Batch - Perfusion Analysis

To do perfusion analysis in batch, 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/check the settings for image loading in the Pre-process tab.

3. Define all settings for the analysis you would like to do for the perfusion analysis (Main, AIF, Advanced AIF, Deconvolution, Options, Leakage correction and Signal conversion, as applicable).

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

5. Run the analysis by selecting Process.

See additional details below.

The Main tab

• Subdirectory name: the name of the subdirectory containing the perfusion series. If several studies are to be analyzed, the name of the subdirectory containing the perfusion series must be the same for all studies.
• If ‘Included if partial’ match is checked, the subdirectories can have similar names.
• Input image type can be either DICOM or nifti.
• File extension can also be left open.
• Output image type can be either DICOM or nifti. This means, that if the input data is DICOM, and output data can be either DICOM or nifti.
• You can specify a dedicated folder for the output images that are produced in the analysis. If this is left blank, all output maps are stored directly in the directory of the study.
• You can specify a prefix to the output images.
• If Output Dicom as greyscale images is not checked, all output maps are saved as RGB images. Thus, in most cases, one would like to check this box. Note that you can add a palette to the map if you open the map in nordicICE. This checkbox is only applicable for Dicom output data. For nifti output data, images will always be saved as greyscale images.

Output images: Some output images are only available when specific settings are used:

• Leakage map is available when leakage correction is used.
• Extraction map is available if residue function leakage correction method is selected.
• Uncorrected rBV is available when leakage correction is used.
• Unmasked rBV is available when vessel removal is used.
• Chi-square map is available when gamma variate is used for parametric modelling.

Defining the arterial input function (AIF)

Analysis can be done with:

• No AIF
• Auto-detect AIF: a global search in the entire dataset will be performed. The used AIF can be saved as a text-file.
• Load from file: use a selected AIF of your choosing.
• Population based AIF: select between two predefined AIF based on literature studies.

All other settings and options are the same as in the GUI perfusion module.