diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_1.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_1.bdo
new file mode 100644
index 0000000..d5648c9
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_1.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="6,755200" y="45,745100" z="-55,388100" />
+    <WorldTransformMatrix>
+        <Row col1="4,000000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="4,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="4,000000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_2.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_2.bdo
new file mode 100644
index 0000000..c4c3900
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_2.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-8,900000" y="42,813900" z="-55,374200" />
+    <WorldTransformMatrix>
+        <Row col1="4,050000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="4,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="4,000000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_3.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_3.bdo
new file mode 100644
index 0000000..5d4a41c
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_3.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-8,432100" y="9,987672" z="-15,439300" />
+    <WorldTransformMatrix>
+        <Row col1="5,000000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="5,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="5,000000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_4.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_4.bdo
new file mode 100644
index 0000000..0120a3c
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Controlat_4.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-8,432100" y="1,987700" z="-6,460000" />
+    <WorldTransformMatrix>
+        <Row col1="3,000000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="3,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="3,000000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_CS_1.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_CS_1.bdo
new file mode 100644
index 0000000..efdc7ef
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_CS_1.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="1,366900" y="35,324708" z="-9,217520" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_CS_2.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_CS_2.bdo
new file mode 100644
index 0000000..c27979e
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_CS_2.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="7,033100" y="17,980100" z="-9,835100" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_CS_3.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_CS_3.bdo
new file mode 100644
index 0000000..69d1b98
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_CS_3.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="13,587600" y="34,577400" z="-28,329727" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_1.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_1.bdo
new file mode 100644
index 0000000..fabfd30
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_1.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-1,000000" y="34,000000" z="-16,000000" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_2.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_2.bdo
new file mode 100644
index 0000000..67f00ef
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_2.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="11,764700" y="26,869900" z="-27,582100" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_3.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_3.bdo
new file mode 100644
index 0000000..5a261b7
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_3.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="1,674000" y="31,671100" z="-9,190500" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_4.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_4.bdo
new file mode 100644
index 0000000..53cbc7c
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_4.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="11,351700" y="30,520000" z="-26,106500" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="3,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_5.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_5.bdo
new file mode 100644
index 0000000..e9be78c
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_5.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="6,086400" y="17,050400" z="-8,364900" />
+    <WorldTransformMatrix>
+        <Row col1="5,000000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="5,000000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_6.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_6.bdo
new file mode 100644
index 0000000..4482d68
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_6.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="5,106300" y="20,922400" z="-13,704200" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_7.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_7.bdo
new file mode 100644
index 0000000..02faeed
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_7.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="8,729500" y="19,607300" z="-10,063961" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_8.bdo b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_8.bdo
new file mode 100644
index 0000000..61ea6d0
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/DTTT_Ipsilat_dPSN_8.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="0,700000" y="24,537400" z="-5,318400" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="4,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="6,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/VTTT_Controlat_OSandIS_1.bdo b/ROIs_clean/MNI/from_left/new_ROIs/VTTT_Controlat_OSandIS_1.bdo
new file mode 100644
index 0000000..bbc7149
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/VTTT_Controlat_OSandIS_1.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Cuboid">
+    <origin x="7,723900" y="38,507800" z="-33,217500" />
+    <WorldTransformMatrix>
+        <Row col1="4,000000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="4,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="9,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_left/new_ROIs/VTTT_Controlat_OSandIS_2.bdo b/ROIs_clean/MNI/from_left/new_ROIs/VTTT_Controlat_OSandIS_2.bdo
new file mode 100644
index 0000000..6becd1f
--- /dev/null
+++ b/ROIs_clean/MNI/from_left/new_ROIs/VTTT_Controlat_OSandIS_2.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-2,000000" y="8,000000" z="-9,000000" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_1.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_1.bdo
