def dicom2nifti(folders,outdir=None,extension=None):
'''dicom2nifti will take a list of folders and produce nifti files
in an output directory. If not defined, they will be output in their
original directory.
'''
if isinstance(folders,dict):
folders = list(folders.keys())
if not isinstance(folders,list):
folders = [folders]
outfiles = []
for folder in folders:
lookup = find_dicoms(folder,extension)
for base,dicomlist in lookup.items():
nii = read_series(dicomlist)
if outdir != None:
outfile = "%s/%s.nii.gz" %(outdir,os.path.basename(base))
else:
outfile = "%s/%s.nii.gz" %(base,os.path.basename(base))
bot.info("Saving %s" %outfile)
nibabel.save(nii,outfile)
outfiles.append(outfile)
return outfiles
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