THE CORE 6 LANDMARKS
Registration Only Borders:
 central sulcus (CeS) (quick ref: 18mm off dorsal; 19mm off ventral)
 Sylvian fissure (SF) [border is drawn along the circular sulcus within the fissure] (quick ref: 9mm
posterior to the intersection of the superior and inferior branches of the circular sulcus on FLAT)
 anterior half of the superior temporal gyrus (aSTG)
Flattening and Registration Borders:
 calcarine sulcus (CaS) (quick ref: 24mm from occipital pole)
 medial wall dorsal segment (quick ref: 19mm gap at frontal junction)
 medial wall ventral segment (quick ref: 16mm gap at calcarine junction)
Required Datasets:
 Atlas target dataset: Human.PALS_B12.LR.REGISTER-with-INDIVIDUAL.73730.spec
 Colin ref-for-landmarks left: Human.Colin.LEFT.REG-with-PALS-B12.71785.spec
 Colin ref-for-landmarks right: Human.Colin.RIGHT.REG-with-PALS-B12.71723.spec
Specific Guidelines for Drawing Registration Borders:
1. After opening CARET, or while CARET is open, make sure you have no borders loaded.
2. Draw the central sulcus, Sylvian fissure, and anterior half of the superior temporal gyrus
landmarks. Project and save these borders.
3. Append the “LANDMARKS.fromFlattening” borders to the current borders that were drawn.
Modify the medial wall and calcarine borders per instructions below. Project and save these
borders.
4. Perform registration.
Note: Using another order than stated above may cause errors!!! Not making sure that no borders are
loaded before drawing the lateral borders (CeS, SF, aSTG) may lead to duplicate borders on the medial
surface – CARET will not complete the registration process!!!!!!!!!!!
GENERAL GUIDELINES
1. The extent of each landmark is constrained to regions where it is reasonable to expect good
correspondence across nearly all subjects. Where distances are used, the reference surface is
specified. The inflated surface is the reference surface for all landmarks except the Sylvian fissure,
for which the flat surface is used; make sure you use the specified reference surface when
checking ID distances.
2. By "inflated," we mean the SureFit-generated (inflate_surface with smooth_iters1=60;
smooth_factor1=1.0; num_cycles=6; inflate_factor=0.6). This is a moderately inflated surface that
shows major sulcal/gyral structures. Do not use the VERY_INFLATED or Freesurfer (highly)
inflated surfaces.
3. While we use Colin as an example target when drawing landmark borders, the objective is to
match the average values represented by the PALS_B12 Case 1-12 averages. The guidelines
specified here reflect those averages, which may differ from those seen in the Colin reference
datasets by a few mm (for details, see the case-by-case extent reference measurements, averages,
and standard deviations for both hemispheres in PALS_B12_Core6_LANDMARKmeasurements_11May05.xls).
4. Distances are +/- 10%. If your individual's brain is sufficiently bigger or smaller than 711-2C
(wustl.edu atlas space used for PALS_B12, Colin -- closer to MNI305 than Talairach, but not
quite as big as MNI305), then you might need to use your judgment. If using these distances to
determine starting and end points results in borders that look disproportionate to Colin's (e.g.,
posterior-most point of calcarine border is closer to medial wall than occipital pole for a very
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small brain), then adjust the distances to better match proportions. At this point, we're not
recommending you compute the ratio of your subject's surface area or volume to Colin's and
reduce your distances based on the resulting geometric distance ratio; rather, "eyeball it" and make
sure there's a logical explanation for large deviations from these reference distances (e.g., very big
or small brain). Ultimately, the most important rule is to draw landmarks consistently from one
subject to the next. Minor deviations from these guidelines are relatively unimportant if they are
applied consistently. Of course, the worst deviations are those applied to one group of subjects,
but not another, if the goal is to compare results across those groups. Consistency is essential.
