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1. Introduction

* Alternation and distribution

This software is implemented in relation to the GNU General Public License. It is free to use, and free to modify and change the program contents with self responsibility. Only the obligation of use is that indicate the name of this software (multi_color) and the URL address ( on your publication which is made by using this software.

* Discharge from responsibility

We have tried to take all possible measures to ensure that building the software. However, we do not assure the safety of use and will not be responsible for any direct or indirect damages or losses of your work by using this software. We make no warranties/recompenses of any kind for it. You are solely responsible for using this program. Also, we have no obligation to solve any problems and to make modification of this software when it has unsatisfactory matters in the program.

* System requirements

This software requires MATLAB larger than R13(version 6.5).
<< We recommend larger than MATLAB R14 Service Pack 2(Version 7.0.4). >>
The software is developed and checked its operation by the MATLAB R2006a(V7.2.0) through the CentOS Linux (linux kernel:2.6.9-34.0.2.ELsmp).

* Program Summary

This software is a MATLAB program to overlay a number of resulting imaging data maps of the contrast on a single brain structure image. It is also possible to express the overlapped contrast maps into the Three Dimensions.

Need to prepare,
  1. Contrast data file
  2. Structural image file
  3. ROI(Region Of Interest) image file (OPTION)

The contrast data file, the structural image file and the ROI image file can be formatted as the ANALYZE 7.5, NIFTI1, MATLAB(*1), and Text file (*2). The resolution of the structural image file should be higher (smaller VOX size) than the contrast data file. Especially for the structural image file, the resolution with integral multiplication is recommended to the Contrast data file.

The reference_file variable and the voxmat variable are preserved in the data file of MATLAB form (.mat). The file name of the ANALYZE 7.5 form or the NIFTI1 model is set to the reference_file variable. Header information such as Voxel size and Dim size is read from the reference file specified by the reference_file variable. On the other hand, the voxmat variable sets X, Y, and Z coordinates in the Voxel coordinate system in the third row from the first row in arrange two dimensions of four N line rows and the data value is set to the fourth row. In the data file of the MATLAB form, it treats as NaN(Not-a-Number) excluding coordinates specified by the voxmat variable.

>> data = load('voxmatrix_new.mat')
data =
    reference_file: 'con_0000.img'
            voxmat: [129x4 double]
>> data.voxmat(1:10,:)
ans =
   33.0000   38.0000    2.0000    2.5600
   34.0000   37.0000   12.0000    2.5800
   34.0000   38.0000   12.0000    2.6300
   35.0000   32.0000   13.0000    2.5900
   38.0000   35.0000   12.0000    2.6100
   39.0000   31.0000   12.0000    2.3200
   42.0000   31.0000   10.0000    2.3000
   45.0000   27.0000    8.0000    2.0000
   45.0000   31.0000    9.0000    2.0012
   45.0000   31.0000    8.0000    2.1333

In the data file of text form (.txt), the file name of the ANALYZE 7.5 form or the NIFTI1 model that refers to header information is set to the reference_file line. Moreover, the number of data is specified for the voxel_num line, and data is set to the vox_val line. In the data file of the text form, it treats as NaN(Not-a-Number) excluding coordinates specified by the vox_val line.

>> cat voxmatrix_new.txt
# reference_file = name of a reference data file.
# voxel_num = number of vox_val data.
# vox_val(X,Y,Z) = Value
reference_file = con_0000.img
voxel_num = 129
vox_val(33,38,2) = 2.560000
vox_val(34,37,12) = 2.580000
vox_val(34,38,12) = 2.630000
vox_val(35,32,13) = 2.590000
vox_val(38,35,12) = 2.610000
vox_val(39,31,12) = 2.320000
vox_val(42,31,10) = 2.300000
vox_val(45,27,8) = 1.999998
vox_val(45,31,9) = 2.001221
vox_val(45,31,8) = 2.133333
vox_val(45,32,7) = 2.002345
vox_val(46,32,8) = 2.000000

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