3. 'Select files' panel
Choose the Contrast data file(*1) or the Structure image file in the
'Select files' panel. Then, choose the picture file you want to use on
the Select file' window that appears
after clicking the 'Select' button of each file. Please click 'Load'
button after selecting all necessary files. Data is
read from all selected picture files. All selections will be cleared
when 'Cancel' button is clicked. ROI file (*2) which describes three
dimension shape of the brain structure can be selected at this step.
The ROI is the file which sets '0(zero)' for the outside of the brain
structure and '1(one)' for the inside of the structure. This file can
be made easily with MRIcro.
[Note]
The contrast data file, the structural image file and the ROI image
file can be formatted as the ANALYZE
7.5, NIFTI1,
MATLAB(*3), and Text file (*4). 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.
(*1)
Contrast data files can be specified up to 64. Contrast data file name
can be displayed three names at the same time. You can click the button
on the right and left for scrolling up/down the data name.
(*2)
ROI files can be specified up to 64. Popup menu displays the ROI file
numbers. To see more, you can specify up to the selected ROI file
numbers plus one more file name. Please set the ROI file name after
selecting the ROI file number with this popup menu.
(*3)
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
(*4)
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
:
:
:
3.1. 'Select file' window
The 'Select file' window is started by either of the following two
selection modes.
(a) Load file selection mode
In this mode, you can select saved file to read the data.
(b) Save file selection mode
In this mode, you can edit saved files, and make and save new files.
Please choose the file you want to edit, or write the name of new file.
