made changes to account for nii.gz image format

regscript

@@ -120,29 +120,37 @@ cp ~dtiuser/etc/dof3 .
 #Load FID files
 if [ -e ${nodiffid}.fid ]; then
     echo Loading nodif
-     load_varian $nodiffid $output_dir/nodif -auto -float -buo -egrv $option
+    load_varian $nodiffid $output_dir/nodif -auto -float -buo -egrv $option
 else
     echo $nodiffid.fid: FID not found
     exit;
 fi
 
-nvols_nodif=`avwval $output_dir/nodif dim4`;
-
-if [ $nvols_nodif -gt 1 ]; then
-    echo nodif has $nvols_nodif volumes - file name will be changed to data
+avwsplit nodif
+if [ -e vol0002.nii.gz ]; then
+    nvols_nodif=2
+    echo nodif has more than 1 volume - file name will be changed to data
     echo first volume will be saved as nodif
-    mv nodif.hdr dti1.hdr
-    mv nodif.img dti1.img
-    avwsplit dti1
-    mv vol0000.hdr nodif.hdr
-    mv vol0000.img nodif.img
-    rm vol* -f	
-    
+    if [ -e nodif.hdr ]; then
+	mv nodif.hdr dti1.hdr
+	mv nodif.img dti1.img
+	mv vol0000.nii.gz nodif.nii.gz
+	rm vol* -f	
+    else
+	mv nodif.nii.gz dti1.nii.gz
+	avwsplit dti1.nii.gz
+	mv vol0000.nii.gz nodif.nii.gz
+	rm nodif.hdr nodif.img -f
+	rm vol* -f
+    fi
+
     count=1
     image_numb=2
     scan_numb=2
     
 else
+    mv vol0000.nii.gz nodif.nii.gz
+    rm nodif.hdr nodif.img -f
     count=0
     image_numb=1
     scan_numb=2
@@ -151,7 +159,7 @@ fi
 while [ $count -lt $number_acqs ]; do  
     if [ -e ${dtifid}${scan_numb}.fid ]; then
        echo Loading dti${image_numb}
-      load_varian ${dtifid}${scan_numb}.fid ${output_dir}/dti${image_numb} -auto -float -buo -egrv $option 
+       load_varian ${dtifid}${scan_numb}.fid ${output_dir}/dti${image_numb} -auto -float -buo -egrv $option 
     else
        echo ${dtifid}${image_numb}.fid: file not found
        exit;    
@@ -207,7 +215,9 @@ case $correc
 			flirt  -in vol000$count -ref nodif -out rvol000$count -nosearch -omat matrices/mat
 			avscale matrices/mat vol000$count >matrices/tmp
 			head -4 matrices/tmp | tail -3 > matrices/MAT000${count}${tmp_acqs}
+			rm vol000${count}.nii.gz -f
 			count=`expr $count + 1`;
+			
 		    done
 		    while [ ${count} != ${nvols} ];do
 			    echo FLIRT on volume ${count}
@@ -216,7 +226,8 @@ case $correc
 			head -4 matrices/tmp | tail -3 > matrices/MAT00${count}${tmp_acqs}
 			rm -f matrices/mat
 			rm -f matrices/tmp
-			count=`expr $count + 1`; 
+			rm vol000${count}.nii.gz -f
+			count=`expr $count + 1`;
 		    done
          		fi
 	        #Clean up unecessary files
@@ -226,10 +237,10 @@ case $correc
 		if [ $number_acqs -eq 1 ]
 		then
 		    echo creating file: data
-		    avwmerge -t data rvol00*.hdr
+		    avwmerge -t data rvol00*
 		else
 		    echo creating file: data${tmp_acqs}
-		    avwmerge -t data${tmp_acqs} rvol00*.hdr
+		    avwmerge -t data${tmp_acqs} rvol00*
 		fi
 	    
 		#Clean up unecessary files
@@ -272,10 +283,10 @@ case $correc
 	    if [ $number_acqs -eq 1 ]
 	    then
 		echo creating file: data
-		avwmerge -t data rvol00*.hdr
+		avwmerge -t data rvol00*
 	    else
 		echo creating file: data${tmp_acqs}
-		avwmerge -t data${tmp_acqs} rvol00*.hdr
+		avwmerge -t data${tmp_acqs} rvol00*
 	    fi
 
 	    #Clean up unecessary files
@@ -290,14 +301,10 @@ esac
 #Brain Extraction
 echo BE
 bet nodif mask -f 0.025 -m
-
-rm mask.hdr -f
-rm mask.img -f
-mv mask_mask.hdr nodif_brain_mask.hdr
-mv mask_mask.img nodif_brain_mask.img
+mv mask_mask.nii.gz nodif_brain_mask.nii.gz
+rm mask.* -f
 rm dof3 -f 
 
-
 #Copy relevant bvals and bvecs file
 n_vols=`echo $nvols`;