5. Since the template cuts often are redrawn during flattening, many of the inflated and
sphericalviews shown were captured with the CUT topo file assigned to show the
starting/termination points of these cuts. During normal flattening and registration, the CLOSED
topo file should be assigned to all 3-D surfaces; the CUT topo file should be used only with the
flat map.
EXTENT GUIDELINES FOR REGISTRATION ONLY BORDERS
central sulcus -- CeS extenti:
1. The central sulcus landmark border begins about 19mm above the margin of the Sylvian fissure
(distance reference: inflated surface).
2. Rotate the inflated surface as needed to approximate AC-PC alignment.
3. The CeS landmark terminates dorso-medially about 18mm from the medial wall (distance
reference: inflated surface).
4.
Sylvian fissure -- SF extentii:
1. The Sylvian fissure landmark begins along the posterior segment of the Sylvian fissure, starting
about 9mm posterior to the intersection of the superior (blue dotted line in the surfaces below) and
inferior (green dots in the surface below) branches of the circular sulcus. The flat surface should
be used to determine the 9 mm posterior starting point.
a. Open a second window and load the inflated surface. Inspect this image to ensure that you
have correctly identified the inferior branch of the circular sulcus; using the flat map alone
can be unreliable. On the inflated map, the intersection is located just anterior to the initial
segment of the posterior branch of the Sylvian fissure and appears slightly posterior to the
gyral inflation that is just posterior to the postcentral sulcus.
Flat
Atero-Lateral Inflated
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2. The landmark continues along the superior branch of the circular sulcus. In the screen captures
above (blue dotted line in the surfaces above).
3. Anteriorly, the landmark extends almost to the anterior and ventral limit of the superior branch of
the circular sulcus, 10 mm dorsal to the ventral margin of the frontal lobe.
anterior half of the superior temporal gyrus -- aSTG extent:
1. The starting point ID for aSTG is found by an imagined plumb line from the central sulcus
border's ventral tip to the STG (i.e., directly below the CeS ventral tip -- not projecting along the
path of the CeS).
2. Rotate the inflated surface as needed to visualize the ID node and the crest of the superior
temporal gyrus. This crest will appear white on the flat surface.
3. Mark the crest of the gyrus on the inflated surface with a series of ID nodes.
4. Draw the border on the flat surface anterior from the ID node and along the crest.
5. Terminate the border at the anterior limit of the temporal pole.
Registration Only Borders
Anterior
Lateral
EXTENT GUIDELINES FOR FLATTENING AND REGISTRATION BORDERS
calcarine sulcus -- CaS extent:
1. Getting started:
a. Use a second window showing a segmented volume (anatomical underlay and
segmentation overlay) for ease in identifying the fundus of the calcarine sulcus.
b. Points on the volume must be selected within the grey matter, just outside the segmentation
boundary.
c. All distances are in reference to the 711-2B atlas.
d. ID nodes will appear only on the surface representations, but can be selected by left
clicking on any representation, including the volume.
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2. Identify the full extent of the calcarine sulcus:
a. On a coronal Volume slice, the posterior extent can be clearly identified at ~Y=between 90 and -100. Place an ID node at this level.
b. Continue anterior in steps of every 2-3 mm until reaching the anterior end of the calcarine
sulcus.
c. In Figure 1 below, the crosshairs mark the fundus of the calcarine sulcus (~Y=100(Figure1a) to ~ Y=-50(Figure1e)).
3. Factors to consider as you proceed:
a. If there is a split/fork in the sulcus, mark a point in the ventral fork.
b. If the sulcus is interrupted by a gyrus (“speed bump”), cross it at its minimum height. The
latter might be easier to visualize by inspecting the inflated brain image.
c. The calcarine sulcus extends from the occipital pole almost to the parahippocampal gyrus.
