mri_surf2volseg. #NF. Added WM in the input segmentation with surface…

… annotation</explanation>
ayendiki · Feb 6, 2022 · 9236c86 · 9236c86
1 parent 11696c6
commit 9236c86
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Showing 2 changed files with 14 additions and 4 deletions.
diff --git a/mri_aparc2aseg/mri_surf2volseg.cpp b/mri_aparc2aseg/mri_surf2volseg.cpp
@@ -54,6 +54,7 @@ class Surf2VolSeg {
   std::string lhcortexlabelpath, rhcortexlabelpath;
   std::string lhannotname="lh.aparc.annot", lhannotpath, rhannotname="rh.aparc.annot", rhannotpath;
   int lhbaseoffset = 1000, rhbaseoffset = 2000;
+  int lhwmunlabeled = 5001,rhwmunlabeled = 5002;
   int nHopsMax = 5;
   int RipUnknown = 0;
   int LabelHypoAsWM = 0;
@@ -227,6 +228,13 @@ static int parse_commandline(int argc, char **argv)
       s2vseg.RipUnknown = 1;
       s2vseg.LabelHypoAsWM = 1;
     }
+    else if (!strcmp(option, "--label-wm-unknown")){
+      // Set values for the unknown label in labeling WM, default is 5001 and 5002
+      if(nargc < 2) CMDargNErr(option,2);
+      sscanf(pargv[0],"%d",&s2vseg.lhwmunlabeled);
+      sscanf(pargv[1],"%d",&s2vseg.rhwmunlabeled);
+      nargsused = 2;
+    }
     else if (!strcmp(option, "--lh-white")){
       if (nargc < 1) CMDargNErr(option,1);
       s2vseg.lhwhitepath = pargv[0];
@@ -478,11 +486,11 @@ int Surf2VolSeg::RelabelSegVox(int c, int r, int s, int *ndotcheck, int *hemi, i
     if(*dmin > wmparc_dist_thresh) newsegid = 0;
     if(*hemi == 1) {
       if(newsegid > 0) newsegid += lhbaseoffset;
-      else             newsegid = 5001;
+      else             newsegid = lhwmunlabeled;
     }
     if(*hemi == 2){
       if(newsegid > 0) newsegid += rhbaseoffset;
-      else             newsegid = 5002;
+      else             newsegid = rhwmunlabeled;
     }
   }
   if(debug) printf("RelabelSegVox(): %d %d %d   %d %d   %d %d %d %g\n",c,r,s,volsegid,newsegid,*ndotcheck,*hemi,*surftype,*dmin);

diff --git a/mri_aparc2aseg/mri_surf2volseg.help.xml b/mri_aparc2aseg/mri_surf2volseg.help.xml
@@ -23,8 +23,8 @@
 ]>
 
 <help>
-  <name>mri_surf2segvol</name>
-  <synopsis>mri_surf2segvol [options]</synopsis>
+  <name>mri_surf2volseg</name>
+  <synopsis>mri_surf2volseg [options]</synopsis>
 	<description> Performs three functions: (1) cleans up presurf aseg cortex and WM. (2) maps cortical labels from an annotation into a volume, and (3) labels cerebral WM with closest cortical label.  This is a replacement for mri_aparc2aseg.
 </description>
 
@@ -62,6 +62,8 @@
       <explanation>Relabel cortex in the input segmentation with surface annotation</explanation>
       <argument>--label-wm</argument>
       <explanation>Relabel cerebral WM in the input segmentation with surface annotation</explanation>
+      <argument>--label-wm-unknown lhval rhval</argument>
+      <explanation>Relabel unknown WM as lhval and rhval (default is 5001 and 5002)</explanation>
 
       <argument>--lh-annot lhannotation lhbaseoffset</argument>
       <explanation>lh annotation for --label-cortex and --label-wm</explanation>