How to load a 3D volume image file (.vol extension) into MATLAB, edit individual 2D slices and save it back as a 3D image

I have a .vol extension 3D image file (an x-ray tomogram of my experimental setup). Its dimensions are x=555, y=556, z=500 i.e. 500 slices. I want to load this file into MATLAB and do the following: remove some slices from the top and bottom and then set the outer voxels (at a distance greater than a fixed distance, r) of the remaining slices to black. Then I want to save this modified volume as a 3D image of the same extension. How can I do this? If someone can help me with just how to load the .vol file and access individual slices, it would be a big help. Any help would be appreciated, thanks in advance.

Edit: Link for the .vol file

[Guillaume]

As far as I know there is no standard .vol format. In any case, that's not something that matlab knows how to handle.

Possibly your .vol file is the same format as in this answer so you could try the code there. If not, it may be the format described here, it would be easy to write a decoder for that, but possibly it's a proprietary format for which you'd need the documentation from the vendor of your software.

Answer 1

[Guillaume]

From your information about the size of the volume and from the number of bytes in the file it would appear that it just contains the raw pixels encoded as 16-bit integers with absolutely nothing else, in particular, no information on the order of dimensions. A little bit of experimentation will be needed

fid = fopen('scan1.vol');
voxels = fread(fid, '*uint16');  %read as 16 bit unsigned. I'm assuming they're unsigned
fclose(fid);

voxels = reshape(voxels, [555, 556, 500]);  %you may need to permute the numbers here
%and you may need to permute the dimensions afterward

[Sagar Chaudhary]

Thanks! This code works for me. Can you suggest how can I convert this 3d matrix 'voxels' back to a 3d image and save as a .vol file?

[Guillaume]

voxels is a 3d image. You can pass it directly to the volume viewer or any matlab function that expects a volume.

volumeViewer(voxels);

You already have the .vol file, so I'm not sure why you'd want to recreate it. If you want to save another volume according to the format of that .vol file, bear in mind that it is a very raw format. In particular, the file does not include any information about:

• size of any dimension
• storage precision of the voxels
• order of dimensions

Therefore, whatever will read the file needs to be told this information.

To write a 3D matrix the same way your current one is encoded:

function writevol(filename, voxels)
    %writevol: Write a volume to a .vol file
    %Warning: the .vol file does not contain any metadata, just the raw voxels intensity. In particular, it does not store the volume size.
    %The voxels are stored as 16-bit unsigned integer, row then column major.
    %inputs:
    %    filename: char vector or scalar string, specifying the file name, ideally as a full path
    %    voxels: a 3D matrix of type double, single, uint8 or uint16
    [fid, errmsg] = fopen(filename, 'w');
    assert(fid > 0, 'Failed to open file "%s" for writing, the error is: %s', filename, errmsg);
    cleanup = onCleanup(@() fclose(fid));  %close file on function completion or on error
    voxels = im2uint16(voxels);  %convert to 16 bit unsigned if the voxels aren't already in this format
    fwrite(fid, voxels(:), 'uint16');  %write voxels intensity.
end

[Sagar Chaudhary]

I actually want to edit the individual 2D slices (e.g. voxels(:,:,250)) of the 3d matrix 'voxels' (i.e. set some of the pixels to black in each image) and then want to save it back as .vol 3d image to be able to open it with Fiji (ImageJ)

[Sagar Chaudhary]

Using fwrite worked for me. Thanks for the solution!

[Hege]

Hi, I am also using this script.but I am getting reshape error. Appreciate your comments

fid = fopen('F:\REICOFIL\reicofil_D_7mm_6um_1d42s_01\reicofil_D_7mm_6um_1d42s.vol');
voxels = fread(fid, '*uint16');  %read as 16 bit unsigned. I'm assuming they're unsigned
fclose(fid);
voxels = reshape(voxels, [1920, 1920, 1536]);  %you may need to permute the numbers here
% %and you may need to permute the dimensions afterward

Error-vol

Error using reshape

To RESHAPE the number of elements must not change.

Error in vol (line 4)

voxels = reshape(voxels, [1920, 1920, 1536]); %you may need to permute the numbers here