spm_readwrite_nii

https://github.com/VUIIS/spm_readwrite_nii

This is the 1% of the SPM12 Matlab code that is needed to read and write data and headers of Nifti files. The purpose of this is to provide a reliable tool to use Nifti files in Matlab when the rest of SPM isn't needed.

Source is https://github.com/spm/spm12/tree/c28485d, which is SPM12 r7771 but updated for Mac Silicon binaries. This version has not been actually released as of 2024 Mar 28.

SPM12 info: http://www.fil.ion.ucl.ac.uk/spm/software/spm12/

SPM12 license: See LICENCE.txt

For newer Macs, execute permissions can be granted all at once with this command in Terminal:

sudo xattr -dr com.apple.quarantine <path>

Where <path> is the base path where this code was installed.

Files included from the SPM distribution

spm_vol.m
    spm_fileparts.m
    spm_existfile.m*
    spm_unlink.m*
    spm_vol_nifti.m
    @nifti/*
@file_array/*
spm_read_vols.m
    spm_check_orientations.m
        spm_mesh_detect.m
    spm_slice_vol.m*
    spm_matrix.m
    spm_type.m
spm_write_vol.m
    spm_create_vol.m
    spm_file.m
spm_write_plane.m

Usage

Also see the help text for the various functions. Compressed nifti files (.nii.gz) can generally be read on linux, but not written. Matlab's gzip function can be applied to written .nii files if desired.

Single 3D .nii

% Read a single 3D nifti file. V contains Nifti header information in 
% an SPM-specific format. Y contains the image data after applying the 
% header scaling factor. XYZ contains world space coordinates in mm, 
% computed from the Nifti header sform/qform.
fname = 'image.nii';
V = spm_vol(fname);
[Y,XYZ] = spm_read_vols(V);

Single 4D .nii

% If it's a 4D series like fMRI, we can reshape to a 2D time x voxel
% matrix, which is often useful for processing
origsize = size(Y);
numvols = origsize(4);
Yr = reshape(Y,[],numvols)';

% Then we can reshape it back later to be ready to write to file
Yout = reshape(Yr',origsize);

% To write, we set a filename, then we have to write a single volume 
% at a time.    
outfname = 'processed_image.nii';

for v = 1:numvols

    % Re-use the original V to get correct headers, but remove
    % the scaling info so SPM can rescale appropriately. Same 
    % scale factor is used for all volumes.
    thisV = rmfield(V(v),'pinfo');
    
    % Choose a data type. float32 is a good compromise between
    % low digitization error and small file size
    thisV.dt(1) = spm_type('float32');
    
    % Alternatively, for integer valued data like ROI images, we
    % should NOT let SPM autoscale, because it may store not-quite-integer
    % values. Instead fix the scaling factor at 1 and use an integer 
    % datatype
    %thisV = V(v);
    %thisV.pinfo(1:2) = [1;0];
    %thisV.dt(1) = spm_type('uint16');
    
    % Don't forget to set the filename so we don't overwrite existing
    thisV.fname = outfname;
    
    % And write this volume
    spm_write_vol(thisV,Yout(:,:,:,v));
    
end