │   ├── sub-01_ses-01_task-story_run-04_bold.json
        │       │   ├── sub-01_ses-01_task-story_run-04_bold.nii.gz
        │       │   └── sub-01_ses-01_task-story_run-04_events.tsv
        │       └── sub-01_ses-01_scans.tsv
        ├── task-faces_bold.json
        ├── task-sound_bold.json
        └── task-story_bold.json

12 directories, 70 files

Validate the BIDS dataset

That looks like a BIDS dataset! Let’s check using the BIDS Validator:

bids-validator-deno Norman/Mennen/5516_greenEyes

Code Output

   [WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended.

        GeneratedBy

        /dataset_description.json - Field description: Used to specify provenance of the dataset.



        SourceDatasets

        /dataset_description.json - Field description: Used to specify the locations and relevant attributes of all source datasets.

Valid keys in each object include "URL", "DOI" (see

URI (https://bids-specification.readthedocs.io/en/stable/common-principles.md#uniform-resource-indicator)), and

"Version" with

string (https://www.w3schools.com/js/js_json_datatypes.asp)

values.



 Please visit https://neurostars.org/search?q=JSON_KEY_RECOMMENDED for existing conversations about this issue.



    [WARNING] README_FILE_SMALL The recommended file '/README' is very small.

Please consider expanding it with additional information about the dataset.

        /README



 Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.



    [WARNING] SIDECAR_FIELD_OVERRIDE Sidecar files should not override values assigned at a higher level.

        ImageOrientationPatientDICOM

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (0.999714,-0.00838295,0.0224008,0.00575803,0.993375,0.114774) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (0.999714,-0.00838295,0.0224008,0.00575803,0.993375,0.114774) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        ImageType

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (ORIGINAL,PRIMARY,M,ND,NORM,MOSAIC,MAGNITUDE) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (ORIGINAL,PRIMARY,M,ND,NORM,MOSAIC,MAGNITUDE) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        ShimSetting

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (3381,8615,9370,473,199,-206,243,231) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (3381,8615,9370,473,199,-206,243,231) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        TablePosition

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (0,0,0) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (0,0,0) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        TaskName

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (TODO: full task name for story) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (TODO: full task name for sound) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        dcmmeta_affine

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (-2.9991416931152344,0.01727408915758133,0.092858225107193,92.07717895507812,0.025148851796984673,2.9801249504089355,0.45844852924346924,-111.91024780273438,0.06720245629549026,-0.3443218469619751,3.9725561141967773,-23.962722778320312,0,0,0,1) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (-2.9991416931152344,0.01727408915758133,0.092858225107193,92.07717895507812,0.025148851796984673,2.9801249504089355,0.45844852924346924,-111.91024780273438,0.06720245629549026,-0.3443218469619751,3.9725561141967773,-23.962722778320312,0,0,0,1) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        dcmmeta_reorient_transform

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (0,-1,0,63,1,0,0,0,0,0,1,0,0,0,0,1) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (0,-1,0,63,1,0,0,0,0,0,1,0,0,0,0,1) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        dcmmeta_shape

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (64,64,27,485) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (64,64,27,179) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        BidsGuess

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (func,_acq-epfid2p2_dir-AP_run-8_bold) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json - Sidecar key defined in /task-faces_bold.json overrides previous value (func,_acq-epfid2p2_dir-AP_run-13_bold) from /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json



        SliceTiming

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (0,0.7675,0.055,0.8225,0.11,0.8775,0.165,0.9325,0.22,0.985,0.2725,1.04,0.3275,1.095,0.3825,1.15,0.4375,1.205,0.4925,1.26,0.5475,1.315,0.6025,1.37,0.6575,1.425,0.7125) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json - Sidecar key defined in /task-faces_bold.json overrides previous value (0,0.765,0.0525,0.82,0.1075,0.875,0.1625,0.93,0.2175,0.985,0.2725,1.04,0.3275,1.095,0.3825,1.15,0.4375,1.205,0.4925,1.26,0.5475,1.315,0.6025,1.37,0.6575,1.425,0.7125) from /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json



        global

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value ([object Object]) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json - Sidecar key defined in /task-faces_bold.json overrides previous value ([object Object]) from /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json



        time

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value ([object Object]) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json - Sidecar key defined in /task-faces_bold.json overrides previous value ([object Object]) from /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json



 Please visit https://neurostars.org/search?q=SIDECAR_FIELD_OVERRIDE for existing conversations about this issue.



    [WARNING] SIDECAR_KEY_RECOMMENDED A data file's JSON sidecar is missing a key listed as recommended.

        PulseSequenceType

        /sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz - Field description: A general description of the pulse sequence used for the scan.