new file mode 100644
index 0000000..abeb8bd
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_1.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="9,294814" y="43,190900" z="-48,360720" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_2.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_2.bdo
new file mode 100644
index 0000000..cdca61c
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_2.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-4,978000" y="43,279700" z="-54,178165" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="3,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_3.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_3.bdo
new file mode 100644
index 0000000..827c260
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_3.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-3,592371" y="12,859644" z="-10,096700" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_4.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_4.bdo
new file mode 100644
index 0000000..480308d
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Controlat_4.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="3,735000" y="1,895000" z="-7,003992" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_CS_1.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_CS_1.bdo
new file mode 100644
index 0000000..54eb273
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_CS_1.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-3,000000" y="20,000000" z="-4,000000" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_CS_2.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_CS_2.bdo
new file mode 100644
index 0000000..4d63d3a
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_CS_2.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-5,000000" y="21,000000" z="3,000000" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_CS_3.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_CS_3.bdo
new file mode 100644
index 0000000..36fa8a6
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_CS_3.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-14,262900" y="23,628600" z="-7,692605" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_1.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_1.bdo
new file mode 100644
index 0000000..4c4b7a4
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_1.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-10,118100" y="40,983700" z="-43,641300" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_2.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_2.bdo
new file mode 100644
index 0000000..d4f1c5d
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_2.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-0,417463" y="24,012207" z="-4,224579" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="11,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_3.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_3.bdo
new file mode 100644
index 0000000..c68c84d
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_3.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-0,671400" y="29,673646" z="-12,706862" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="13,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_4.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_4.bdo
new file mode 100644
index 0000000..54dca32
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_4.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Cuboid">
+    <origin x="-1,251300" y="37,916500" z="-28,879000" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_5.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_5.bdo
new file mode 100644
index 0000000..ce041af
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_5.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-3,501100" y="24,419600" z="-20,915821" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_6.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_6.bdo
new file mode 100644
index 0000000..01fad24
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_6.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-8,876900" y="17,284095" z="-9,040400" />
+    <WorldTransformMatrix>
+        <Row col1="7,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="3,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_7.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_7.bdo
new file mode 100644
index 0000000..636001a
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_7.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-8,972300" y="29,465000" z="-25,534500" />
+    <WorldTransformMatrix>
+        <Row col1="7,000000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_8.bdo b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_8.bdo
new file mode 100644
index 0000000..d69d97d
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/DTTT_Ipsilat_dPSN_8.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-11,873300" y="13,497900" z="3,332400" />
+    <WorldTransformMatrix>
+        <Row col1="5,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="6,000000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/VTTT_Controlat_OSandIS_1.bdo b/ROIs_clean/MNI/from_right/new_ROIs/VTTT_Controlat_OSandIS_1.bdo
new file mode 100644
index 0000000..bbc7149
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/VTTT_Controlat_OSandIS_1.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Cuboid">
+    <origin x="7,723900" y="38,507800" z="-33,217500" />
+    <WorldTransformMatrix>
+        <Row col1="4,000000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="4,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="9,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/ROIs_clean/MNI/from_right/new_ROIs/VTTT_Controlat_OSandIS_2.bdo b/ROIs_clean/MNI/from_right/new_ROIs/VTTT_Controlat_OSandIS_2.bdo
new file mode 100644
index 0000000..6becd1f
--- /dev/null
+++ b/ROIs_clean/MNI/from_right/new_ROIs/VTTT_Controlat_OSandIS_2.bdo
@@ -0,0 +1,9 @@
+<?xml version="1.0" ?>
+<mitkBoundingObject type="Ellipsoid">
+    <origin x="-2,000000" y="8,000000" z="-9,000000" />
+    <WorldTransformMatrix>
+        <Row col1="2,500000" col2="0,000000" col3="0,000000" />
+        <Row col1="0,000000" col2="2,500000" col3="0,000000" />
+        <Row col1="0,000000" col2="0,000000" col3="2,500000" />
+    </WorldTransformMatrix>
+</mitkBoundingObject>
diff --git a/trigeminal_second_order.sh b/trigeminal_second_order.sh
index 6b241da..49fe685 100755
--- a/trigeminal_second_order.sh
+++ b/trigeminal_second_order.sh
@@ -27,6 +27,7 @@ while getopts "s:m:o:g:" args; do
         *) usage;;
     esac
 done
+
 shift $((OPTIND-1))
 