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4. Connecting the CaS border to the medial wall border:
a. Place an ID node at the crest of the parahippocampal gyrus in the coronal slice where the
posterior column of the fornix connects the hippocampus and the splenium of the corpus
callosum (~Y=-40).
i. Figure 2a also illustrates this node placement on the volume image (also black
arrow of Figures 2d,e).
b. Move posterior until the calcarine sulcus is at or superior to the axial plane of the node
identified at the parahippocampal gyrus (blue crosshairs of Figure 2b).
i. Mark the fundus of the calcarine sulcus at this point (Figure 2c).
ii. Remove any ID nodes that are further inferior-anterior of the previously placed
node (white arrow) on the compressed medial wall (Figure 2e). The resulting
inflated and compressed medial wall surfaces are seen in Figure 2d and e,
respectively. The black arrow marks the crest of the parahippocampal gyrus. The
white arrow marks the last node of the calcarine sulcus.
5. Drawing the CaS Border:
a. Start with the most posterior point and connect the ID nodes. When you reach the last ID
node, the one at the white arrow, cross the “Medial.Wall” border using the shortest
possible distance (Figure 3).
6. Changes to CaS border that are needed for registrationiii:
a. Place the INFLATTED view in the main CARET window and on this view nibble off
border points at the posterior end until there is a 24mm gap on the inflated surface between
the occipital pole and the posterior end of the CaS landmark border.
i. First select the posterior view of the surface (P on CARET toolbar) to locate the
border point over the occipital pole, which normally is shown in red. Place an ID
node over this point.
ii. Switch to a medial view of the surface (M on CARET toolbar) and place a second
ID point about 24mm anterior.
iii. Inspect the last entry in the Identify Window where the distance between the last
two ID nodes is posted for the Main Window. Repeat the ID node placements until
they mark 24 mm anterior from the occipital pole.
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Medial wall dorsal and ventral segments:

The following atlas has several images and drawings that are extremely useful for identifications.
(Mai J.K., Assheuer J., Paxinos G. (1997). Atlas of the Human Brain. Academic Press. (see pages
124-236))

These borders are drawn during flattening as a single closed border. During flattening, the border is
named the “Medial.Wall”. Several key landmarks should be identified with green ID nodes before
drawing the border on the compressed medial wall surface. The sequence of ID node placements can
be done in any order, but for simplicity use the following sequence of steps.

Use a second CARET window showing a segmented volume for ease in identifying node placements.
a. Points on the volume must be selected within the grey matter, just outside the segmentation
boundary.
b. ID nodes will appear only on the surface representations, but can be selected by left
clicking on any representation, including the volume.

All distances are in reference to the 711-2B atlas.
1. Marking the olfactory sulcus and defining the anterior extent of the medial wall border:
a. (Figure 1) Identify the posterior extent of the olfactory sulcus on a coronal slice (~Y=7)
where the sulcus is still straight. Place an ID node at the fundus (Figure 1a,b,c).
i. In some cases, there is a lateral hook to the sulcus that is visible in the coronal
plane; in these cases select as the posterior extent the slice just before the hook
appears (i.e. the sulcus is straight).
b. Next move 10mm posterior and place a second ID node at the same lateral position at the
superiorly located segmentation boundary (Figure 1d, e, f). The second ID node will be
used later.
1a
1b
1c
1d
1e
1f
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2. Identifying the superior portion of the medial wall.
a. (Figure 2a) Turn off segmentation on volume representation.
b. Go to Y=0 on the coronal slice (Hit R (reset), which moves to Y=0 if you are in the
coronal plane). Place an ID node where the cingulate gyrus. (Figure 2a) abuts the superior
surface of the corpus callosum. The cross hairs in figure 2a mark the location where the
gray matter of the cingulate gyrus, CSF, and white matter of the corpus callosum intersect
each other; place the node at this location.
c. (Figure 2b) Moving posterior, place ID nodes every ~5-10mm (Figure 2b.i-vii) until the
posterior column of the fornix is visible (Figure 2b.vi, Figure 3c.i; ~y=-40).
d. Place an ID node at the callosal sulcus in this coronal slice.
e. Immediately after placing the last ID node, switch to the parasagittal view (Figure 2b.viii)
and place 4-5 ID nodes along the posterior boundary of the corpus callosum splenium. Do
not extend the ID nodes inferior-anterior of a line tangent to the posterior extent (Figure
2b.ix, green line). Figure 2b.x illustrates how these ID nodes should look on the
compressed medial wall. The olfactory sulcus marks are also shown.
