function cropPadNii(niiIn,niiOut,compressFlag,normalizeFlag,padNum)

%% crop the zero padding around nifti file

% Author: Da Ma (da_ma@sfu.ca)

% compressFlag: whether to compress the output nifti file (Default: False)

% normalizeFlag: whether/how to normalize the input volume

%    0 (default): donot normalize

%    1 : normalize to [0,1]

% [Yet to be implemented]:

% padNum: Number of voxels to pad around the cropped images

%%

% By default, don't compress .nii file to .nii.gz

if ~exist('compressFlag','var'); compressFlag=false;end

% By default, compress to [0,1]

if ~exist('normalizeFlag','var'); normalizeFlag=0;end

%% Read input nifti

disp('loading nifti file ...')

% read nifti volume

vol = niftiread(niiIn);

% % read nifti head

disp('read nifti header ...')

niiHead = niftiinfo(niiIn);

%% crop zero pad

disp('cropping nifti volume ...')

vol = cropPad(vol);

% [Yet to be implemented]:

% padNum: Number of voxels to pad around the cropped images%% normalze

if normalizeFlag == 1

    vol = mat2gray(vol);

    vol = single(vol);

end

%% update header dimension

niiHead.ImageSize = size(vol);

niiHead.raw.dim(2:4) = size(vol);

%% save nifti

disp('saving nifti file ...')

% determine if need to save as a '.nii.gz' compression file

[niiPath,niiName,niiExt] = fileparts(niiOut);

[~,~,internalExt] = fileparts(niiName);

if internalExt == ".nii" ||niiExt == ".gz"

    compressFlag = 1; % = true

end

savePath = fullfile(niiPath,niiName);

%% save nii

niftiwrite(vol,savePath,niiHead,'Compressed',compressFlag);