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

--2026-05-06 19:51:01--  https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz
Resolving zenodo.org (zenodo.org)... 188.184.98.114, 188.185.48.75, 188.184.103.118, ...
Connecting to zenodo.org (zenodo.org)|188.184.98.114|:443... connected.
HTTP request sent, awaiting response... 301 MOVED PERMANENTLY
Location: /records/3677090/files/0219191_mystudy-0219-1114.tar.gz [following]
--2026-05-06 19:51:02--  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%[                    ]  51.49K   229KB/s                       0219191_mys   0%[                    ] 265.79K   520KB/s                      0219191_myst   0%[                    ] 725.60K   910KB/s                     0219191_mystu   0%[                    ]   1.60M  1.47MB/s                    0219191_mystud   0%[                    ]   3.02M  2.20MB/s                   0219191_mystudy   1%[                    ]   4.73M  2.86MB/s                  0219191_mystudy-   2%[                    ]   8.75M  4.51MB/s                 0219191_mystudy-0   4%[                    ]  16.86M  7.87MB/s                0219191_mystudy-02   6%[>                   ]  23.66M  10.1MB/s               0219191_mystudy-021   8%[>                   ]  31.91M  12.2MB/s               219191_mystudy-0219  10%[=>                  ]  39.71M  14.0MB/s               19191_mystudy-0219-  12%[=>                  ]  47.49M  15.6MB/s    eta 22s    9191_mystudy-0219-1  14%[=>                  ]  55.15M  17.0MB/s    eta 22s    191_mystudy-0219-11  16%[==>                 ]  63.74M  18.5MB/s    eta 22s    91_mystudy-0219-111  18%[==>                 ]  72.52M  19.9MB/s    eta 22s    1_mystudy-0219-1114  20%[===>                ]  78.90M  20.6MB/s    eta 22s    _mystudy-0219-1114.  22%[===>                ]  86.54M  21.4MB/s    eta 14s    mystudy-0219-1114.t  24%[===>                ]  94.48M  23.5MB/s    eta 14s    ystudy-0219-1114.ta  26%[====>               ] 103.07M  26.2MB/s    eta 14s    study-0219-1114.tar  28%[====>               ] 111.13M  28.1MB/s    eta 14s    tudy-0219-1114.tar.  30%[=====>              ] 119.63M  30.0MB/s    eta 14s    udy-0219-1114.tar.g  32%[=====>              ] 127.54M  31.8MB/s    eta 10s    dy-0219-1114.tar.gz  34%[=====>              ] 135.31M  32.7MB/s    eta 10s    y-0219-1114.tar.gz   36%[======>             ] 142.96M  34.3MB/s    eta 10s    -0219-1114.tar.gz    39%[======>             ] 152.27M  36.0MB/s    eta 10s    0219-1114.tar.gz     41%[=======>            ] 160.02M  37.1MB/s    eta 10s    219-1114.tar.gz      43%[=======>            ] 167.73M  37.8MB/s    eta 8s     19-1114.tar.gz       45%[========>           ] 176.26M  38.1MB/s    eta 8s     9-1114.tar.gz        47%[========>           ] 185.43M  37.7MB/s    eta 8s     -1114.tar.gz         50%[=========>          ] 193.50M  37.8MB/s    eta 8s     1114.tar.gz          52%[=========>          ] 201.64M  37.9MB/s    eta 8s     114.tar.gz           54%[=========>          ] 210.00M  38.1MB/s    eta 6s     14.tar.gz            56%[==========>         ] 218.38M  38.5MB/s    eta 6s     4.tar.gz             58%[==========>         ] 226.08M  38.4MB/s    eta 6s     .tar.gz              60%[===========>        ] 235.56M  38.1MB/s    eta 6s     tar.gz               63%[===========>        ] 244.42M  38.5MB/s    eta 6s     ar.gz                65%[============>       ] 252.54M  38.6MB/s    eta 4s     r.gz                 67%[============>       ] 260.77M  38.7MB/s    eta 4s     .gz                  68%[============>       ] 266.40M  38.2MB/s    eta 4s     gz                   70%[=============>      ] 274.26M  38.2MB/s    eta 4s     z                    72%[=============>      ] 281.84M  38.1MB/s    eta 4s                          74%[=============>      ] 289.17M  38.3MB/s    eta 3s                       0  76%[==============>     ] 296.89M  38.4MB/s    eta 3s                      02  78%[==============>     ] 304.52M  38.4MB/s    eta 3s                     021  80%[===============>    ] 311.83M  38.1MB/s    eta 3s                    0219  82%[===============>    ] 319.57M  38.1MB/s    eta 3s                   02191  84%[===============>    ] 327.27M  37.9MB/s    eta 2s                  021919  86%[================>   ] 336.49M  38.4MB/s    eta 2s                 0219191  88%[================>   ] 344.07M  38.3MB/s    eta 2s                0219191_  90%[=================>  ] 351.86M  38.1MB/s    eta 2s               0219191_m  92%[=================>  ] 359.51M  38.1MB/s    eta 2s              0219191_my  94%[=================>  ] 367.21M  38.1MB/s    eta 1s             0219191_mys  96%[==================> ] 375.12M  38.1MB/s    eta 1s            0219191_myst  98%[==================> ] 382.66M  38.0MB/s    eta 1s     0219191_mystudy-021 100%[===================>] 386.88M  38.0MB/s    in 12s     