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: A general description of the pulse sequence used for the scan.



        5 more files with the same issue



        SpoilingType

        /sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz - Field description: Specifies which spoiling method(s) are used by a spoiled sequence.



        PartialFourierDirection

        /sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz - Field description: The direction where only partial Fourier information was collected.

Corresponds to DICOM Tag 0018, 9036 (https://dicomlookup.com/dicomtags/(0018,9036)) Partial Fourier Direction.

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: The direction where only partial Fourier information was collected.

Corresponds to DICOM Tag 0018, 9036 (https://dicomlookup.com/dicomtags/(0018,9036)) Partial Fourier Direction.



        5 more files with the same issue



        Instructions

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: Text of the instructions given to participants before the recording.

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.nii.gz - Field description: Text of the instructions given to participants before the recording.



        4 more files with the same issue



        TaskDescription

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: Longer description of the task.

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.nii.gz - Field description: Longer description of the task.



        4 more files with the same issue



        CogPOID

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: URI (https://bids-specification.readthedocs.io/en/stable/common-principles.md#uniform-resource-indicator)

of the corresponding CogPO (http://www.cogpo.org/) term.

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.nii.gz - Field description: URI (https://bids-specification.readthedocs.io/en/stable/common-principles.md#uniform-resource-indicator)

of the corresponding CogPO (http://www.cogpo.org/) term.



        4 more files with the same issue



        StimulusPresentation

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_events.tsv - Field description: Object containing key-value pairs related to the software used to present

the stimuli during the experiment.

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_events.tsv - Field description: Object containing key-value pairs related to the software used to present

the stimuli during the experiment.



        4 more files with the same issue



 Please visit https://neurostars.org/search?q=SIDECAR_KEY_RECOMMENDED for existing conversations about this issue.



    [WARNING] SUSPICIOUSLY_SHORT_EVENT_DESIGN The onset of the last event is less than half the total duration of the corresponding scan.

This design is suspiciously short.

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.nii.gz



        4 more files with the same issue



 Please visit https://neurostars.org/search?q=SUSPICIOUSLY_SHORT_EVENT_DESIGN for existing conversations about this issue.



    [WARNING] TSV_ADDITIONAL_COLUMNS_UNDEFINED A TSV file has extra columns which are not defined in its associated JSON sidecar

        TODO -- fill in rows and add more tab-separated columns if desired

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_events.tsv

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_events.tsv



        4 more files with the same issue



 Please visit https://neurostars.org/search?q=TSV_ADDITIONAL_COLUMNS_UNDEFINED for existing conversations about this issue.



    [ERROR] NOT_INCLUDED Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore (https://github.com/bids-standard/bids-validator#bidsignore) for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.

        /sub-01/ses-01/anat/sub-01_ses-01_scout__dup-023.nii.gz

        /sub-01/ses-01/anat/sub-01_ses-01_scout__dup-023.json



        24 more files with the same issue



 Please visit https://neurostars.org/search?q=NOT_INCLUDED for existing conversations about this issue.





          Summary:                         Available Tasks:                      Available Modalities:

          56 Files, 337 MB                 TODO: full task name for sound        MRI                  

          1 - Subjects 1 - Sessions        TODO: full task name for story                             

                                           TODO: full task name for faces                             

                                           sound                                                      

                                           story                                                      

                                           faces                                                      

Code Output

: 16

Fixing a BIDS Dataset

The BIDS Validator found several errors and issued a number of warnings. This means the dataset is not yet fully BIDS-compliant. You need to manually adjust the relevant files to fix these issues. Start by addressing the errors first. Errors make your dataset BIDS-incompatible and must be resolved for proper validation. Many BIDS Apps (like fMRIPrep and MRIQC) require datasets to be error-free they can run. Warnings indicate that your dataset is technically BIDS-compliant, but improvements are recommended. You should try to resolve all warnings to ensure your dataset is robust and ready for downstream analysis.

