From f71e3479f0961ab1ca786a4405296456c92f1939 Mon Sep 17 00:00:00 2001
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Date: Tue, 7 Dec 2021 10:50:11 -0500
Subject: [PATCH] mri_fill. #NF. Added new standalone option -pointset to fill
 in voxels around a pointset (eg, with ento)

---
 mri_fill/mri_fill.cpp      | 31 +++++++++++++++++++++++++++++++
 mri_fill/mri_fill.help.xml |  2 ++
 2 files changed, 33 insertions(+)

diff --git a/mri_fill/mri_fill.cpp b/mri_fill/mri_fill.cpp
index 61030cb2c1b..8c878a76980 100644
--- a/mri_fill/mri_fill.cpp
+++ b/mri_fill/mri_fill.cpp
@@ -47,6 +47,7 @@
 #include "talairachex.h"
 #include "connectcomp.h"
 #include "mrisegment.h"
+#include "ctrpoints.h"
 
 
 /*-------------------------------------------------------------------
@@ -3765,6 +3766,36 @@ get_option(int argc, char *argv[])
   else if (!stricmp(option, "no-auto-man"))  {
     DoAutoMan = 0;
   }
+  else if (!stricmp(option, "pointset")) {
+    /* Stand-alone option: takes one or more point sets and fills in
+       the all the voxels that intersect lines connecting any two
+       points within a given point set.  Fill value determined by the
+       sign of the xcentroid of a point set. The orginal use case for
+       this was to help correct the surface in entorhinal cortex where
+       there would often be a "bite" out of the surface. See docs for
+       MRIreadControlPoints().
+    */
+    if(argc < 4){
+      printf("-pointset invol outvol ps1 <ps2 ...>\n");
+      exit(1);
+    }
+    printf("Reading input %s\n",argv[2]);
+    MRI *invol = MRIread(argv[2]);
+    if(invol == NULL) exit(1);
+    char *outvolfile = argv[3];
+    int n;
+    for(n=0; n < argc-4; n++){
+      int count, useRealRAS;
+      printf("Reading control point file %s\n",argv[4+n]);
+      MPoint *mp = MRIreadControlPoints(argv[4+n], &count, &useRealRAS);
+      if(mp == NULL) exit(1);
+      MRIfillPoints(invol, 0, count, useRealRAS, mp);
+      free(mp);
+    }
+    printf("Writing output %s\n",outvolfile);
+    int err = MRIwrite(invol,outvolfile);
+    exit(err);
+  }
   else switch (toupper(*option))
     {
     case 'P':
diff --git a/mri_fill/mri_fill.help.xml b/mri_fill/mri_fill.help.xml
index fb8c76488a1..ad91ee8c3f6 100644
--- a/mri_fill/mri_fill.help.xml
+++ b/mri_fill/mri_fill.help.xml
@@ -66,6 +66,8 @@
       <explanation>Get edits based on the difference between auto and man and apply to the output. Edit col,row,slice,autoval,manval will be written to the edits.txt file</explanation>
       <argument>-no-auto-man </argument>
       <explanation>Turns off -auto-man</explanation>
+      <argument>-pointset invol outvol ps {ps2 ...} </argument>
+      <explanation>Stand-alone option: takes one or more pointsets and fills in the all the voxels that intersect lines connecting any two points within a given point set.</explanation>
       <argument>-ctab colortable  </argument>
       <explanation>Embed color table in the output </explanation>
     </optional-flagged>