2026-05-06 19:51:15 (32.3 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
0219191_mystudy-0219-1114/dcm/12-82-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-224-1.dcm.gz
0219191_mystudy-0219-1114/dcm/12-88-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-285-1.dcm.gz
0219191_mystudy-0219-1114/dcm/1-116-1.dcm.gz
0219191_mystudy-0219-1114/dcm/9-49-1.dcm.gz
0219191_mystudy-0219-1114/dcm/8-47-1.dcm.gz
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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
│   ├── 10-196-1.dcm.gz
│   ├── 10-197-1.dcm.gz
│   ├── 10-198-1.dcm.gz
│   ├── 10-199-1.dcm.gz
│   ├── 10-2-1.dcm.gz
│   ├── 10-20-1.dcm.gz
│   ├── 10-200-1.dcm.gz
│   ├── 10-201-1.dcm.gz
│   ├── 10-202-1.dcm.gz
│   ├── 10-203-1.dcm.gz
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│   ├── 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: 500 Server Error: Internal Server Error for url: https://rig.mit.edu/et/projects/nipy/heudiconv
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')
260506-19:51:36,588 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixo_z6pygw/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixo_z6pygw/convert".
260506-19:51:36,590 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:51:36,697 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.697912:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:51:36.697912:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:51:36,698 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.697912:Found 3 DICOM file(s)
INFO: stdout 2026-05-06T19:51:36.697912:Found 3 DICOM file(s)
260506-19:51:36,698 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.697912:Slices not stacked: orientation varies (vNav or localizer?) [0.999146 -0.0147051 0.0386074 -0.000473197 0.930373 0.366613] != [0.996918 -0.0146115 0.077075 -0.00902414 0.954619 0.297693]
INFO: stdout 2026-05-06T19:51:36.697912:Slices not stacked: orientation varies (vNav or localizer?) [0.999146 -0.0147051 0.0386074 -0.000473197 0.930373 0.366613] != [0.996918 -0.0146115 0.077075 -0.00902414 0.954619 0.297693]
260506-19:51:36,698 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.697912:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv447_i00003 (162x162x1x1)
INFO: stdout 2026-05-06T19:51:36.697912:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv447_i00003 (162x162x1x1)
260506-19:51:36,701 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.701802:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv447_i00001 (162x162x1x1)
INFO: stdout 2026-05-06T19:51:36.701802:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv447_i00001 (162x162x1x1)
260506-19:51:36,705 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.705768:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv447_i00002 (162x162x1x1)
INFO: stdout 2026-05-06T19:51:36.705768:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_heudiconv447_i00002 (162x162x1x1)
260506-19:51:36,709 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.709168:Conversion required 0.015478 seconds (0.015472 for core code).
INFO: stdout 2026-05-06T19:51:36.709168:Conversion required 0.015478 seconds (0.015472 for core code).
260506-19:51:36,732 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.074894s.
INFO: [Node] Finished "convert", elapsed time 0.074894s.
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')
260506-19:51:36,803 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixf8xgy4v1/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixf8xgy4v1/convert".
260506-19:51:36,838 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:51:36,933 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.933104:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:51:36.933104:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:51:36,933 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.933104:Found 192 DICOM file(s)
INFO: stdout 2026-05-06T19:51:36.933104:Found 192 DICOM file(s)
260506-19:51:36,933 nipype.interface INFO:
     stdout 2026-05-06T19:51:36.933104:Convert 192 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_T1w_heudiconv122 (256x256x192x1)
INFO: stdout 2026-05-06T19:51:36.933104:Convert 192 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_T1w_heudiconv122 (256x256x192x1)
260506-19:51:39,731 nipype.interface INFO:
     stdout 2026-05-06T19:51:39.731691:Conversion required 2.855896 seconds (2.855695 for core code).
INFO: stdout 2026-05-06T19:51:39.731691:Conversion required 2.855896 seconds (2.855695 for core code).
260506-19:51:39,755 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 2.916513s.
INFO: [Node] Finished "convert", elapsed time 2.916513s.
260506-19:51:46,262 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetapzar_rsf/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetapzar_rsf/embedder".
260506-19:51:46,273 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:51:49,249 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 2.975431s.
INFO: [Node] Finished "embedder", elapsed time 2.975431s.
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')
