modified the script so it will be compatible with any type of images

replace_and_average_fmrib

@@ -52,8 +52,8 @@ current_dir=`pwd`
 
 acq=1
 while [ $acq -le $numb_acqs ];do
-  if [ ! -e ${input_file}${acq}.hdr ]; then
-      echo Cant find $input_file
+  if [ ! `imtest ${input_file}${acq}` ]; then
+      echo Cant find $input_file 
       exit
   fi
   acq=`expr $acq + 1`;
@@ -74,24 +74,21 @@ nvols=`avwval ${input_file}1 dim4`;
 acq=1
 while [ $acq -le $numb_acqs ]; do
   echo splitting $input_file$acq
-  avwsplit $input_file$acq.hdr
+  avwsplit $input_file$acq
   volume=0;
   if [ $nvols -lt 10 ]; then
      while [ $volume -lt $nvols ]; do
-        mv vol000$volume.hdr vol000${volume}_${acq}.hdr
-        mv vol000$volume.img vol000${volume}_${acq}.img
+        immmv vol000$volume vol000${volume}_${acq}
         volume=`expr $volume + 1`
      done
   else
      volume=0
      while [ $volume -lt 10 ]; do
-        mv vol000${volume}.hdr vol000${volume}_${acq}.hdr
-        mv vol000${volume}.img vol000${volume}_${acq}.img
+        immv vol000${volume} vol000${volume}_${acq}
         volume=`expr $volume + 1`
      done
      while [ $volume -lt $nvols ]; do
-        mv vol00${volume}.hdr vol000${volume}_${acq}.hdr
-        mv vol00${volume}.img vol000${volume}_${acq}.img
+        immv vol00${volume} vol000${volume}_${acq}
 	volume=`expr $volume + 1`
      done
   fi
@@ -103,23 +100,21 @@ num_dodgy_vols=`expr $#`
 while [ $vol -lt $num_dodgy_vols ]; do
   v=$1
   shift
-  if [ -e vol000${v}_1.hdr ]; then
-    rm vol000${v}_*.hdr -f
-    rm vol000${v}_*.img -f
-  fi
+  if [ `imtest vol000${v}_1` ]; then
+    rm vol000${v}_* -f
+  fi 
+  if [ `imtest vol00${v}_1` ]; then
+    rm vol00${v}_* -f
+  fi 
 
-  if [ -e vol00${v}_1.hdr ]; then
-    rm vol00${v}_*.hdr -f
-    rm vol00${v}_*.img -f
-  fi
   vol=`expr $vol + 1`
 done
 
 acq=1
 while [ $acq -le $numb_acqs ]; do
-   rm ${input_file}${acq}*
-   avwmerge -t data$acq vol*_$acq.hdr
-   acq=`expr $acq + 1`;
+   rm ${input_file}${acq}* -f
+   avwmerge -t data$acq `$FSLDIR/bin/imglob -oneperimage vol*_$acq`
+   acq=`expr $acq + 1`; 
 done
 
 matlab -nodisplay -nojvm -nosplash 1> matlab.out1 2>&1 <<EOF
@@ -179,36 +174,36 @@ if [ $# -gt 1 ]; then
 
   check_vols $n_vols $numb_acqs
   
-  if [ -e dodgy_vols ]; then
-       dodgy=`cat dodgy_vols`
-  rem_vols data $numb_acqs $dodgy
+ if [ -e dodgy_vols ]; then
+      dodgy=`cat dodgy_vols`
+      rem_vols data $numb_acqs $dodgy
   else
-   echo No volumes need to be removed
+      echo No volumes need to be removed
   fi
-
+  
   nvols=`avwval data1 dim4`;
-
+  
   echo output will have $nvols volumes
-
+  
   dodgy_volumes=`cat vol_list`
   dodgy_volumes=`echo $dodgy_volumes`
- 
+  
   if [ -e dodgy_vols ]; then
-     if [ "$dodgy_volumes" != "" ]; then 
-	 echo dogdy volumes updated taking into account removed volumes
-	 echo dodgy volumes are now: $dodgy_volumes
-     fi
+      if [ "$dodgy_volumes" != "" ]; then 
+	  echo dogdy volumes updated taking into account removed volumes
+	  echo dodgy volumes are now: $dodgy_volumes
+      fi
   fi
-
+  
   if [ "$dodgy_volumes" != "" ]; then  
       acq=1
       
       echo "">file_list  
       
       while [ $acq -le $numb_acqs ];do
-	  echo data$acq.hdr >> file_list
+	  echo data$acq >> file_list
 	  acq=`expr $acq + 1`;
-      done
+      done  
       
       file_list=`cat file_list`
       avwmerge -t bigdata $file_list
@@ -223,9 +218,9 @@ if [ $# -gt 1 ]; then
 	  echo "$first $second">>average_file;
 	  acq=`expr $acq + 1`;
       done
-       
+      
       echo "">>average_file
-    
+      
       acq=0 
       n_vols=`echo $nvols`
       
@@ -247,6 +242,10 @@ if [ $# -gt 1 ]; then
 	  done;  
       fi
       
+      if [ $FSLOUTPUTTYPE != 'ANALYZE' ]; then
+	  avwchfiletype ANALYZE bigdata
+	  rm bigdata.nii.gz -f
+      fi
       replacevols bigdata average_file $dodgy_volumes tmp_file
       
       if [ -e tmp_file.img.gz ]; then
@@ -256,6 +255,10 @@ if [ $# -gt 1 ]; then
 	  fi
       fi
 
+      if [ $FSLOUTPUTTYPE != 'ANALYZE' ]; then
+	  avwchfiletype $FSLOUTPUTTYPE tmp_file
+      fi
+
       nvols=`avwval tmp_file dim4`;
       n_vols=`echo $nvols` 
       volsacqs=`avwval data1 dim4`;
@@ -277,15 +280,16 @@ if [ $# -gt 1 ]; then
 	      fi
 	      vol=`expr $vol + 1`;
 	  done
-	  avwmerge -t data${acq}_all vol${acq}_*.hdr
+	 
+	  avwmerge -t data${acq}_all `$FSLDIR/bin/imglob -oneperimage vol${acq}_*`
 	  avwmaths data${acq}_all -div ${numb_acqs} data${acq}_all;
-	  add4d data data${acq}_all data;
+	  avwmaths data -add data${acq}_all data;
           rm data${acq}_all* vol${acq}* -f  
       	  acq=`expr $acq + 1`;
-      done
-      rm tmp*
+      done 
       rm *_all* -f
-      rm average_file -f
+       rm tmp* -f
+       rm average_file -f
   else
       echo averaging the data
       volsacqs=`avwval data1 dim4`;
@@ -295,7 +299,7 @@ if [ $# -gt 1 ]; then
       acq=1;
       while [ ${acq} -le ${numb_acqs} ]; do
 	  avwmaths data${acq} -div ${numb_acqs} data${acq};
-	  add4d data data${acq} data;
+	  avwmaths data -add data${acq} data;
 	  acq=`expr $acq + 1`;
       done
   fi
@@ -314,14 +318,12 @@ else
     acq=1;
     while [ ${acq} -le ${numb_acqs} ]; do
         avwmaths data${acq} -div ${numb_acqs} data${acq};
-	add4d data data${acq} data;
+	avwmaths data -add data${acq} data;
 	acq=`expr $acq + 1`;
     done
 fi
 
 echo extracting nodif image from averaged data
-avwsplit data
-mv vol0000.hdr nodif.hdr -f
-mv vol0000.img nodif.img -f
+avwroi data nodif 0 1
 rm tmp* -f
 rm vol* -f