#!/bin/bash
echo "" > index.html
echo "" >> index.html
for sub in $(ls ${SUBJECTS_DIR});
do
echo "" >> index.html
echo "![](\""$sub".lh.lat.lr.tif\") | " >> index.html
echo "![](\""$sub".lh.med.lr.tif\") | " >> index.html
echo "![](\""$sub".rh.lat.lr.tif\") | " >> index.html
echo "![](\""$sub".rh.med.lr.tif\") | " >> index.html
echo "
" >> index.html
echo "" >> index.html
echo ""$sub"
| " >> index.html
echo "
" >> index.html
echo "labl_import_annotation \"aparc.annot\"" > tmp.tcl
echo "scale_brain 1.35" >>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 "resize_window 300" >>tmp.tcl
echo "rotate_brain_y -180.0" >>tmp.tcl
echo "redraw" >>tmp.tcl
echo "save_tiff "$sub".lh.lat.lr.tif" >>tmp.tcl
echo "rotate_brain_y 180.0" >>tmp.tcl
echo "redraw" >>tmp.tcl
echo "save_tiff "$sub".lh.med.lr.tif" >>tmp.tcl
echo "exit 0" >>tmp.tcl
tksurfer $sub lh white -tcl tmp.tcl
echo "labl_import_annotation \"aparc.annot\"" > tmp.tcl
echo "scale_brain 1.35" >>tmp.tcl
echo "redraw" >>tmp.tcl
echo "save_tiff "$sub".rh.lat.hr.tif" >>tmp.tcl
echo "rotate_brain_y 180.0" >>tmp.tcl
echo "redraw" >>tmp.tcl
echo "save_tiff "$sub".rh.med.hr.tif" >>tmp.tcl
echo "rotate_brain_y -180.0" >>tmp.tcl
echo "resize_window 300" >>tmp.tcl
echo "redraw" >>tmp.tcl
echo "save_tiff "$sub".rh.lat.lr.tif" >>tmp.tcl
echo "rotate_brain_y 180.0" >>tmp.tcl
echo "redraw" >>tmp.tcl
echo "save_tiff "$sub".rh.med.lr.tif" >>tmp.tcl
echo "exit 0" >>tmp.tcl
tksurfer $sub rh white -tcl tmp.tcl
rm tmp.tcl
done;
echo "
" >> index.html
echo "" >> index.html