260506-19:51:49,272 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixa3buuxa5/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixa3buuxa5/convert".
260506-19:51:49,305 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:51:49,401 nipype.interface INFO:
     stdout 2026-05-06T19:51:49.401451:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:51:49.401451:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:51:49,401 nipype.interface INFO:
     stdout 2026-05-06T19:51:49.401451:Found 179 DICOM file(s)
INFO: stdout 2026-05-06T19:51:49.401451:Found 179 DICOM file(s)
260506-19:51:49,401 nipype.interface INFO:
     stdout 2026-05-06T19:51:49.401451:Convert 179 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold_heudiconv311 (64x64x27x179)
INFO: stdout 2026-05-06T19:51:49.401451:Convert 179 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-sound_run-01_bold_heudiconv311 (64x64x27x179)
260506-19:51:52,940 nipype.interface INFO:
     stdout 2026-05-06T19:51:52.940249:Conversion required 3.597856 seconds (3.597487 for core code).
INFO: stdout 2026-05-06T19:51:52.940249:Conversion required 3.597856 seconds (3.597487 for core code).
260506-19:51:52,967 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 3.660996s.
INFO: [Node] Finished "convert", elapsed time 3.660996s.
260506-19:52:00,205 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetarcyvd2sb/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetarcyvd2sb/embedder".
260506-19:52:00,215 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:52:03,906 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 3.690099s.
INFO: [Node] Finished "embedder", elapsed time 3.690099s.
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')
260506-19:52:03,939 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niix3inu217f/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix3inu217f/convert".
260506-19:52:04,25 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:52:04,214 nipype.interface INFO:
     stdout 2026-05-06T19:52:04.214308:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:52:04.214308:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:52:04,214 nipype.interface INFO:
     stdout 2026-05-06T19:52:04.214308:Found 485 DICOM file(s)
INFO: stdout 2026-05-06T19:52:04.214308:Found 485 DICOM file(s)
260506-19:52:04,214 nipype.interface INFO:
     stdout 2026-05-06T19:52:04.214308:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_bold_heudiconv679 (64x64x27x485)
INFO: stdout 2026-05-06T19:52:04.214308:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-01_bold_heudiconv679 (64x64x27x485)
260506-19:52:13,783 nipype.interface INFO:
     stdout 2026-05-06T19:52:13.783491:Conversion required 9.720259 seconds (9.719472 for core code).
INFO: stdout 2026-05-06T19:52:13.783491:Conversion required 9.720259 seconds (9.719472 for core code).
260506-19:52:13,810 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 9.78394s.
INFO: [Node] Finished "convert", elapsed time 9.78394s.
260506-19:52:33,463 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmeta_vkivam3/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmeta_vkivam3/embedder".
260506-19:52:33,488 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:52:43,792 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 10.303487s.
INFO: [Node] Finished "embedder", elapsed time 10.303487s.
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')
260506-19:52:43,854 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixq7pflxjz/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixq7pflxjz/convert".
260506-19:52:43,944 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:52:44,133 nipype.interface INFO:
     stdout 2026-05-06T19:52:44.133712:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:52:44.133712:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:52:44,133 nipype.interface INFO:
     stdout 2026-05-06T19:52:44.133712:Found 485 DICOM file(s)
INFO: stdout 2026-05-06T19:52:44.133712:Found 485 DICOM file(s)
260506-19:52:44,133 nipype.interface INFO:
     stdout 2026-05-06T19:52:44.133712:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_bold_heudiconv744 (64x64x27x485)
INFO: stdout 2026-05-06T19:52:44.133712:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_bold_heudiconv744 (64x64x27x485)
260506-19:52:53,820 nipype.interface INFO:
     stdout 2026-05-06T19:52:53.820349:Conversion required 9.837152 seconds (9.836543 for core code).
INFO: stdout 2026-05-06T19:52:53.820349:Conversion required 9.837152 seconds (9.836543 for core code).
260506-19:52:53,858 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 9.913485s.
INFO: [Node] Finished "convert", elapsed time 9.913485s.
260506-19:53:13,82 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetajlce4j_h/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetajlce4j_h/embedder".
260506-19:53:13,107 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:53:23,274 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 10.166665s.
INFO: [Node] Finished "embedder", elapsed time 10.166665s.
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')