Create a .bidsignore file

Let the BIDS validator ignore /sourcedata and .heudiconv. To this end, we create a .bidsignore file:

touch Norman/Mennen/5516_greenEyes/.bidsignore
echo "/sourcedata" > Norman/Mennen/5516_greenEyes/.bidsignore
echo ".heudiconv" >> Norman/Mennen/5516_greenEyes/.bidsignore

Let’s look at the contents of the .bidsignore file:

cat  Norman/Mennen/5516_greenEyes/.bidsignore

/sourcedata
.heudiconv

Remove data from the MRI loalizer

rm -rf Norman/Mennen/5516_greenEyes/sub-*/ses-*/*/*scout*

Remove repeated runs (resulting in duplications)

rm -rf Norman/Mennen/5516_greenEyes/sub-*/ses-*/*/*_dup*

Adjust the scans.tsv file:

1. Import the pandas library for data manipulation.
2. Load the *scans.tsv file into a DataFrame.
3. Remove rows where the 'filename' column contains '_dup' (duplicate runs).
4. Further remove rows where 'filename' contains 'scout' (localizer scans).
5. Save the cleaned DataFrame back to the original*scans.tsv file, overwriting it.

awk -F'\t' 'NR==1 || (!/scout/ && !/_dup/)' Norman/Mennen/5516_greenEyes/sub-01/ses-01/sub-01_ses-01_scans.tsv > temp_scans.tsv && mv temp_scans.tsv Norman/Mennen/5516_greenEyes/sub-01/ses-01/sub-01_ses-01_scans.tsv

You can also run Python code to achieve the same result:

import pandas as pd
df = pd.read_csv('Norman/Mennen/5516_greenEyes/sub-01/ses-01/sub-01_ses-01_scans.tsv', sep='\t')
df_clean = df[~df['filename'].str.contains('_dup')]
df_clean = df_clean[~df_clean['filename'].str.contains('scout')]
df_clean.to_csv('Norman/Mennen/5516_greenEyes/sub-01/ses-01/sub-01_ses-01_scans.tsv', sep='\t', index=False)

Validate again

Run the BIDS Validator repeatedly to verify that you resolved remaining errors and warnings:

bids-validator-deno Norman/Mennen/5516_greenEyes/

Code Output

   [WARNING] SIDECAR_FIELD_OVERRIDE Sidecar files should not override values assigned at a higher level.

        ImageOrientationPatientDICOM

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (0.999714,-0.00838295,0.0224008,0.00575803,0.993375,0.114774) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (0.999714,-0.00838295,0.0224008,0.00575803,0.993375,0.114774) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        ImageType

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (ORIGINAL,PRIMARY,M,ND,NORM,MOSAIC,MAGNITUDE) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (ORIGINAL,PRIMARY,M,ND,NORM,MOSAIC,MAGNITUDE) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        ShimSetting

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (3381,8615,9370,473,199,-206,243,231) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (3381,8615,9370,473,199,-206,243,231) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        TablePosition

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (0,0,0) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (0,0,0) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        TaskName

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (TODO: full task name for story) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (TODO: full task name for sound) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        dcmmeta_affine

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (-2.9991416931152344,0.01727408915758133,0.092858225107193,92.07717895507812,0.025148851796984673,2.9801249504089355,0.45844852924346924,-111.91024780273438,0.06720245629549026,-0.3443218469619751,3.9725561141967773,-23.962722778320312,0,0,0,1) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (-2.9991416931152344,0.01727408915758133,0.092858225107193,92.07717895507812,0.025148851796984673,2.9801249504089355,0.45844852924346924,-111.91024780273438,0.06720245629549026,-0.3443218469619751,3.9725561141967773,-23.962722778320312,0,0,0,1) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        dcmmeta_reorient_transform

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (0,-1,0,63,1,0,0,0,0,0,1,0,0,0,0,1) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (0,-1,0,63,1,0,0,0,0,0,1,0,0,0,0,1) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        dcmmeta_shape

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json - Sidecar key defined in /task-story_bold.json overrides previous value (64,64,27,485) from /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (64,64,27,179) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json



        4 more files with the same issue



        BidsGuess

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (func,_acq-epfid2p2_dir-AP_run-8_bold) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json - Sidecar key defined in /task-faces_bold.json overrides previous value (func,_acq-epfid2p2_dir-AP_run-13_bold) from /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json



        SliceTiming

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value (0,0.7675,0.055,0.8225,0.11,0.8775,0.165,0.9325,0.22,0.985,0.2725,1.04,0.3275,1.095,0.3825,1.15,0.4375,1.205,0.4925,1.26,0.5475,1.315,0.6025,1.37,0.6575,1.425,0.7125) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json - Sidecar key defined in /task-faces_bold.json overrides previous value (0,0.765,0.0525,0.82,0.1075,0.875,0.1625,0.93,0.2175,0.985,0.2725,1.04,0.3275,1.095,0.3825,1.15,0.4375,1.205,0.4925,1.26,0.5475,1.315,0.6025,1.37,0.6575,1.425,0.7125) from /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json



        global

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value ([object Object]) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json - Sidecar key defined in /task-faces_bold.json overrides previous value ([object Object]) from /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json



        time

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json - Sidecar key defined in /task-sound_bold.json overrides previous value ([object Object]) from /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.json

        /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json - Sidecar key defined in /task-faces_bold.json overrides previous value ([object Object]) from /sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold.json



 Please visit https://neurostars.org/search?q=SIDECAR_FIELD_OVERRIDE for existing conversations about this issue.



