The code of EPICA is FREELY available to the community of PET data analysis. Matlab software is required for EPICA. |
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Background of EPICA | →top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
In the kinetic analysis of dynamic positron emission tomography (PET) data, the input function of the compartment model [the plasma time-activity curve (pTAC)] was obtained by serial arterial blood sampling. It is of clinical interest to develop a method for PET studies that estimates the pTAC without needing serial arterial blood sampling. For this purpose, we proposed a method to extract the pTAC from the dynamic brain PET images using a modified independent component analysis [extraction of the pTAC using independent component analysis (EPICA). EPICA performs the appropriate preprocessing and spatial independent component analysis (ICA) using a cost function that takes the various properties of the pTAC into account. Spatial ICA seeks statistically independent images from mixed data. This code implements an EPICA algorithm proposed in an article, "Extraction of the Plasma Time-activity Curve based on Independent Component Analysis", (M. Naganawa, Y. Kimura, K. Ishii, K. Oda, K. Ishiwata, A. Matani). This paper can be downloaded from (the Web site). We adopted the FastICA algorithm developed by Dr. Hyvärinen. This code is also used in an article, "Omission of Serial Arterial Blood Sampling in Neuroreceptor Imaging with Independent Component Analysis", (M. Naganawa, Y. Kimura, T. Nariai, K. Ishii, K. Oda, Y. Manabe, K. Chihara, K. Ishiwata) in NeuroImage (in press). The code included in this program is written in Matlab (version 6.5), Mathworks, tested on PC and Linux. |
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Unpacking the EPICA Zip File | →top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The EPICA codes are compressed into EPICA.zip.
The ZIP file includes the following files:
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Required Data | →top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The input data, which are required to perform EPICA, are demonstrated below.
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Usage | →top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
To run EPICA, type>> Est = Epica(Data, Options); Example: >> Epica(FDGData); >> Epica(FDGData, {'Para',[-50, 0.3]}, {'NSlice', [1,20]}, {'NFrame',[1 23]},{'NComp', 3}....); |
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Summary of Inputs, Outputs, and Options | →top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
INPUTS: The function of EPICA takes only one mandatory argument, a structure. Its fields has the following meanings.
OPTIONS: The function of EPICA has various options to modify its algorithm. The option must be a cell that contains two elements. The 1st element is a string to denote the option and the 2nd element is a value for the option. (PC = Principal Component)
OUTPUTS: A result is returned as a structure. (IC = Independent Component)
ICA LINEAR MODEL The relationship among the above inputs and outputs is represented as the following equations. IC (Data)
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Demonstration | →top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Clinical FDG data and noise added simulated data are prepared for demonstration.
The demonstration program is run by typing:>> Demo_Epica(Sw); Sw is either 'clinical' or 'simulate'.Example: >> Demo_Epica('clinical'); The initial vector for FastICA is a random vector, therefore a shape of the 1st estimated IC is pTAC-like or tTAC-like. If the estimated IC is tTAC-like as shown in Fig. 5, type 'y'; >> Continue? (y/n) y
>> Continue? (y/n) n
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Copyright | →top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The EPICA codes are Copyright (C) 2005-2013 by Mika Naganawa and Yuichi Kimura.
The software package is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License
as published by the Free Software Foundation;
either version 2 of the License, or any later version. The software package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. |
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Licensing the Software Package for Proprietary Programs | →top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
As stated in the GNU General Public License,
it is not possible to include this software library in a proprietary program without written
permission from the owners of the copyright. If you wish to obtain such permission, you can reach us by paper mail: Yale PET Center, Yale University, 801 Howard Avenue, PO Box 208048 New Haven, CT, 06520-8048, USA or by sending email to Mika Naganawa (mika.naganawa[at]yale.edu). |