Preprocessing utilities

ConvertDicomToNiiVolume

This conversion utility will convert a dicom series image into a single NIfTI file. It can be run on a single dicom series or in batch mode.

The utility can be found here:

.
└─ ImageQuizzer/
      └─ PrePost_Processing/
          └─ ConvertDicomToNiiVolume.py

How to run

From a command terminal

This assumes you have Python (minimum version 3) installed on your PC.

Run cmd.exe

>>>cd path/to/ImageQuizzer/PrePost_Processing

        for single run - one dicom series
>>>py ConvertDicomToNiiVolume.py -i path/to/input/dicom/folder -o path/to/output/folder

        for multiple runs
>>>py ConvertDicomToNiiVolume.py -b path/to/batchfile.csv

From Slicer's Python Interactor

If you don't have Python installed on your PC, you can use the Python Interactor in Slicer. Following are the python commands to run the conversion.

Open Slicer
View > Python Interactor

>>>import sys
>>>os.chdir("path/to/ImageQuizzer/PrePost_Processing")

        for single run - one dicom series
>>>sys.argv=["ConvertDicomToNiiVolume.py","-i","path/to/input/dicom/folder","-o","path/to/output/folder"]
>>>exec(open("ConvertDicomToNiiVolume.py").read())

        for multiple runs
>>>sys.argv=["ConvertDicomToNiiVolume.py","-b","path/to/batchfile.csv"]
>>>exec(open("ConvertDicomToNiiVolume.py").read())

Batch file syntax

To run this conversion utility multiple times, create a comma separated values (csv) file with the syntax as follows:

parent database folder, input dicom folder 1, output nii volume folder 1
parent database folder, input dicom folder 2, output nii volume folder 2
# Comment line
parent database folder, input dicom folder 3, output nii volume folder 3
parent database folder, input dicom folder 4, output nii volume folder 4
...
    (continue for each dicom series to convert)

Lines beginning with '#' are comment lines and are ignored.

After a batch run, a log file is created in the same directory where the csv batch file is located. It has the same name as the batch file with 'Log' as the suffix.

Utility syntax help

>>>py ConvertDicomToNiiVolume.py -h

usage: ConvertDicomToNiiVolume.py [-h] [-i PATH] [-o PATH] [-b CsvFilePATH]

ConvertDicomToNiiVolume preprocessor

optional arguments:
  -h, --help            show this help message and exit
  -i PATH, --input-folder PATH
                        Folder of input DICOM files (can contain sub-folders)
  -o PATH, --output-folder PATH
                        Folder to save converted datasets
  -b CsvFilePATH, --batch-csv CSVFILEPATH
                        Full path to csv file for batch processing