adding conversion file image type .mha .nii

fabibo3 · Apr 25, 2022 · 8682c30 · 8682c30
1 parent 51110ea
commit 8682c30
Showing 1 changed file with 46 additions and 0 deletions.
diff --git a/conversion_image_type.py b/conversion_image_type.py
@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 20 22:14:40 2022
+
+@author: lw19
+"""
+
+
+import SimpleITK as sitk
+import numpy as np 
+import nibabel as nb
+
+
+#### Load gifti image using nibabel ####
+#image = nb.load('/data/Data/data_release_gDL_benchmarking/Data/Regression/Native_Space/regression_native_space_features/sub-CC00051XX02_ses-7702_L.shape.gii')
+image = nb.load('/home/sd20/data/dHCP/merged_metrics/ico6_template/original/CC01215XX11_146331_right_merged.shape.gii')
+
+#### Define number of channels in gifti ####
+channels=4
+
+img_array=[]
+
+
+#### Iterate over each channel, extract array and append to img_array object/list ####  
+for i in range(channels):
+    array = image.darrays[i].data
+    img_array.append(array)
+
+
+#### Swap axes so that img_array dim is 40962,4 #### 
+#img_array = np.swapaxes(img_array, 0,1)
+
+
+#### Create .mha image using sitk ####
+mha_img = sitk.GetImageFromArray(img_array)
+
+#### Write out .mha image ####
+sitk.WriteImage(mha_img,'/home/sd20/workspace/SLCN_algorithm/test/sub-CC01215XX111_ses-14633_L.mha')
+
+#### Read in .mha image again ####
+mha_img1 = sitk.ReadImage('/home/sd20/workspace/SLCN_algorithm/test/sub-CC01215XX111_ses-14633_L.mha')
+
+
+#### Get array from image using sitk ####
+img1_array = sitk.GetArrayFromImage(mha_img1)