> For the complete documentation index, see [llms.txt](https://docs.ccv.brown.edu/bnc-user-manual/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar/oscar-utility-script/extra-tools-and-features.md).

# Extra tools & features

## Correct DICOM headers during XNAT export

{% hint style="warning" %}
Use this tool responsibly! Modifying DICOM headers can create corrupt or invalid DICOM data if not done correctly. (Although your data on XNAT will not be modified, so you can always re-export if necessary)
{% endhint %}

If you have any corrections you need to make to your DICOMs, you can create a .json file that lists the scan(s) to be modified, DICOM field(s) to be changed, and the new value(s) you'd like to change it/them to. This can be useful, for example if your participant was registered with their actual birthdate but you'd like to change it to a pseudo birthdate (e.g. Jan 1st, birth year) before further analyzing and/or sharing the data.

For example, say that I am exporting the data from demodat subject 004, and I would like to 1) correct the birth date to 19880101 and 2) change the Patient ID to "Anonymous".

<details>

<summary>This is how I would set up my json file</summary>

```json
{
    "mappings": [
        {
            "scans_to_correct": [
                "anat-scout_acq-localizer",
                "anat-scout_acq-aascout",
                "anat-scout_acq-aascoutMPRsag",
                "anat-scout_acq-aascoutMPRcor",
                "anat-scout_acq-aascoutMPRtra",
                "anat-T1w_acq-memprage",
                "anat-T1w_acq-memprageRMS",
                "fmap_acq-boldGRE",
                "func-bold_task-checks_run-01",
                "func-bold_task-checks_run-02",
                "func-bold_task-motionloc",
                "func-bold_task-resting",
                "dwi_acq-b1500_dir-ap_SBRef",
                "dwi_acq-b1500_dir-ap",
                "dwi_acq-b1500_dir-apTENSOR",
                "fmap_acq-diffSE_dir-ap",
                "dwi_acq-b1500_dir-pa_SBRef",
                "dwi_acq-b1500_dir-pa",
                "dwi_acq-b1500_dir-paTENSOR",
                "fmap_acq-diffSE_dir-pa"
            ],
            "dicom_field": "PatientBirthDate",
            "new_value": "19880101"
        },
        {
            "scans_to_correct": [
                "anat-scout_acq-localizer",
                "anat-scout_acq-aascout",
                "anat-scout_acq-aascoutMPRsag",
                "anat-scout_acq-aascoutMPRcor",
                "anat-scout_acq-aascoutMPRtra",
                "anat-T1w_acq-memprage",
                "anat-T1w_acq-memprageRMS",
                "fmap_acq-boldGRE",
                "func-bold_task-checks_run-01",
                "func-bold_task-checks_run-02",
                "func-bold_task-motionloc",
                "func-bold_task-resting",
                "dwi_acq-b1500_dir-ap_SBRef",
                "dwi_acq-b1500_dir-ap",
                "dwi_acq-b1500_dir-apTENSOR",
                "fmap_acq-diffSE_dir-ap",
                "dwi_acq-b1500_dir-pa_SBRef",
                "dwi_acq-b1500_dir-pa",
                "dwi_acq-b1500_dir-paTENSOR",
                "fmap_acq-diffSE_dir-pa"
            ],
            "dicom_field": "PatientID",
            "new_value": "Anonymous"
        }
    ]
}
```

</details>

After saving it as "x2b\_demodat\_dicomfix\_config.json" on Oscar, I just need to add one line to the \[xnat2bids-args] section of my [configuration file](https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar/oscar-utility-script/pages/LIKGICqZUzrJRb8hGD8W#id-2.-configure-xnat2bids-parameters):

```md
dicomfix-config="/oscar/home/elorenc1/scripts/demodat/x2b_demodat_dicomfix_config.json"
```

Then, launch run\_xnat2bids.py as usual. Be sure to check your output log file when your job completes - it will print INFO messages as it makes changes to DICOMs:

`INFO Modified PatientBirthDate in /users/elorenc1/bids-export/bnc/study-demodat/xnat-export/sub-004/ses-01/anat-scout_acq-localizer/1.3.12.2.1107.5.2.43.67050.30000022051915365316000000043-1-1-n8iroc.dcm: 19880101`

and WARNING messages if it runs into any trouble:

`WARNING PatientsBirthDate field is not present in /users/elorenc1/bids-export/bnc/study-demodat/xnat-export/sub-004/ses-01/fmap_acq-boldGRE/1.3.12.2.1107.5.2.43.67050.30000022051915365316000000043-8-11-178dtrw.dcm.`


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://docs.ccv.brown.edu/bnc-user-manual/xnat-to-bids-intro/using-oscar/oscar-utility-script/extra-tools-and-features.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.