Arterial Input Function (AIF) Resampler

If you have some measures of contrast agent plasma concentration, perhaps with uneven spacing in time or perhaps from more than one subject, you can perform a least-squares fit to the data using a model of blood recirculation to obtain an AIF suitable for use in perfusion or DCE-MRI calculation. You can also use this tool to resample an AIF with one time between samples (possibly irregular) to a different time between samples.

Bring up the stand-alone AIF Resampler tool by clicking on the icon in the Jim install folder, or in the installed menu for Jim, or using the AIFREsamplerTool command (on Unix systems). This brings up the AIF Resampler tool:

Now set:

• The AIF input file. This text file must contain two columns separated by white space or a comma (","). The first column is the time at which the gadolinium concentration was measured, and the second column is the contrast agent concentration at that time. The values do not need to be evenly-spaced in time.

• Whether to fit a recirculation model to the data before resampling. If you select this option, the recirculation model detailed in this paper will be fitted to the data, and then th fitted recirculation model curve will be resampled to the required time between samples. If you do not select this option, a cubic spline interpolator will used to resample the input data at regular time intervals. If the input data comes from more than one subject, then you must select to fit the recirculation model.

• Whether you want to manually set the time of contrast agent arrival. If you do, then set that time in the text field underneath the check box. If you do not, then the time of arrival will be taken as the first time point in the input file where the contrast agent concentration, rises above zero or it will be set from the recirculation model fit.

• The (regular) time between samples you require in the output AIF file.

• The number of zero concentration values to be output before the time of arrival of the contrast bolus, in the output AIF file. The output will simply be padded with this number of zero concentration values.

• The file name for the output AIF file.

You can save these settings for future use by pressing the button, or revert to default settings by pressing the button.

This tool can also be run from the command-line with the program entry point com.xinapse.apps.perfusion.AIFResampler