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f. (Figure 2c) Switch back to the coronal view and move to Y=1 (Hit R (reset)), which moves
to Y=0 if you are in the coronal plane, and move anterior one slice to get to Y=1).
g. Continue placing ID nodes anterior along the callosal sulcus (Figures 2c.i-2c.v) until the
superior and inferior segments of the genu fuse (Figure 2c.v).
h. Immediately after placing the last ID node, switch to the parasagittal view (Figure 2c.vi)
and place ID nodes along the superior and anterior boundaries of the genu of the corpus
callosum. Do not extend ID nodes posterior-inferior of a line tangent to the anterior extent
of the genu (Figure 2c.vii , vertical green line). The nodes on the surface should look
similar to Figures 2c.viii and 2c.ix.
2c.i
2c.ii
2c.vi
2c.viii
2c.iii
2c.iv
2c.v
2c.vii
2c.ix
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i. (Figure 2d) On the compressed medial wall surface connect, with a series of ID nodes, the
last ID node marking the anterior extent of the callosal sulcus (see step 2c) to the ID node
previously placed ~10mm posterior to the olfactory sulcus (see step 1). The series should
make a slightly bowed arc, avoiding ventral prefrontal cortex as illustrated below.
2d.i
2d.ii
3. (Figure 3) Identifying the ventral portion of the medial wall:
a. (Figure 3a) Start by identifying the anterior extent of the uncus on coronal slices. Deep to
the anterior uncus is the amygdala. The gray matter of the uncus makes a hook laterally
(Figure 3a, black arrow) where there is an area of inferior convexity (Figure 3a.i, white
arrow). Use the first coronal slice that both can be identified. Note: At the hook and the
area of inferior convexity, the gray matter will appear darker than the other gray matter in
the region because the gray matter is mixing with CSF. This indicates that there is a very
thin hippocampal sulcus here. This sulcus marks the anterior extent of the hippocampus.
3a
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b. (Figure 3b) Turn segmentation on. Place an ID at the crest of the segmentation that
underlies the uncus (Figure 3b.i). This ID node can be noted on the inflated surface.
c. On the same slice, place a second ID node at the lateral edge of the amygdala next to the
segmentation boundary (Figure 3b.ii).
d. Place a third ID node half the distance between the first two nodes on the coronal slice
(Figure 3b.iii). On the surfaces, the nodes should now appear similar to Figures 3b.iv and
3b.v.
3b.i
3b.ii
3b.iii
3b.iv
3b.v
e. (Figure 3c) On the compressed medial wall surface connect with a series of 3-4 ID nodes
the second ID node marked in step 3b (Figures 3b.ii and 3b.iv) to the second ID node
placed posterior to the olfactory sulcus in step 1 (Figures 1d,e,f). The series of nodes
should then resemble the image below. Note: your surface will already have nodes for the
parahippocampal crest and subiculum marked. They are not shown below.
3c
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f. (Figure 3d) Move 5-7mm posterior and place a node at the crest of the segmentation
underlying the entorhinal gyrus or parahippocampal gyrus (Figures 3d.i,iii,v,vi). This is at
the medial most boundary of segmentation.
g. Next place a second ID node ~12 mm laterally, which should fall on the subiculum
(inferior-most convexity of segmentation) (Figures 3d.ii,iv,vi,viii).
i. NOTE: The L-R position of the subiculum node should be approximately the same
throughout, but will drift lateral as you move posterior along the hippocampal
formation.
h. Continue the process of placing nodes every 5-7mm posterior at the medial edge of the
segmentation and another 12 mm lateral until reaching the posterior column of the fornix
(Figure 3d.ix, black arrows, ~y=-40; the white arrow marks the corpus callosum).
i. At this point, only mark the crest of the parahippocampal gyrus (Figure 3d.x). DO NOT
mark the subiculum on this slice. Figures 3d.xi and 3d.xii (next page) show how the
compressed medial wall and inflated surfaces should look after this step has been
completed.
