Add files via upload

BET_CTimages.py

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+# -*- coding: utf-8 -*-
+"""
+Created on Tue Nov 30 06:01:05 2021
+
+@author: cbri3325
+"""
+import SimpleITK as sitk
+import os
+from ImageAnalysisFunctions import *
+
+data_supradir = 'Path to data directory' #Set working directory
+
+subjs_path = [ f.path for f in os.scandir(data_supradir) if f.is_dir() ] #Create a list of the paths to the subjects directories
+subjs_name = [ f.name for f in os.scandir(data_supradir) if f.is_dir() ] #Create a lisdt of subjects names
+
+n_subj = len(subjs_name) #Total number of subjects
+
+
+
+for current in subjs_name:
+    subj_dir = data_supradir+current
+    subj_name = current
+
+    # PETFET= sitk.ReadImage(subj_dir +'/'+ subj_name +'_PET_FET_inFETCT.nii')
+    # CTFET= sitk.ReadImage(subj_dir +'/'+ subj_name +'_CT_FET.nii')
+
+    # brain=sitk.BinaryThreshold(CTFET, 0.0, 100.0)
+    # brain2=sitk.BinaryFillhole(brain)
+    # brain2=sitk.BinaryMorphologicalOpening(brain2, (8,8,8), sitk.sitkBall, 0.0, 1.0)
+    # sitk.WriteImage(brain2, subj_dir+'/brain_mask.nii')
+
+      #Perform brain extraction on PET image
+    print('Perform brain extraction on PET image for '+subj_name)
+    PET_FET = sitk.ReadImage(subj_dir +'/'+ subj_name +'_PET_FET_inFETCT.nii', sitk.sitkFloat32) #read PET FET image
+    brain_mask = sitk.ReadImage(subj_dir +'/brain_mask.nii') #read brain mask
+
+    brain_mask_filled = sitk.BinaryMorphologicalClosing(brain_mask, (1,1,1), sitk.sitkBall, 1.0) #fill holes in brain mask
+    # sitk.WriteImage(brain_mask_filled, subj_dir +'/brain_mask_filled.nii') #save filled mask
+
+    brain_mask_cleaned = sitk.BinaryMorphologicalOpening(brain_mask_filled, (1,1,1), sitk.sitkBall, 0.0, 1.0) #remove small structures in brain mask filled
+    # sitk.WriteImage(brain_mask_cleaned, subj_dir +'/brain_mask_cleaned.nii') #save cleaned mask
+
+    # brain_mask_cleaned = sitk.ReadImage(subj_dir +'/brain_mask_cleaned.nii')
+
+    PET_FET_bet = generate_mask(PET_FET, brain_mask_cleaned)
+    sitk.WriteImage(PET_FET_bet, subj_dir +'/' + subj_name + '_PET_FET_bet.nii')

CopyImages.py

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+# -*- coding: utf-8 -*-
+"""
+Created on Mon Feb  6 13:21:43 2023
+
+@author: Caterina Brighi
+"""
+
+#%% Import functions 
+
+import os
+import shutil
+
+#%% Set Working directory
+
+data_supradir = 'Path to data directory' #Set working directory
+
+subjs_path = [ f.path for f in os.scandir(data_supradir) if f.is_dir() ] #Create a list of the paths to the subjects directories
+subjs_name = [ f.name for f in os.scandir(data_supradir) if f.is_dir() ] #Create a lisdt of subjects names
+subjs_name.remove('Analysis Results Plots')
+
+n_subj = len(subjs_name) #Total number of subjects
+
+dest_dir = 'C:/Users/cbri3325/OneDrive - The University of Sydney (Staff)/Caterina Brighi/Data/test/'
+
+#%%Create a for loop to perform image analysis on each subject sequentially
+
+for current in subjs_name:
+    subj_dir = data_supradir+current
+    subj_name = current
+
+    print('Copying images for '+current)
+
+    #Make new patient directory
+    if not os.path.exists(dest_dir+current):#if it does not already exist, create a directory of patient data
+        os.mkdir(dest_dir+current)
+    pt_dir = dest_dir+current
+
+    if not os.path.exists(pt_dir+'/Original/'):#if it does not already exist, create a directory of patient data
+        os.mkdir(pt_dir+'/Original/')
+    orig_dir = pt_dir+'/Original/'
+
+    if not os.path.exists(pt_dir+'/ROIs/'):#if it does not already exist, create a directory of patient data
+        os.mkdir(pt_dir+'/ROIs/')
+    roi_dir = pt_dir+'/ROIs/'
+
+    if not os.path.exists(pt_dir+'/Registered/'):#if it does not already exist, create a directory of patient data
+        os.mkdir(pt_dir+'/Registered/')
+    reg_dir = pt_dir+'/Registered/'
+
+    if not os.path.exists(pt_dir+'/Transforms/'):#if it does not already exist, create a directory of patient data
+        os.mkdir(pt_dir+'/Transforms/')
+    tfm_dir = pt_dir+'/Transforms/'
+
+    #Copy images into test folder
+    shutil.copy2(subj_dir+'/Original images/'+current+'_CT_FET.nii', orig_dir+'CT_FET.nii')
+    shutil.copy2(subj_dir+'/Original images/'+current+'_CT_TER.nii', orig_dir+'CT_PSMA.nii')
+    shutil.copy2(subj_dir+'/Original images/'+current+'_PET_FET.nii', orig_dir+'PET_FET.nii')
+    shutil.copy2(subj_dir+'/Original images/'+current+'_PET_TER.nii', orig_dir+'PET_PSMA.nii')
+
+    # shutil.copy2(subj_dir+'/Registered images/'+current+'_PET_FET_inFETCT.nii', img_dir+'PET_FET.nii')
+    # shutil.copy2(subj_dir+'/Registered images/'+current+'_CT_TER_inFETCT.nii', img_dir+'CT_PSMA.nii')
+    # shutil.copy2(subj_dir+'/Registered images/'+current+'_PET_TER_inFETCT.nii', img_dir+'PET_PSMA.nii')
+