Update fsqc.sh

Convert tif files to png files

fsqc.sh

@@ -5,10 +5,10 @@ echo "<table>"																						>> index.html
 for sub in $(ls ${SUBJECTS_DIR});
 do
 	echo "<tr>"																						>> index.html
-	echo "<td><a href=\"file:"$sub".lh.lat.hr.tif\"><img src=\""$sub".lh.lat.lr.tif\"></a></td>"	>> index.html
-	echo "<td><a href=\"file:"$sub".lh.med.hr.tif\"><img src=\""$sub".lh.med.lr.tif\"></a></td>"	>> index.html
-	echo "<td><a href=\"file:"$sub".rh.lat.hr.tif\"><img src=\""$sub".rh.lat.lr.tif\"></a></td>"	>> index.html
-	echo "<td><a href=\"file:"$sub".rh.med.hr.tif\"><img src=\""$sub".rh.med.lr.tif\"></a></td>"	>> index.html
+	echo "<td><a href=\"file:"$sub".lh.lat.hr.png\"><img src=\""$sub".lh.lat.lr.png\"></a></td>"	>> index.html
+	echo "<td><a href=\"file:"$sub".lh.med.hr.png\"><img src=\""$sub".lh.med.lr.png\"></a></td>"	>> index.html
+	echo "<td><a href=\"file:"$sub".rh.lat.hr.png\"><img src=\""$sub".rh.lat.lr.png\"></a></td>"	>> index.html
+	echo "<td><a href=\"file:"$sub".rh.med.hr.png\"><img src=\""$sub".rh.med.lr.png\"></a></td>"	>> index.html
 	echo "</tr>"																					>> index.html
 	echo "<tr>"																						>> index.html
 	echo "<td colspan=4><center>"$sub"</center><br></td>"											>> index.html
@@ -53,3 +53,10 @@ do
 done;
 echo "</table>"										>> index.html
 echo "</html>"										>> index.html
+
+# Convert tif to PNG and remove TIFF files
+for f in *.tif; do
+    echo "Converting $f";
+    convert "$f"  "$(basename "$f" .tif).png";
+    rm $f
+done
\ No newline at end of file