260506-19:53:23,334 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niix57h7sgku/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix57h7sgku/convert".
260506-19:53:23,423 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:53:23,610 nipype.interface INFO:
     stdout 2026-05-06T19:53:23.610481:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:53:23.610481:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:53:23,610 nipype.interface INFO:
     stdout 2026-05-06T19:53:23.610481:Found 485 DICOM file(s)
INFO: stdout 2026-05-06T19:53:23.610481:Found 485 DICOM file(s)
260506-19:53:23,610 nipype.interface INFO:
     stdout 2026-05-06T19:53:23.610481:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold_heudiconv300 (64x64x27x485)
INFO: stdout 2026-05-06T19:53:23.610481:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-03_bold_heudiconv300 (64x64x27x485)
260506-19:53:33,263 nipype.interface INFO:
     stdout 2026-05-06T19:53:33.263034:Conversion required 9.802395 seconds (9.801308 for core code).
INFO: stdout 2026-05-06T19:53:33.263034:Conversion required 9.802395 seconds (9.801308 for core code).
260506-19:53:33,296 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 9.871857s.
INFO: [Node] Finished "convert", elapsed time 9.871857s.
260506-19:53:52,326 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetau9amugcr/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetau9amugcr/embedder".
260506-19:53:52,350 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:54:02,544 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 10.193919s.
INFO: [Node] Finished "embedder", elapsed time 10.193919s.
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')
260506-19:54:02,605 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixt94wjkky/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixt94wjkky/convert".
260506-19:54:02,693 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:54:02,879 nipype.interface INFO:
     stdout 2026-05-06T19:54:02.879703:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:54:02.879703:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:54:02,879 nipype.interface INFO:
     stdout 2026-05-06T19:54:02.879703:Found 485 DICOM file(s)
INFO: stdout 2026-05-06T19:54:02.879703:Found 485 DICOM file(s)
260506-19:54:02,879 nipype.interface INFO:
     stdout 2026-05-06T19:54:02.879703:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-04_bold_heudiconv197 (64x64x27x485)
INFO: stdout 2026-05-06T19:54:02.879703:Convert 485 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-story_run-04_bold_heudiconv197 (64x64x27x485)
260506-19:54:12,543 nipype.interface INFO:
     stdout 2026-05-06T19:54:12.543614:Conversion required 9.813188 seconds (9.812394 for core code).
INFO: stdout 2026-05-06T19:54:12.543614:Conversion required 9.813188 seconds (9.812394 for core code).
260506-19:54:12,576 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 9.882836s.
INFO: [Node] Finished "convert", elapsed time 9.882836s.
260506-19:54:32,916 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetaws8z796b/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetaws8z796b/embedder".
260506-19:54:32,940 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:54:43,76 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 10.134693s.
INFO: [Node] Finished "embedder", elapsed time 10.134693s.
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')
260506-19:54:43,131 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixdmadt5vp/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixdmadt5vp/convert".
260506-19:54:43,165 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:54:43,266 nipype.interface INFO:
     stdout 2026-05-06T19:54:43.266784:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:54:43.266784:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:54:43,266 nipype.interface INFO:
     stdout 2026-05-06T19:54:43.266784:Found 196 DICOM file(s)
INFO: stdout 2026-05-06T19:54:43.266784:Found 196 DICOM file(s)
260506-19:54:43,267 nipype.interface INFO:
     stdout 2026-05-06T19:54:43.266784:Convert 196 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold_heudiconv749 (64x64x27x196)
INFO: stdout 2026-05-06T19:54:43.266784:Convert 196 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/func/sub-01_ses-01_task-faces_run-01_bold_heudiconv749 (64x64x27x196)
260506-19:54:47,177 nipype.interface INFO:
     stdout 2026-05-06T19:54:47.177049:Conversion required 3.974533 seconds (3.974101 for core code).
INFO: stdout 2026-05-06T19:54:47.177049:Conversion required 3.974533 seconds (3.974101 for core code).
260506-19:54:47,209 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 4.043446s.
INFO: [Node] Finished "convert", elapsed time 4.043446s.
260506-19:54:55,7 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetang4luhrx/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetang4luhrx/embedder".
260506-19:54:55,19 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:54:58,936 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 3.91686s.
INFO: [Node] Finished "embedder", elapsed time 3.91686s.
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')
