Batch Module - Getting Started

To do batch analysis, follow these steps:

1. Organize input data to be analyzed in a base directory and give the subdirectories containing the series to be analyzed a given name.

2. Select the settings for image loading in Pre-process.

3. Define all settings for the analysis you would like to do.

4. Set base directory, and do Search for files.

5. Run the analysis.

See additional details below:

Introduction

The batch module can analyze data in DICOM or nifti formats. Some functionality is only available for nifti data. However, image conversion from DICOM to nifti can always be performed first.

It is important that all data to be analyzed in the same batch is of equivalent type, so that they can be analyzed in the same manner.

The different types of analysis (Perfusion, ROI analysis, DCE analysis etc.) are selected in the tabs in the lower row. In the example above, the perfusion analysis tab has been selected. For some analysis, such as for perfusion, there are several tabs to define analysis settings. These are seen in the middle of the image above (Main, AIF, Advanced AIF...).

After defining settings, the analysis is done by pressing Process. This is true for all analysis tabs except for Pre-process. This tab is used as input for the other types of analysis.

Batch analysis can be done for one or several series. Results will be saved in specified output subdirectories, or copied to clipboard, depending on type of analysis.

Before you start - search for files

When processing data in the batch module, the application will analyze all data of a specific type (for example perfusion data) in a selected base directory. For the application to find the specific perfusion data, one needs to specify the name of the folder. This means that all subdirectories containing data to be analysed in the same batch must have the same name. In the example above, the perfusion subdirectory is named 'Perf', and we see that the application found six subdirectories with this name, meaning that each of the six studies in this example all had one perfusion series. If any of the perfusion series were in subdirectory with a different name, it would not have been included in the analysis.

Search for files can be refined based on:

• Include subdirectories: if not checked, only subdirectories one level down from base directory will be included.
• Include if partial match: if checked, analysis will include subdirectories even if name specified only partially matches the subdirectory name, as shown in image below.

Loading of images

An important first step in a batch analysis is to ensure that images are loaded in the correct order. This is defined in the Pre-process tab.

For DICOM data, Sort using instance number seems to work best for most data, but this will always depend on the input data. If image time is used, the specific tag to be used can be defined in General Options (Select Options in the main GUI frame).

Performing analysis

After image loading has been set correctly, analysis can start. Any preprocessing to be done can be defined in the same tab.

To start the analysis, one first need to specify all settings. For Perfusion, DCE and T1 mapping analysis, remember to specify settings in all tabs.

It is smart to run the analysis with a minimum number of cases first, to make sure that analysis runs as expected, and to familiarize yourself with the analysis, before starting a large batch.

Tips

• Motion correction can be done as part of the analysis for perfusion and DCE, but it is recommended to do this as a separate step before you run the dedicated analysis, using the Motion correction tab. This will save you time in case you would want to repeat the batch analysis, but do not want to repeat the motion correction.