 if [ -z "${s}" ] || [ -z "${m}" ] || [ -z "${o}" ]; then
@@ -88,6 +89,7 @@ do
     orig_rois_dir=${out_dir}/${nsub}/orig_space/rois
     mni_rois_dir=${out_dir}/${nsub}/mni_space/rois
     orig_tracking_dir=${out_dir}/${nsub}/orig_space/tracking_second_order
+
     mni_tracking_dir_first_order=${out_dir}/${nsub}/mni_space/tracking_first_order
     mni_tracking_dir_second_order=${out_dir}/${nsub}/mni_space/tracking_second_order
 
@@ -127,6 +129,8 @@ do
     scil_labels_combine ${orig_rois_dir}/${nsub}_left_thalamus_orig.nii.gz \
         --volume_ids ${orig_rois_dir}/${nsub}_aparc.DKTatlas+aseg_orig.nii.gz ${Left_Thalamus[*]} --merge_groups -f
 
+
+
     scil_labels_combine ${mni_rois_dir}/${nsub}_left_thalamus_mni.nii.gz \
         --volume_ids ${mni_rois_dir}/${nsub}_aparc.DKTatlas+aseg_mni.nii.gz ${Left_Thalamus[*]} --merge_groups -f
 
@@ -140,7 +144,7 @@ do
             ${orig_rois_dir}/${nsub}_${nside}_spinal_density_second_order_seed_orig.nii.gz \
             ${orig_rois_dir}/${nsub}_wm_mask_${fa_threshold}_orig.nii.gz \
             ${orig_tracking_dir}/orig/${nsub}_${nside}_from_spinal_track_npv1000.trk \
-            --npv ${npv_from_spinal_track_long} \
+            --npv ${npv_from_spinal_track_long} \ 
             -v -f ${gpu}
 
         # Tracking from Spinal bundle - npv 100
@@ -161,6 +165,7 @@ do
             ${orig_rois_dir}/${nsub}_wm_mask_${fa_threshold}_orig.nii.gz\
             ${orig_tracking_dir}/orig/${nsub}_${nside}_from_thalamus_npv500.trk \
             --npv ${npv_from_thalamus_track} \
+
             -v -f ${gpu}
     done
 
@@ -249,7 +254,7 @@ do
             ${out_dir}/mni_space/tracking_first_order/final/all_${nside}_remaining_cp_density_mni.nii.gz \
             ${mni_rois_dir}/${nsub}_${nside}_second_order_VTTT_Controlat_vPSN_Cuts_mni.nii.gz \
             --data_type uint8 -f
-        scil_labels_from_mask ${mni_rois_dir}/${nsub}_${nside}_second_order_VTTT_Controlat_vPSN_Cuts_mni.nii.gz \
+        scil_labels_from_mask ${mni_rois_dir}/${nsub}_${nside}_second_order_VTTT_Controlat_vPSN_Cuts_mni.nii.gz \ 
             ${mni_rois_dir}/${nsub}_${nside}_second_order_VTTT_Controlat_vPSN_Cuts_labels_mni.nii.gz \
             -f
     done
@@ -279,7 +284,12 @@ do
             --drawn_roi ${mni_dir}/MNI/from_${nside}/VTTT_Controlat_EXC_CaudalMedulla_Controlat.nii.gz 'any' 'exclude' \
             --drawn_roi ${mni_dir}/MNI/from_${nside}/VTTT_Controlat_INC_VTT_Area.nii.gz 'any' 'include' \
             --drawn_roi ${mni_dir}/MNI/from_${nside}/VTTT_Controlat_EXC_Pons_Ipsilat.nii.gz 'any' 'exclude' \
-            --drawn_roi ${mni_dir}/MNI/cs_plaque.nii.gz 'any' 'exclude' -f
+            --drawn_roi ${mni_dir}/MNI/cs_plaque.nii.gz 'any' 'exclude'\
+            --drawn_roi ${mni_dir}/MNI/from_${nside}/VTTT_Controlat_INC_VTT_Area.nii.gz 'any' 'include'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/VTTT_Controlat_OSandIS_1.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/VTTT_Controlat_OSandIS_2.bdo 'any' 'exclude'\
+			-f
+
 