260506-19:54:58,964 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niix5am238u9/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix5am238u9/convert".
260506-19:54:58,987 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:54:59,60 nipype.interface INFO:
     stdout 2026-05-06T19:54:59.059960:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:54:59.059960:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:54:59,60 nipype.interface INFO:
     stdout 2026-05-06T19:54:59.059960:Found 128 DICOM file(s)
INFO: stdout 2026-05-06T19:54:59.059960:Found 128 DICOM file(s)
260506-19:54:59,60 nipype.interface INFO:
     stdout 2026-05-06T19:54:59.059960:Convert 128 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-01_heudiconv492 (160x160x128x1)
INFO: stdout 2026-05-06T19:54:59.059960:Convert 128 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-01_heudiconv492 (160x160x128x1)
260506-19:54:59,721 nipype.interface INFO:
     stdout 2026-05-06T19:54:59.721928:Conversion required 0.697874 seconds (0.697786 for core code).
INFO: stdout 2026-05-06T19:54:59.721928:Conversion required 0.697874 seconds (0.697786 for core code).
260506-19:54:59,746 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.757844s.
INFO: [Node] Finished "convert", elapsed time 0.757844s.
260506-19:55:05,196 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetaloqr63xt/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetaloqr63xt/embedder".
260506-19:55:05,204 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:55:07,49 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 1.844597s.
INFO: [Node] Finished "embedder", elapsed time 1.844597s.
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')
260506-19:55:07,63 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixdvs6mi9f/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixdvs6mi9f/convert".
260506-19:55:07,66 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:55:07,109 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.109011:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:55:07.109011:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:55:07,109 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.109011:Found 5 DICOM file(s)
INFO: stdout 2026-05-06T19:55:07.109011:Found 5 DICOM file(s)
260506-19:55:07,109 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.109011:Slices not stacked: orientation varies (vNav or localizer?) [-0.512268 0.806544 0.295072 0.0413103 0.366319 -0.929572] != [0.515908 0.788925 0.333821 0.0413103 0.366319 -0.929572]
INFO: stdout 2026-05-06T19:55:07.109011:Slices not stacked: orientation varies (vNav or localizer?) [-0.512268 0.806544 0.295072 0.0413103 0.366319 -0.929572] != [0.515908 0.788925 0.333821 0.0413103 0.366319 -0.929572]
260506-19:55:07,109 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.109011:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv714_i00004 (162x162x1x1)
INFO: stdout 2026-05-06T19:55:07.109011:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv714_i00004 (162x162x1x1)
260506-19:55:07,113 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.113198:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv714_i00002 (162x162x1x1)
INFO: stdout 2026-05-06T19:55:07.113198:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv714_i00002 (162x162x1x1)
260506-19:55:07,117 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.117119:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv714_i00003 (162x162x1x1)
INFO: stdout 2026-05-06T19:55:07.117119:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv714_i00003 (162x162x1x1)
260506-19:55:07,121 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.121007:Convert 2 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv714_i00001 (162x162x2x1)
INFO: stdout 2026-05-06T19:55:07.121007:Convert 2 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-02_heudiconv714_i00001 (162x162x2x1)
260506-19:55:07,128 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.128241:Conversion required 0.024765 seconds (0.024760 for core code).
INFO: stdout 2026-05-06T19:55:07.128241:Conversion required 0.024765 seconds (0.024760 for core code).
260506-19:55:07,152 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.084978s.
INFO: [Node] Finished "convert", elapsed time 0.084978s.
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')
260506-19:55:07,267 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixmmjdfin6/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixmmjdfin6/convert".
260506-19:55:07,270 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:55:07,311 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.311423:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:55:07.311423:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:55:07,311 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.311423:Found 3 DICOM file(s)
INFO: stdout 2026-05-06T19:55:07.311423:Found 3 DICOM file(s)
260506-19:55:07,311 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.311423: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 2026-05-06T19:55:07.311423: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]
