From 511c168f8bc9f5350f4d0f97bba275dbb8b59778 Mon Sep 17 00:00:00 2001
From: Pierre-Louis Benveniste <pierrelouis.benveniste03@gmail.com>
Date: Wed, 2 Aug 2023 09:47:59 -0400
Subject: [PATCH] trying to register M0 to M12

---
 .../time_point_lesion_evolution.py            | 29 ++++++++++++-------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/lesion_analysis/time_point_lesion_evolution.py b/lesion_analysis/time_point_lesion_evolution.py
index c83c049..216cc64 100644
--- a/lesion_analysis/time_point_lesion_evolution.py
+++ b/lesion_analysis/time_point_lesion_evolution.py
@@ -7,8 +7,8 @@
 Args:
     -i-1, --input-first_image: path to the first image 
     -i-2, --input-second_image: path to the second image
-    -seg-1, --segmentation-first_image: path to the segmentation of the first image
-    -seg-2, --segmentation-second_image: path to the segmentation of the second image
+    -seg-1, --segmentation-first_image: path to the lesion segmentation of the first image
+    -seg-2, --segmentation-second_image: path to the lesion segmentation of the second image
     -o, --output_folder: path to the output folder
     --plot: whether to plot the results or not
 
@@ -17,6 +17,7 @@
 
 Example:
     python time_point_lesion_evolution.py -i-1 path/to/first/image -i-2 path/to/second/image -seg-1 path/to/first/segmentation -seg-2 path/to/second/segmentation -o path/to/output/folder
+    python3 lesion_analysis/time_point_lesion_evolution.py -i-1 /Users/plbenveniste/Desktop/lesion_comparison_copy/sub-cal072_ses-M0_STIR.nii.gz -i-2 /Users/plbenveniste/Desktop/lesion_comparison_copy/sub-cal072_ses-M12_STIR.nii.gz -seg-1 /Users/plbenveniste/Desktop/lesion_comparison_copy/M0_inference_results.nii.gz -seg-2 /Users/plbenveniste/Desktop/lesion_comparison_copy/M12_inference_results.nii.gz -o /Users/plbenveniste/Desktop/lesion_comparison_copy/output
 
 To do:
     *
@@ -49,13 +50,13 @@ def get_parser():
     parser.add_argument('-i-2', '--input-second_image', required=True,
                         help='Path to the second image')
     parser.add_argument('-seg-1', '--segmentation-first_image', required=True,
-                        help='Path to the segmentation of the first image')
+                        help='Path to the lesion segmentation of the first image')
     parser.add_argument('-seg-2', '--segmentation-second_image', required=True,
-                        help='Path to the segmentation of the second image')
+                        help='Path to the lesion segmentation of the second image')
     parser.add_argument('-o', '--output_folder', required=True,
                         help='Path to the output folder')
-    parser.add_argument('--plot', action='store_true',
-                        help='Whether to plot the results or not')
+    parser.add_argument('--show', action='store_true',
+                        help='Whether to show the results or not')
     return parser
 
 def main():
@@ -75,12 +76,18 @@ def main():
     #get the images and the segmentations
     first_image = nib.load(args.input_first_image)
     second_image = nib.load(args.input_second_image)
-    first_segmentation = nib.load(args.segmentation_first_image)
-    second_segmentation = nib.load(args.segmentation_second_image)
+    first_lesion_segmentation = nib.load(args.segmentation_first_image)
+    second_lesion_segmentation = nib.load(args.segmentation_second_image)
 
-    #first we perform a registration of the images and the segmentations
-    #we use the first image and the first segmentation as the reference
-    
+    #first we segment the spinal cord on the two images using sct_deepseg_sc
+    os.system('sct_deepseg_sc -i ' + args.input_first_image + ' -c t2 -o ' + args.output_folder + '/first_image_sc_segmentation.nii.gz')
+    os.system('sct_deepseg_sc -i ' + args.input_second_image + ' -c t2 -o' + args.output_folder + '/second_image_sc_segmentation.nii.gz')
+
+    #then we register the images and the segmentations with the first image as reference using sct_register_multimodal
+    os.system('sct_register_multimodal -i ' + args.input_second_image + ' -d ' + args.input_first_image + ' -iseg ' + args.output_folder + '/second_image_sc_segmentation.nii.gz' + ' -dseg ' + args.output_folder + '/first_image_sc_segmentation.nii.gz' + ' -o ' + args.output_folder + '/second_image_registered.nii.gz' + ' -owarp ' + args.output_folder +'/warping_M0_to_M12.nii.gz')
+
+    #then we apply the warping field to the segmentation of the lesions on the second images using sct_apply_transfo
+    os.system('sct_apply_transfo -i ' + args.segmentation_second_image + ' -d ' + args.segmentation_first_image + ' -w ' + args.output_folder + '/warping_M0_to_M12.nii.gz' + ' -o ' + args.output_folder + '/second_image_lesion_segmentation_registered.nii.gz' + ' -x linear')
 
     return None