<dicom>.zip
<dicom>.tgz
<parrec>.zip
<parrec>.tgz
image.PARimage.REC
max 1 nested level
image.parimage.rec
INPUT
OUTPUT
PROCESS
prepare
dcm2niix
pydeface
resolve
remove_incomplete_volumes
decompress_dicoms
comment -> “”
compress_images -> yes
compression_level -> 6
convert_only_series -> all
crop
filename -> %f
ignore_derived
ignore_errors
lossless_scaling -> no
merge2d
output_nrrd
philips_scaling
single_file_mode
text_notes_private
dcm2niix_verbose
a
a
pydeface
pydeface_cost -> mutualinfo
pydeface_nocleanup
pydeface_verbose
<template>.nifti
<facemask>.nifti
One Required
Optional
anonymize_bids
bids_sidecar -> no
<filename>.nii
a
coil_combine
<filename>.nii.gz
<filename>.json
<filename>.bval<filename>.bvec
<filename>.nhdr<filename>.raw.gz
<filename>.nrrd
Default:
if diffusion:
Modifications:
a
no
defaced version:<filename>.nii.gz
<f>_pydeface_mask.nii.gz<f>_pydeface.mat
yes
a
may impact anonymization, if altered
default config set to False
default config set to True
change config option
default gear configs