fsqc-lgi.sh 1.76 KB
Newer Older
Bo-Chun Chen's avatar
Bo-Chun Chen committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
#!/bin/bash

echo "<html>" 												>  index.html
echo "<table>"												>> index.html
for sub in $(ls ${SUBJECTS_DIR});
do
	echo "sclv_read_from_volume 0 "$sub"/surf/lh.pial_lgi 1"	> tmp.tcl
	echo "redraw"									>>tmp.tcl
	echo "save_tiff "$sub".lh.lat.hr.tif"			>>tmp.tcl
	echo "rotate_brain_y 180.0"						>>tmp.tcl
	echo "redraw"									>>tmp.tcl
	echo "save_tiff "$sub".lh.med.hr.tif"			>>tmp.tcl
	echo "exit 0"									>>tmp.tcl
	tksurfer $sub lh inflated -tcl tmp.tcl

	echo "sclv_read_from_volume 0 "$sub"/surf/rh.pial_lgi 1"	> tmp.tcl
	echo "redraw"									>>tmp.tcl
	echo "save_tiff "$sub".rh.lat.hr.tif"			>>tmp.tcl
	echo "rotate_brain_y 180.0"						>>tmp.tcl
	echo "redraw"									>>tmp.tcl
	echo "save_tiff "$sub".rh.med.hr.tif"			>>tmp.tcl
	echo "exit 0"									>>tmp.tcl
	tksurfer $sub rh inflated -tcl tmp.tcl && {
		echo "<tr>"										>> index.html
		echo "<td><a href=\"file:"$sub".lh.lat.hr.png\"><img width=\"300\" src=\""$sub".lh.lat.hr.png\"></a></td>"	>> index.html
		echo "<td><a href=\"file:"$sub".lh.med.hr.png\"><img width=\"300\" src=\""$sub".lh.med.hr.png\"></a></td>"	>> index.html
		echo "<td><a href=\"file:"$sub".rh.lat.hr.png\"><img width=\"300\" src=\""$sub".rh.lat.hr.png\"></a></td>"	>> index.html
		echo "<td><a href=\"file:"$sub".rh.med.hr.png\"><img width=\"300\" src=\""$sub".rh.med.hr.png\"></a></td>"	>> index.html
		echo "</tr>"										>> index.html
		echo "<tr>"										>> index.html
		echo "<td colspan=4><center>"$sub"</center><br></td>"					>> index.html
		echo "</tr>"										>> index.html
	}

	rm tmp.tcl
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