    [WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended.

        GeneratedBy

        /dataset_description.json - Field description: Used to specify provenance of the dataset.



        SourceDatasets

        /dataset_description.json - Field description: Used to specify the locations and relevant attributes of all source datasets.

Valid keys in each object include "URL", "DOI" (see

URI (https://bids-specification.readthedocs.io/en/stable/common-principles.md#uniform-resource-indicator)), and

"Version" with

string (https://www.w3schools.com/js/js_json_datatypes.asp)

values.



 Please visit https://neurostars.org/search?q=JSON_KEY_RECOMMENDED for existing conversations about this issue.



    [WARNING] README_FILE_SMALL The recommended file '/README' is very small.

Please consider expanding it with additional information about the dataset.

        /README



 Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.



    [WARNING] SIDECAR_KEY_RECOMMENDED A data file's JSON sidecar is missing a key listed as recommended.

        PulseSequenceType

        /sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz - Field description: A general description of the pulse sequence used for the scan.

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: A general description of the pulse sequence used for the scan.



        5 more files with the same issue



        SpoilingType

        /sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz - Field description: Specifies which spoiling method(s) are used by a spoiled sequence.



        PartialFourierDirection

        /sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz - Field description: The direction where only partial Fourier information was collected.

Corresponds to DICOM Tag 0018, 9036 (https://dicomlookup.com/dicomtags/(0018,9036)) Partial Fourier Direction.

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: The direction where only partial Fourier information was collected.

Corresponds to DICOM Tag 0018, 9036 (https://dicomlookup.com/dicomtags/(0018,9036)) Partial Fourier Direction.



        5 more files with the same issue



        Instructions

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: Text of the instructions given to participants before the recording.

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.nii.gz - Field description: Text of the instructions given to participants before the recording.



        4 more files with the same issue



        TaskDescription

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: Longer description of the task.

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.nii.gz - Field description: Longer description of the task.



        4 more files with the same issue



        CogPOID

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz - Field description: URI (https://bids-specification.readthedocs.io/en/stable/common-principles.md#uniform-resource-indicator)

of the corresponding CogPO (http://www.cogpo.org/) term.

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.nii.gz - Field description: URI (https://bids-specification.readthedocs.io/en/stable/common-principles.md#uniform-resource-indicator)

of the corresponding CogPO (http://www.cogpo.org/) term.



        4 more files with the same issue



        StimulusPresentation

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_events.tsv - Field description: Object containing key-value pairs related to the software used to present

the stimuli during the experiment.

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_events.tsv - Field description: Object containing key-value pairs related to the software used to present

the stimuli during the experiment.



        4 more files with the same issue



 Please visit https://neurostars.org/search?q=SIDECAR_KEY_RECOMMENDED for existing conversations about this issue.



    [WARNING] SUSPICIOUSLY_SHORT_EVENT_DESIGN The onset of the last event is less than half the total duration of the corresponding scan.

This design is suspiciously short.

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold.nii.gz

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold.nii.gz



        4 more files with the same issue



 Please visit https://neurostars.org/search?q=SUSPICIOUSLY_SHORT_EVENT_DESIGN for existing conversations about this issue.



    [WARNING] TSV_ADDITIONAL_COLUMNS_UNDEFINED A TSV file has extra columns which are not defined in its associated JSON sidecar

        TODO -- fill in rows and add more tab-separated columns if desired

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_events.tsv

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_events.tsv



        4 more files with the same issue



 Please visit https://neurostars.org/search?q=TSV_ADDITIONAL_COLUMNS_UNDEFINED for existing conversations about this issue.





          Summary:                         Available Tasks:                      Available Modalities:

          30 Files, 331 MB                 TODO: full task name for sound        MRI                  

          1 - Subjects 1 - Sessions        TODO: full task name for story                             

                                           TODO: full task name for faces                             

                                           sound                                                      

                                           story                                                      

                                           faces                                                      

Cool, no more errors!

What’s next?

Once you have a fully BIDS-compatible dataset, you can run BIDS Apps (like fMRIPrep and MRIQC) and more! And you have a well-documented dataset that follows best community practices! Congrats!

References

Nastase, S. A., Mennen, A. C., Brooks, P. P., & McDevitt, E. A. (2020). Princeton Handbook for Reproducible Neuroimaging: Sample Data. Zenodo. https://doi.org/10.5281/ZENODO.3677090