Reading voxel values from binary file into matlab

Question

I have a 16bit voxel data set from which I need to extract the integer values for each voxel. The data set can be downloaded from here, it is the 'Head Aneuyrism 16Bits' data set (You need to click on the blood vessels image to download the 16bit version). Its size is 512x512x512, but I don't know whether it is greyscale or color, nor if that matters. Looking at the image on the website I'd guess that it is color, but I am not sure whether the image should be taken literally.

A related question on SO is the following: How can I read in a RAW image in MATLAB?

and the following on mathworks: http://www.mathworks.com/matlabcentral/answers/63311-how-to-read-an-n-dimensioned-matrix-from-a-binary-file

Thanks to the information in the answers to these questions I managed to extract some information from the file with matlab as follows:

fileID=fopen('vertebra16.raw','r');

A=fread(fileID,512*512*512,'int16');

B=reshape(A,[512 512 512]);

I don't need to visualise the image, I only need to have the integer values for each voxel, but I am not sure whether I am reading the information in the correct way with my script. The only way I found to try and check whether I have the correct voxel values is to visualise B using the following:

implay(B)

Now, with the code above, and then using implay(B) I get a black and white movie with a white disc in the center and black background and some black pixels moving in the disc (I tried to upload a frame of the movie, but it didn't work). Looking at the image on the website from which I downloaded the file, the movie frames I get seem quite different from that image, so I'd conclude that I do not have the correct voxel values.

Here are some questions related to my problem:

Do I need to know whether the image is in grey scale or color to read the voxel values correctly?
On the data set website there is only written that the data set is in 16bit format, so how do I know whether I am dealing with signed or unsigned integers?
In the SO question linked to above they use 'uint8=>uint8'. I could not find this in the matlab manual, so I wonder whether 'uint8=>uint8' is an obsolete matlab notation for 'uint8' or if it does something different. I suspect that it does something different since if I use 'int16=>int16' instead of 'int16' in my code above I get a completely black movie with implay.

Lisa Lisa · Accepted Answer · 2016-02-18T11:18:47

It looks like you read the data correctly.

The problem when displaying it is the scale of the values. implay seems to assume the values to be in [0,1] and therefore clamps all values to be in that range, where are your data range is [0,3000].

Simply doing

B = B / max(B(:))

will rescale your data to [0,1] and looking at the data again with

implay(B)

shows you something much more sensible.

Reading voxel values from binary file into matlab

1 Answers