260506-19:55:07,311 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.311423:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv898_i00002 (162x162x1x1)
INFO: stdout 2026-05-06T19:55:07.311423:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv898_i00002 (162x162x1x1)
260506-19:55:07,315 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.315152:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv898_i00001 (162x162x1x1)
INFO: stdout 2026-05-06T19:55:07.315152:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv898_i00001 (162x162x1x1)
260506-19:55:07,318 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.318743:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv898_i00003 (162x162x1x1)
INFO: stdout 2026-05-06T19:55:07.318743:Convert 1 DICOM as /app/Norman/Mennen/5516_greenEyes/sub-01/ses-01/anat/sub-01_ses-01_scout_dup-03_heudiconv898_i00003 (162x162x1x1)
260506-19:55:07,321 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.321601:Conversion required 0.014962 seconds (0.014956 for core code).
INFO: stdout 2026-05-06T19:55:07.321601:Conversion required 0.014962 seconds (0.014956 for core code).
260506-19:55:07,345 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.07392s.
INFO: [Node] Finished "convert", elapsed time 0.07392s.
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')
260506-19:55:07,401 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niix14_vsm22/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix14_vsm22/convert".
260506-19:55:07,404 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:55:07,445 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.445677:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:55:07.445677:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:55:07,445 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.445677:Found 3 DICOM file(s)
INFO: stdout 2026-05-06T19:55:07.445677:Found 3 DICOM file(s)
260506-19:55:07,445 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.445677: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_heudiconv560 (64x64x27x3)
INFO: stdout 2026-05-06T19:55:07.445677: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_heudiconv560 (64x64x27x3)
260506-19:55:07,505 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.505130:Conversion required 0.063888 seconds (0.063883 for core code).
INFO: stdout 2026-05-06T19:55:07.505130:Conversion required 0.063888 seconds (0.063883 for core code).
260506-19:55:07,528 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.124012s.
INFO: [Node] Finished "convert", elapsed time 0.124012s.
260506-19:55:07,668 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetaf6yg9cir/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetaf6yg9cir/embedder".
260506-19:55:07,672 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:55:07,739 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 0.067137s.
INFO: [Node] Finished "embedder", elapsed time 0.067137s.
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')
260506-19:55:07,747 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixr3pj71ss/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixr3pj71ss/convert".
260506-19:55:07,751 nipype.workflow INFO:
     [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
INFO: [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
260506-19:55:07,795 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.795321:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
INFO: stdout 2026-05-06T19:55:07.795321:Chris Rorden's dcm2niiX version v1.0.20250505  GCC10.2.1 x86-64 (64-bit Linux)
260506-19:55:07,795 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.795321:Found 12 DICOM file(s)
INFO: stdout 2026-05-06T19:55:07.795321:Found 12 DICOM file(s)
260506-19:55:07,795 nipype.interface INFO:
     stdout 2026-05-06T19:55:07.795321: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_heudiconv912 (64x64x27x12)
INFO: stdout 2026-05-06T19:55:07.795321: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_heudiconv912 (64x64x27x12)
260506-19:55:08,31 nipype.interface INFO:
     stdout 2026-05-06T19:55:08.031148:Conversion required 0.243272 seconds (0.243189 for core code).
INFO: stdout 2026-05-06T19:55:08.031148:Conversion required 0.243272 seconds (0.243189 for core code).
260506-19:55:08,57 nipype.workflow INFO:
     [Node] Finished "convert", elapsed time 0.304735s.
INFO: [Node] Finished "convert", elapsed time 0.304735s.
260506-19:55:08,555 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetaguqi44gc/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetaguqi44gc/embedder".
260506-19:55:08,559 nipype.workflow INFO:
     [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
INFO: [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
260506-19:55:08,805 nipype.workflow INFO:
     [Node] Finished "embedder", elapsed time 0.245342s.
INFO: [Node] Finished "embedder", elapsed time 0.245342s.
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] 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] 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] SIDECAR_FIELD_OVERRIDE Sidecar files should not override values assigned at a higher level.

