Good Morning,
I tried to import DICOM Nifti into ImageJ and save to xyz format with getVoxelCloud plugin based on this discussion thread:
https://www.researchgate.net/post/How_can_I_obtain_voxel_coordinates_and_intensity_for_all_voxels_in_a_MRI_imageThe Nifti file is 16-bit and can download at:
http://bit.ly/2TJb9GvI was told it needs to change to image>type>32-bit in order to generate more accurate intensity value. The following is some of the output xyz txt file. The first column is the image serial number, and 2-4 columns are xyz valuve. I did not see the intensity value.
125 33 7 171
126 33 7 264
127 33 7 217
128 33 7 64
129 33 7 68
130 33 7 70
131 33 7 43
132 33 7 92
133 33 7 29
134 33 7 175
135 33 7 353
136 33 7 416
137 33 7 37
138 33 7 259
139 33 7 133
140 33 7 112
141 33 7 45
142 33 7 47
here are the codes of the plugin:
run("Clear Results");
requires("1.32f");
title = getTitle;
width = getWidth;
height = getHeight;
depth = nSlices;
getPixelSize(unit, pw, ph, pd);
path = getDirectory("image");
Vp_tmp = 0;
f = File.open("");
for (z=0; z<nSlices; z++) {
setSlice(z+1);
for (y=0; y<getHeight; y++) {
for (x=0; x<getWidth; x++) {
value = calibrate(getPixel(x,y));
print(f, x + " \t" + y + " \t" + z+ " \t" + value);
}
}
}
Does anyone know how to convert a series of DICOM files into xyz coordinate with intensity value?
Thanks
SJ
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.htmlimagejoutput.JPG (146K) <
http://imagej.1557.x6.nabble.com/attachment/5021498/0/imagejoutput.JPG>