<html><head><meta name="color-scheme" content="light dark"></head><body><pre style="word-wrap: break-word; white-space: pre-wrap;">'''
Copyright (c) 2015 Computational Biomechanics (CoBi) Core, Department of
Biomedical Engineering, Cleveland Clinic

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to permit
persons to whom the Software is furnished to do so, subject to the
following conditions:

The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
-------------------

dcm2nii.py

DESCRIPTION:

Python script to read a DICOM directory and split and save the individual series into separate NIFTI files.

REQUIREMENTS:

Python (http://www.python.org)
SimpleITK (http://www.simpleitk.org/)

DEVELOPERS:

Ahmet Erdemir
Computational Biomodeling (CoBi) Core
Department of Biomedical Engineering
Lerner Research Institute
Cleveland Clinic
Cleveland, OH
erdemira@ccf.org

Modified by:
Tyler Schimmoeller
schimmt@ccf.org
'''
import sys
import dicom  # TS
import SimpleITK as sitk
import os

subjectID = 'CMULTIS' + '011-1'
dir ='/Users/schimmt/Multis/app/FileAssociation/MULTIS_trials/'
modality = 'MRI' # MRI or CT
modality = 'CT' # MRI or CT
appendage = 'WA'
appendage = 'WL'


if modality == 'MRI':
    nii_dir = dir + subjectID + '/MRI' + '/nii_leg'
    dcm_dir = dir + subjectID + '/MRI' + '/dcm_leg'
    if not os.path.exists(nii_dir):
        os.makedirs(nii_dir)
    # if not os.path.exists(nii_dir + '/T1'):
    #     os.makedirs(nii_dir + '/T1')
    # if not os.path.exists(nii_dir + '/T1_FS'):
    #     os.makedirs(nii_dir + '/T1_FS')

    def dcm2nii(dcm_dir):
        # Set DICOM directory name
        # dcm_dir = argv
        i = 1  # TS
        if dcm_dir != '/':
            dcm_dir = dcm_dir + '/'

        folders = os.listdir(dcm_dir)
        print folders


        for groups in folders:
            if groups != '.DS_Store':
                reader = sitk.ImageSeriesReader()
                IDS = reader.GetGDCMSeriesIDs(dcm_dir+groups)



                for ID in IDS:

                    files = reader.GetGDCMSeriesFileNames(dcm_dir+groups, ID)
                    reader.SetFileNames(files)
                    dataset = dicom.read_file(files[0], stop_before_pixels=True) #TS
                    protocolName = dataset.ProtocolName #TS
                    images = reader.Execute()
                    if len(str(i)) &lt; 2:
                        ii = '0' + str(i)
                    else:
                        ii = str(i)
                    print ii
                    print protocolName
                    # sitk.WriteImage(images, nii_dir + protocolName[0:-1] + '_' + ii + '.nii')  # TS for ct
                    sitk.WriteImage(images, nii_dir + protocolName[0:-1] + '_' + ii + '_' + protocolName[-1:] + '.nii') #TS for mri
                    i += 1

if modality == 'CT':
    nii_dir = dir + subjectID + '/CT' + '/nii/'
    dcm_dir = dir + subjectID + '/CT/' + subjectID + '_' + appendage + '_CT/'
    print dcm_dir
    if not os.path.exists(nii_dir):
        os.makedirs(nii_dir)
    # if not os.path.exists(nii_dir + '/T1'):
    #     os.makedirs(nii_dir + '/T1')
    # if not os.path.exists(nii_dir + '/T1_FS'):
    #     os.makedirs(nii_dir + '/T1_FS')

    def dcm2nii(dcm_dir):
        # Set DICOM directory name
        # dcm_dir = argv
        i = 1  # TS
        # if dcm_dir != '/':
        #     dcm_dir = dcm_dir + '/'
        # folders = os.listdir(dcm_dir)
        # print folders


        # for groups in folders:
        # if groups != '.DS_Store':
        reader = sitk.ImageSeriesReader()
        IDS = reader.GetGDCMSeriesIDs(dcm_dir)



        for ID in IDS:

            files = reader.GetGDCMSeriesFileNames(dcm_dir, ID)
            reader.SetFileNames(files)
            dataset = dicom.read_file(files[0], stop_before_pixels=True) #TS
            protocolName = dataset.ProtocolName #TS
            images = reader.Execute()
            if len(str(i)) &lt; 2:
                ii = '0' + str(i)
            else:
                ii = str(i)
            print ii
            print protocolName
            sitk.WriteImage(images, nii_dir + subjectID + '_' + appendage + '_CT' + '.nii')  # TS for ct
            i += 1

if __name__ == "__main__":
    dcm2nii(dcm_dir)</pre></body></html>