pydicom_split is a simple script than splits the DICOM into a specified number of volumes along the specified axis into equal sized volumes without resampling. The series and SOP instance UIDs are updated with an appended period and integer for the split number. The image position (patient) is updated as necessary. Each split volume is saved in the same parent directory as the parent volume, in a directory with an appended period and integer for the split number. The script currently works for DICOM directories only.
pydicom_split.py [-h] [-o] [-a AXIS]
[-d [DESCRIPTIONS [DESCRIPTIONS ...]]]
(-n N | -u [UIDS [UIDS ...]])
DICOM_DIRECTORY
positional arguments:
DICOM_DIRECTORY
optional arguments:
-h, --help show this help message and exit
-o, --origin origin position from offset from original volume,
default no
-a AXIS, --axis AXIS axis (0 for rows, 1 for columns), default columns
-d [DESCRIPTIONS [DESCRIPTIONS ...]], --descriptions [DESCRIPTIONS [DESCRIPTIONS ...]]
set the series descriptions
-u [UIDS [UIDS ...]], --uids [UIDS [UIDS ...]]
split into a volume for each forward slashseparated
SOP/series instance UID pair
-Outdir output, --output_dir
Output directory to save split result
For single column or single row dataset
-n N split into N volumes
-order order if there is an empty volumn in dataset,
specify volume(s) need to be split (1,1,1 means split
all three columns mice, 1,0,1 means middle volumn is empty)
For multiple column and double row dataset
-nTB N1,N2 split top row into N1 volumes, and bottom row into N2
volumes
-orderT orderT if there is an empty volumn in the top row of dataset,
specify volume(s) need to be split (1,1 means split
top row into two columns mice, 1,0 means skip the right mice of top row)
-orderB orderB if there is an empty volumn in the bottom row of dataset,
specify volume(s) need to be split (1,1 means split
bottom row into two columns mice, 1,0 means skip the right mice of bottom row)
-offset offset Offset from center, default 5 percent from center, only
apply to double row dataset
There are some testing examples under the test directory which can give you better understanding.
If you want split all three column volume.
python pydicom_split.py test/SingleRow/ -n 3 -order 1,1,1 -Outdir ./output
If you want remove right column empty volume.
python pydicom_split.py test/SingRowLastOneEmpty/ -n 3 -order 1,1,0 -Outdir ./output
If you want split two rows volume.
python pydicom_split.py test/TwoRows/ -nTB 1,2 -orderT 1 -orderB 1,1 -Outdir ./output
Hint: For two rows volume, make sure patient name contains special characters (Rp for bottom right)(L for bottom left)(T for top) to make a correct split. e.g. Patient_name: Session1_716(T)_719(Rp)_730(L)
NCI ABCS IVG provides girder based dicom split workflow interface for user to quick and easy visualize and utilize this script, contact IVG group for more informations. (Two rows volume split has not been implemented in web interface yet.)
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