mri_segstats.cpp. #NF. Added stand-alone --xfm2etiv

mri_segstats/mri_segstats.cpp

@@ -1701,6 +1701,20 @@ static int parse_commandline(int argc, char **argv)
     {
       InVolRegHeader = 1;
     }
+    else if(!strcmp(option, "--xfm2etiv"))
+    {
+      if(nargc < 2) argnerr(option,1);
+      double etiv_scale_factor = 1948.106, determinant = 0, atlas_icv;
+      atlas_icv = MRIestimateTIV(pargv[0],etiv_scale_factor,&determinant);
+      printf("%12.4lf\n",atlas_icv);
+      if(strcmp(pargv[1],"nofile")!=0){
+	FILE *fp = fopen(pargv[1],"w");
+	if(fp == NULL) exit(1);
+	fprintf(fp,"%12.4lf\n",atlas_icv);
+	fclose(fp);
+      }
+      exit(0);
+    }
     else if ( !strcmp(option, "--in-intensity-name") )
     {
       if (nargc < 1)

mri_segstats/mri_segstats.help.xml

@@ -150,6 +150,8 @@ white surface. This is more accurate than from the aseg. The aseg values for the
       <explanation>compute intracranial volume from subject/mri/transforms/talairach_with_skull.lta and exit</explanation>
       <argument>--talxfm fname</argument>
       <explanation>specify path to talairach.xfm file for etiv</explanation>
+      <argument>--xfm2etiv xfm outfile</argument>
+      <explanation>Stand-alone option to convert xfm to eTIV and write to outfile (unless nofile)</explanation>
       <argument>--euler</argument>
       <explanation>Write out number of defect holes in orig.nofix based on the euler number. This is the orig file prior to topology fixing. </explanation>
       <intro>Average waveform options</intro>