Cleanup analysis overview

Analysis.ipynb

@@ -30,21 +30,16 @@
     "~~~\n",
     "\n",
     "\n",
-    "## Analysis\n",
+    "## Overview of processing pipeline\n",
     "\n",
     "For each subject:\n",
-    "-->For each RF shim directory\n",
     "\n",
-    "---->Analyze GRE scans by:\n",
-    "----->Segment the SC from the GRE scan\n",
-    "----->Extract the signal intensity within this mask from the GRE scans\n",
-    "\n",
-    "---->Analyze B1+ maps by:\n",
-    "----->Coregistering the anatomical image of the TFL_B1map scan to the corresponding GRE scan (noshim to noshim, CVred to CVred, etc)\n",
-    "----->Warp the previously created mask to the TFL_B1map space\n",
-    "----->Convert the B1+ maps to nT/V units\n",
-    "----->Extract the B1+ value within the coregistered mask\n",
-    "\n"
+    "- Segment the SC from the GRE scan\n",
+    "- Extract the signal intensity within this mask from the GRE scans\n",
+    "- Coregister the TFL_B1map to the corresponding GRE scan from each subfolder (CVred, Noshim, etc.)\n",
+    "- Apply the computed warping field to bring the SC segmentation to the TFL_B1map\n",
+    "- Convert the B1+ maps to nT/V units\n",
+    "- Extract the B1+ value within the registered mask"
    ]
   },
   {