New versions of avwcreatehd and other minor mods

avwcpgeom.c

@@ -84,8 +84,9 @@ int main(argc,argv)
   /* {{{ copy geom */
 
 /* memcpy(hdr2.dime.vox_units,hdr.dime.vox_units,4); */
-  FslGetVoxUnits(src, thestring);
-  FslSetVoxUnits(dest, thestring);
+  /* Note that Get and Set VoxDim work exclusively in mm and sec now */ 
+  /* FslGetVoxUnits(src, thestring); */
+  /* FslSetVoxUnits(dest, thestring); */
 
 /* for(i=0;i<8;i++) */
 /* { */

avwcreatehd.c

@@ -13,7 +13,7 @@ void usage(void)
   printf("\nUsage: avwcreatehd <xsize> <ysize> <zsize> <tsize> <xvoxsize> <yvoxsize> <zvoxsize> <tr> <xorigin> <yorigin> <zorigin> <datatype> <headername> [-r]\n");
   printf("       avwcreatehd <nifti_xml_file> <headername> [-r]\n\n");
   printf("  In all forms, [-r] => reverse byte order (to match byte order in data)\n");
-  printf("  In the second form, an XML form of nifti header is read (as output by avwhd -n)\n");
+  printf("  In the second form, an XML-ish form of nifti header is read (as output by avwhd -x)\n");
   printf("  Note that stdin is used if '-' is used in place of a filename\n");
   exit(1);
 }
@@ -22,19 +22,37 @@ void usage(void)
 int main(int argc, char **argv) 
 {
   FSLIO* fslio;
-  char *buffer, *hdrxml;
+  void *buffer=NULL;
+  char *hdrxml, *filename;
   int fileread=1, filetype;
+  long bufsize=0;
+  short x,y,z,v, dt;
 
   if (argc<2)
     usage();
 
+  
   if ((argc==3) || (argc==4)) {
       /* use the XML form of header specification */
-      fslio = FslOpen(argv[2],"wb");
+      filename = argv[2];
   } else {
-      fslio = FslOpen(argv[13],"wb");
+      filename = argv[13];
+  }
+
+  /* check if file already exists and if so, read the image contents */
+  /* also store the size of this buffer for later in case it is wrong */ 
+  if (FslFileExists(filename)) {
+      /* buffer = FslReadAllVolumes(fslio,filename); */
+      fslio = FslOpen(filename,"rb");
+      FslGetDim(fslio,&x,&y,&z,&v);
+      bufsize = x * y * z * v * FslGetDataType(fslio,&dt) / 8;
+      buffer = (void *) calloc(bufsize,1);
+      FslReadVolumes(fslio,buffer,v);
+      FslClose(fslio);
   }
 
+  fslio = FslOpen(filename,"wb");
+
   filetype = FslGetFileType(fslio);
 
   if (FslBaseFileType(FslGetFileType(fslio))==FSL_TYPE_MINC) {
@@ -59,11 +77,13 @@ int main(int argc, char **argv)
       
   } else {
       /* read XML form */
-      char *newstr;
+      char *newstr, *oldfname, *oldiname;
       FILE *fileptr=NULL;
       if (strcmp(argv[1],"-")==0) {fileread=0;}
-      newstr = (char *)calloc(1,10000);
-      hdrxml = (char *)calloc(1,65534);  /* too long, to be safe */
+      newstr = (char *)calloc(10000,1);
+      oldfname = (char *)calloc(10000,1);
+      oldiname = (char *)calloc(10000,1);
+      hdrxml = (char *)calloc(65534,1);  /* too long, to be safe */
 
       if (fileread) {
 	  fileptr = fopen(argv[1],"rb");
@@ -83,11 +103,19 @@ int main(int argc, char **argv)
 	  strcat(hdrxml,newstr);
       }  while (strcmp(newstr + strlen(newstr) - 2,"/>")!=0);
 
+      strcpy(oldfname,fslio->niftiptr->fname);
+      strcpy(oldiname,fslio->niftiptr->iname);
+
       fslio->niftiptr = nifti_image_from_ascii(hdrxml);
+
       if (fslio->niftiptr == NULL) {
 	  fprintf(stderr,"Incomplete or incorrect text: could not form header info\n");
 	  exit(EXIT_FAILURE);
       }
+
+      fslio->niftiptr->fname = oldfname;
+      fslio->niftiptr->iname = oldiname;
+
       free(hdrxml);
       if (fileread) fclose(fileptr);
   }
@@ -108,9 +136,15 @@ int main(int argc, char **argv)
   /* write header */
   
   FslWriteHeader(fslio);
-  
-  /* make a zero image here */
-  buffer = (char *) calloc(fslio->niftiptr->nvox,fslio->niftiptr->nbyper);
+
+  /* if previously read buffer is wrong size then make a zero image here */
+  FslGetDim(fslio,&x,&y,&z,&v);
+  if ( bufsize != ( x * y * z * v * FslGetDataType(fslio,&dt)/8) ) {
+      if (bufsize>0) free(buffer);  /* only if previously read */
+      buffer = (void *) calloc(x * y * z * v,FslGetDataType(fslio,&dt)/8);
+  }
+
+  /* write the data out - either from previous read or zeros */
   FslWriteVolumes(fslio,buffer,fslio->niftiptr->dim[4]);
   
   FslClose(fslio);

avwsplit.c

@@ -39,7 +39,6 @@ int main(int argc, char **argv)
 
   FslGetDim(src,&x,&y,&z,&v);
   FslGetVoxDim(src,&vx,&vy,&vz,&tr);
-  FslGetVoxUnits(src, units);
 
   bufsz = x * y * z * (FslGetDataType(src, &t) / 8);
   buffer = (void *) calloc(bufsz, sizeof(char));