         ## vPSN
         ## VPM
@@ -293,12 +303,13 @@ do
             --drawn_roi ${mni_dir}/MNI/from_${nside}/VTTT_Controlat_EXC_Ventral_Brainstem.nii.gz 'any' 'exclude' \
             --drawn_roi ${mni_dir}/MNI/from_${nside}/VTTT_Controlat_EXC_CaudalMedulla_Controlat.nii.gz 'any' 'exclude' \
             --drawn_roi ${mni_dir}/MNI/from_${nside}/VTTT_Controlat_INC_VTT_Area.nii.gz 'any' 'include'\
-			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_1.bdo 'any' 'exclude'\ 
-			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_2.bdo 'any' 'exclude'\ 
-			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_3.bdo 'any' 'exclude'\ 
+			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_1.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_2.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_3.bdo 'any' 'exclude'\
 			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_4.bdo 'any' 'exclude'\
 			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_5.bdo 'any' 'exclude'\
-			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_6.bdo 'any' 'exclude' -f
+			--bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_6.bdo 'any' 'exclude'\
+			-f
 
 
 
@@ -311,7 +322,12 @@ do
             --drawn_roi ${mni_dir}/MNI/from_${contra_nside}/VTTT_Controlat_EXC_Ventral_Brainstem.nii.gz 'any' 'exclude' \
             --drawn_roi ${mni_dir}/MNI/from_${contra_nside}/DTTT_Controlat_INC_CaudalMedulla_Ipsilat.nii.gz 'any' 'include' \
             --drawn_roi ${mni_dir}/MNI/from_${contra_nside}/DTTT_Controlat_INC_Medulla_Controlat.nii.gz 'any' 'include' \
-            --drawn_roi ${mni_dir}/MNI/from_${contra_nside}/DTTT_Controlat_EXC_Midbrain_Ipsilat.nii.gz 'any' 'exclude' -f
+            --drawn_roi ${mni_dir}/MNI/from_${contra_nside}/DTTT_Controlat_EXC_Midbrain_Ipsilat.nii.gz 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Controlat_1.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Controlat_2.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Controlat_3.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Controlat_4.bdo 'any' 'exclude'\
+			-f
 
         echo "|------------- 3.3) ${nside} - DTTT (ipsilateral) - dPSN and CS -------------|"
         ## CS
@@ -322,15 +338,30 @@ do
             --drawn_roi ${mni_rois_dir}/${nsub}_${nside}_spinal_density_second_order_seed_mni.nii.gz 'either_end' 'include' \
             --drawn_roi ${mni_rois_dir}/${nsub}_${nside}_VPM_mni.nii.gz 'any' 'include' \
             --drawn_roi ${mni_dir}/MNI/from_${nside}/VTTT_Controlat_EXC_Ventral_Brainstem.nii.gz 'any' 'exclude' \
-            --drawn_roi ${mni_dir}/MNI/midsagittal_plane.nii.gz 'any' 'exclude' -f
-
+			--drawn_roi ${mni_dir}/MNI/midsagittal_plane.nii.gz 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_CS_1.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_CS_2.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_CS_3.bdo 'any' 'exclude'\
+			-f
+			
         ## dPSN
         ## VPM/Thalamus
         scil_tractogram_filter_by_roi \
             ${mni_tracking_dir_second_order}/orig/${nsub}_${nside}_from_spinal_track_npv1000.trk \
             ${mni_tracking_dir_second_order}/filtered/${nsub}_from_${nside}_DTTT_Ipsilat_dPSN.trk \
             --drawn_roi ${mni_rois_dir}/${nsub}_${nside}_VPM_mni.nii.gz 'any' 'include' \
-            --drawn_roi ${out_dir}/mni_space/tracking_first_order/final/all_${nside}_remaining_cp_density_mni.nii.gz 'either_end' 'include' -f
+            --drawn_roi ${out_dir}/mni_space/tracking_first_order/final/all_${nside}_remaining_cp_density_mni.nii.gz 'either_end' 'include'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_1.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_2.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_3.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_4.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_5.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_6.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_7.bdo 'any' 'exclude'\
+			--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_8.bdo 'any' 'exclude'\
+			-f
+			
+			
     done
     echo "|------------- 3) Done -------------|"
     echo ""