Batch - ASL Analysis

To do ASL 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 ASL analysis (Main, Options, Parameters and Quantification, 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 asl 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 <Include if partial match> is checked, the subdirectories can have similar names, as illustrated above.
• Input image type can be either DICOM or nifti.
• 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.

Output:

The batch ASL can produce the perfusion map (blood flow map), and an average map.

The Options tab

The Parameters tab

Parameters:

TR is read from the DICOM header when present.

Other parameters are set in accordance with recommendations in Alsop et al (Recommended implementation of arterial spin-labeled perfusion MRI for clinical applications, Mag Reson Med 2015).

Labelling method:

Labelling method should be in accordance with the acquired data type.

Input data sorting:

Input data sorting can be auto-detected for DICOM data, given that correct tags are present in the DICOM header. If not, this must be specified manually. For nifti data, this needs to be specified correctly, or the analysis will not be valid.

It is always recommended to run the analysis with one series to make sure that the settings for image order is correct on your data. It can also be useful to use the GUI batch module to verify the order.

The Quantification tab

M0 reference:

An M0 image can be used to produce (semi-) quantitative results.

• Fixed M0 value. Note that a M0 value of 1 means that no correction is done.
• M0 from the ASL control image
• M0 from an image file. The M0 image needs to be in nifti-format.