From 3c56ddb364931a81e7f0876615a731ba2cc3b9a8 Mon Sep 17 00:00:00 2001
From: jcohenadad <jcohen@polymtl.ca>
Date: Fri, 22 Dec 2023 23:17:39 -0500
Subject: [PATCH] Extract B1+ values along the cord

---
 data_processing.ipynb | 68 ++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 61 insertions(+), 7 deletions(-)

diff --git a/data_processing.ipynb b/data_processing.ipynb
index 7123f0d..63eb48d 100644
--- a/data_processing.ipynb
+++ b/data_processing.ipynb
@@ -56,7 +56,7 @@
     "\n",
     "For each subject:\n",
     "\n",
-    "- Segment the SC on GRE scan\n",
+    "- Segment the spinal cord on GRE scan\n",
     "- Label vertebral levels on GRE scan using existing manual disc labels\n",
     "- Extract the signal intensity on the GRE scan within the spinal cord\n",
     "- Register each B1 map (CP, CoV, etc.) to the GRE scan\n",
@@ -147,7 +147,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ab6a7dbe",
+   "id": "95cafe0d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -157,7 +157,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4e1a6ae1",
+   "id": "6137bb2b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -173,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "90deb5e5",
+   "id": "862dc562",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,6 +186,33 @@
     "    !sct_crop_image -i {subject}_acq-CoV_T2starw_seg_labeled.nii.gz -m {subject}_acq-CoV_T2starw_seg.nii.gz -dilate 20x20x0 -o {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz    "
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c46e8d9a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Register the other shim methods to the GRE CoV scan\n",
+    "\n",
+    "# TODO"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "90deb5e5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Extract the signal intensity on the GRE scan within the spinal cord\n",
+    "\n",
+    "for subject in subjects:\n",
+    "    # TODO: loop across other shim methods    \n",
+    "    os.chdir(os.path.join(path_data, subject, \"anat\"))\n",
+    "    !sct_extract_metric -i {subject}_acq-CoV_T2starw_crop.nii.gz -f {subject}_acq-CoV_T2starw_crop_seg.nii.gz -method wa -vert 1:9 -vertfile {subject}_acq-CoV_T2starw_crop_seg_labeled.nii.gz -append 1 -perslice 1 -o gre_CoV.csv\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -203,7 +230,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "679f1193",
+   "id": "39de4623",
    "metadata": {},
    "source": [
     "## Verify QC report (B1maps to GRE registration)\n",
@@ -214,7 +241,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "623c26cd",
+   "id": "6a6d7670",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -230,12 +257,39 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ef34c2a1",
+   "id": "a835cdee",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Convert the B1 map to nT/V units\n",
+    "\n",
+    "# TODO"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "740fda91",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Extract B1+ value along the spinal cord\n",
     "\n",
+    "for subject in subjects:\n",
+    "    os.chdir(os.path.join(path_data, subject, \"fmap\"))\n",
+    "    for shim_mode in shim_modes:\n",
+    "        !sct_extract_metric -i {subject}_acq-famp{shim_mode}_TB1TFL.nii.gz -f {subject}_acq-anat{shim_mode}_TB1TFL_seg.nii.gz -method wa -vert 1:9 -vertfile {subject}_acq-anat{shim_mode}_TB1TFL_seg_labeled.nii.gz -append 1 -perslice 1 -o TB1TFL_{shim_mode}.csv"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b0185bb0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Make figure of B1+ values along the spinal cord across shim methods\n",
+    "\n",
     "# TODO"
    ]
   }