CT and MRI scans: studies, series and slices explained

A scan is organised in three levels. A study is one visit to the scanner, a series is one set of images taken within that visit, and a slice is a single image in that set. A CT or MRI study usually contains several series, and each series can contain dozens or hundreds of slices, which is why a patient CD looks like a huge pile of files.

Study: one visit

A study is everything produced during one examination. If someone has a CT of the chest on a given day, that is one study, with its own date, description and unique study identifier stored inside the files.

One disc can hold more than one study. A person who had scans on different days, or different body regions on the same day, may have several. The viewer or the folder structure is what separates them.

Series: one set of images

Inside a study, the scanner produces one or more series. A series is a group of images acquired together with the same settings and the same orientation. Each series has a number and often a short description such as “AXIAL” or “SAG T2”, written by the scanner.

Typical reasons for several series in one study:

• the same region scanned in different planes, for example axial, sagittal and coronal
• the same region scanned with different settings, such as before and after a contrast agent
• extra images made by the scanner software from the original data, such as reformatted views

The series description is only a label chosen by the hospital or the scanner. It can be short and cryptic, and it differs between manufacturers.

Slice: one image

A slice is one image, stored as one DICOM instance. For most CT and MRI, a slice is a thin cross-section of the body. Scrolling through a series moves from one slice to the next, usually from one end of the scanned region to the other.

Each slice file carries its own position and orientation in space. That is what lets software know which slice sits above which, and how far apart they are. You can see these values in the tags. See DICOM tags and metadata for how to read them.

How CT and MRI differ

Both produce stacks of slices, but they are built differently.

• CT is made with X-rays. Pixel values are calibrated in Hounsfield units, so the same material gives roughly the same value on different scanners. A CT study often has a small number of series, commonly the same region reconstructed in a few ways.
• MRI uses a magnetic field and radio waves. Pixel values have no fixed scale like Hounsfield units, so brightness is relative and depends on the sequence and the machine. An MRI study often has many series, because each sequence is its own series.

This is why an MRI folder can look more confusing than a CT folder. More series does not mean more problems. It only means more sequences were run.

Why a disc has so many files

Most scanners write one file per slice. A series of 200 slices is 200 files, and a study with ten series is 2,000 files. Older discs sometimes store files with no extension and put them in nested subfolders with short coded names.

The index that ties everything together is the DICOMDIR file. It lists the patient, studies, series and images on the disc. For how it works, see DICOMDIR explained.

Finding your way around

A few practical habits help when you open a scan yourself:

• Check the series description and number first. They tell you which series is which.
• Check the number of slices. A series with only a few images may be a reference image rather than a full stack.
• Do not assume the first series is the main one. Order depends on how the scan was run.
• Open each plane separately. Axial, sagittal and coronal series are different stacks, not different views of one file.

Radix DICOM opens a whole patient-CD folder, including nested subfolders and files with no extension, so you can browse the series and slices on an Android phone. It is not a medical device and is not meant for diagnosis. The steps are in How to open a DICOM CD on your phone.

Who interprets the images

Reading the images is a task for the radiologist and the doctor who ordered the scan. Knowing the structure of a study helps you navigate and share it. Any decision about what the images mean or what to do next belongs to the patient’s doctor.