No, dcm2niix does not handle DICOMs archived in compressed zip files. You can use your favorite scripting language here. Below is my Matlab script for tgz archives which can easily be modified for zip files:


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function tgz2dcm1
%matlab script to convert DICOM images saved in compressed .tgz archives
tgzDir = '/Volumes/TbStick/DIOCM';
outDir = '/Volumes/TbStick/nifti';
dcm2niix = '/usr/local/bin/dcm2niix';
if ~exist(dcm2niix,'file'), error('Unable to find %s',dcm2niix); end;
d = dir(fullfile(tgzDir,'*.tgz'));
if isempty(tgzDir), error('No tgz files in %s', tgzDir); end
nams ={d.name};
nams =sort(nams);
for i = numel(nams): -1 : 1 %173numel(nams)
nam = nams{i};
[~, n] = fileparts(nam);
fprintf('%d/%d >> %s\n', i, numel(nams), n);
nam2 = fullfile(tgzDir,nam);
outDir2 = fullfile(outDir,n);
if exist(outDir2,'dir'), continue; end;
mkdir(outDir2);
outDir3 = fullfile(outDir2,n);
mkdir(outDir3);
untar(nam2, outDir3);
%convert DICOM -> Json
cmd = sprintf('%s -9 -b y -ba n -z y -i y -f %%t_%%s_%%p %s', dcm2niix, outDir2);
fprintf('Running \n %s\n', cmd);
system(cmd,'-echo');
rmdir(outDir3, 's')
end