Merge branch 'main' of https://github.com/metrics-lab/SLCN_challenge …

…into main
fabibo3 · May 4, 2022 · 57d1831 · 57d1831
2 parents 57023e6 + b6473b2
commit 57d1831
Showing 1 changed file with 10 additions and 8 deletions.
diff --git a/conversion_image_type.py b/conversion_image_type.py
@@ -13,11 +13,11 @@
 
 
 #### 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')
+filename = '' ### Participant to modify
+image = nb.load(filename)
 
 #### Define number of channels in gifti ####
-channels=4
+channels=4 ### Each channel represents a structural cortical metric (myelin, curvature, cortical thickness and sulcal depth - in that order) 
 
 img_array=[]
 
@@ -28,19 +28,21 @@
     img_array.append(array)
 
 
-#### Swap axes so that img_array dim is 40962,4 #### 
-#img_array = np.swapaxes(img_array, 0,1)
+#### Swap axes so that img_array dim is 40962,4 - this will depend on how participants want to work with the image arrays #### 
+img_array = np.swapaxes(img_array, 0,1) 
 
 
 #### Create .mha image using sitk ####
 mha_img = sitk.GetImageFromArray(img_array)
 
+new_filename='' ### Participant to modify
+
 #### Write out .mha image ####
-sitk.WriteImage(mha_img,'/home/sd20/workspace/SLCN_algorithm/test/sub-CC01215XX111_ses-14633_L.mha')
+sitk.WriteImage(mha_img, new_filename)
 
 #### Read in .mha image again ####
-mha_img1 = sitk.ReadImage('/home/sd20/workspace/SLCN_algorithm/test/sub-CC01215XX111_ses-14633_L.mha')
+mha_img1 = sitk.ReadImage(new_filename)
 
 
 #### Get array from image using sitk ####
-img1_array = sitk.GetArrayFromImage(mha_img1)
+img1_array = sitk.GetArrayFromImage(mha_img1)