# Data - First Steps

<figure><img src="/files/XRnE7bpMbHkayUpEpg2N" alt="" width="563"><figcaption></figcaption></figure>

[You can read more about this process via the linked PowerPoint made by the CBI](https://medicine.musc.edu/-/sm/medicine/departments/centers/cbi/f/cbimridataflow20210421.pdf).

## 1. Downloading scan data from CBIHome

* Open Filezilla (or the FTP software of your choice)
* Enter the address to CBIHome (sftp\://cbihome.musc.edu), as well as your NetID and password
* Navigate to the top level directory, then to MRData, then to your PI's folder, then to the study folder of your choice
* Download scans of your choice
  * Note that you can set the output destination for your downloads - set this to the folder on your desktop in which you will organize your newly downloaded data

## 2. Unzipping dicom folders

* You can unzip newly downloaded dicom folders in one of two ways:
  * Manually unzip the folders by double clicking (on Mac) or right clicking and extracting (on Windows)
  * Automate the unzipping process with a command line tool such as the bash tool 'unzip'.
    * See <https://bridge-lab.gitbook.io/docs/general/onboarding/research-specialist-training#id-5.-workspace-setup> for more details
    * To use bash unzip, open a Terminal and pass the following commands:

```bash
cd [filezilla download directory]
find . -type f -name '*.zip' -exec unzip {} \;
```

## 3. Sorting dicoms by sequence type

In order to access dicoms in a manageable way, they need to be sorted. This is done by looking at dicom meta data and sorting each dicom file based on a piece of meta data. There are many tools that allow a user to do this, such as simple-dicom-sort ( see <https://bridge-lab.gitbook.io/docs/general/onboarding/research-specialist-training#id-5.-workspace-setup> for more details).&#x20;

Our study dicoms are typically sorted by series/sequence name - the name of the type of scan to which the dicoms belong. Below is the simple-dicom-sort command to sort a set of dicoms. This can be placed into a for-loop in bash to sort many subjects' dicoms at once.

```bash
dicom_sort [input] [output] %SeriesName%
```

## 4. Convert to nifti and BIDS format

See [BIDS Data Organization](/docs/imaging/data-organization/general-documentation/bids-data-organization.md).


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