        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



        ImageOrientationPatientDICOM

        /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

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_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-02_bold.json



        4 more files with the same issue



        ImageType

        /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

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_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-02_bold.json



        4 more files with the same issue



        ShimSetting

        /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

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_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-02_bold.json



        4 more files with the same issue



        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



        TablePosition

        /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

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_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-02_bold.json



        4 more files with the same issue



        TaskName

        /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

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_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-02_bold.json



        4 more files with the same issue



        dcmmeta_affine

        /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

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_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-02_bold.json



        4 more files with the same issue



        dcmmeta_reorient_transform

        /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

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_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-02_bold.json



        4 more files with the same issue



        dcmmeta_shape

        /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

        /sub-01/ses-01/func/sub-01_ses-01_task-story_run-02_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-02_bold.json



        4 more files with the same issue



        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-02_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-02_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-02_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-02_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-02_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-04_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-sound_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-02_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-04_events.tsv

        /sub-01/ses-01/func/sub-01_ses-01_task-sound_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.json

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



        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 story        MRI                  

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

                                           TODO: full task name for faces                             

                                           story                                                      

                                           sound                                                      

                                           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-02_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-02_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-02_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-02_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-02_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-02_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-02_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-02_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-02_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-02_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-02_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-02_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-02_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-02_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-02_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-02_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] 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] 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] 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-02_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-02_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-02_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-02_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-02_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-04_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-sound_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-02_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



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    [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-04_events.tsv

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



        4 more files with the same issue



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          Summary:                         Available Tasks:                      Available Modalities:

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

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

                                           TODO: full task name for faces                             

                                           story                                                      

                                           sound                                                      

                                           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