From 7e37d272cec301eae0e54747d46168cd47448e37 Mon Sep 17 00:00:00 2001
From: Julien Cohen-Adad <jcohen@polymtl.ca>
Date: Tue, 16 Jan 2024 08:38:50 -0500
Subject: [PATCH] Clarified interpolation choices (#41)

Fixes #40
---
 data_processing.ipynb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/data_processing.ipynb b/data_processing.ipynb
index 33635f2..797bed0 100644
--- a/data_processing.ipynb
+++ b/data_processing.ipynb
@@ -313,7 +313,9 @@
     "for subject in subjects:\n",
     "    os.chdir(os.path.join(path_data, subject, \"fmap\"))\n",
     "    for shim_mode in shim_modes:\n",
+    "        # Use linear interpolation to preserve partial volume information (needed when extracting values along the cord)
     "        !sct_apply_transfo -i ../anat/{subject}_acq-CoV_T2starw_crop_seg.nii.gz -d {subject}_acq-anat{shim_mode}_TB1TFL.nii.gz -w warp_{subject}_acq-CoV_T2starw_crop2{subject}_acq-anat{shim_mode}_TB1TFL.nii.gz -x linear -o {subject}_acq-anat{shim_mode}_TB1TFL_seg.nii.gz\n",
+    "        # Use nearest neighbour (nn) interpolation because we are dealing with non-binary discrete labels
     "        !sct_apply_transfo -i ../anat/{subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -d {subject}_acq-anat{shim_mode}_TB1TFL.nii.gz -w warp_{subject}_acq-CoV_T2starw_crop2{subject}_acq-anat{shim_mode}_TB1TFL.nii.gz -x nn -o {subject}_acq-anat{shim_mode}_TB1TFL_seg_labeled.nii.gz"
    ]
   },