3d.i
3d.ii
3d.iii
3d.iv
3d.v
3d.vi
3d.vii
3d.viii
3d.ix
3d.x
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3d.xi
3d.xii
j. (Figure 3e) On the compressed medial wall surface connect, with a series of 2-3 ID nodes,
the ID node at the most posterior parahippocampal crest (Figure 3d.x) to the ID node
placed at the posterior extent of the splenium (Figure 2b.ix and 2b.x)..The resulting
compressed medial wall and inflated views go from Figure 3b.xi and 3b.xii to Figures 4a
and 4b, respectively.
3e.i
3e.ii
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4. (Figure 5) Drawing the Medial Wall border:
a. Once steps 1-3 are completed, the Medial.Wall border can be drawn through the ID nodes
on the compressed medial surface. ALWAYS make a smooth line!!! Start from the most
posterior subiculum point on the compressed medial wall view (Figure 4a, black arrow).
b. Now go towards the most posterior parahippocampal gyrus ID node (Figure 4a, red
arrow).
c. Continue along the path of ID nodes towards the callosal sulcus nodes. Continue along the
callosal sulcus and wrap around the inferior prefrontal cortex.
d. DO NOT connect the first ID node marking the olfactory sulcus; Figure 1a,b and c; Figure
4a, blue arrow.
e. Continue along the ID nodes going through the node lateral to the amygdala (Figure 4a,
magenta arrow).
f. Continue along the subiculum (Figure 4a, white arrows).
g. Except for the most posterior parahippocampus crest node, no other nodes on the crest of
this gyrus should be included in the border.
h. Whenever there is an ambiguity as to which ID node to choose, choose the node toward the
center of the compressed medial wall. Figure 4b shows the medial wall border when
completed.
4a
4b
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5. Changes to medial border that are needed for registration :
a. After Flattening, the medial wall border will automatically divided into dorsal and ventral
segments based on where the CaS (dorsal ends, ventral starts) and frontal cut (dorsal
begins, ventral ends). The dorsal medial wall border will run from a line parallel and
tangent to the gryus rectus (gryus medial to the olfactory sulcus) to the calcarine sulcus.
The ventral medial wall landmark runs from the same termination points, but in the
opposite direction and along the medial margin of the hippocampal sulcus, and across the
margins of cortex with the basal forebrain.
b. Anterior portion of medial wall modifications:
i. Nibble off dorsal medial wall border points (CARET menu: Layers > Borders >
Delete Border Point with Mouse).
ii. Start at border point marked in red and continue until the red dot is located medial
to a line running through the gryus rectus (medial most gyrus in the ventral view).
iii. Nibble off points of ventral medial wall until the end point is ~19 mm from start of
dorsal border in the fiducial view.
c. Posterior portion of medial wall modifications:
iv. Nibble off border points equally on either side of the calcarine landmark so that
there is a ~16mm gap between the dorsal and ventral medial wall segments in the
Fiducial view.
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RESULTING BORDERS SHOULD LOOK LIKE THESE:
Medial Wall
Medial Wall
Borders_for_ Flattening
Borders_for_REG_with_ATLAS
Flat view of Ces, SF, and aSTG
i
Lateral view of Ces, SF, and
aSTG
Medial-Ventral View of Gaps
between ventral and dorsal
Medial Wall borders
Dorsal view of Ces
Changes from prior instructions: Before 5/11/2005, the guideline was 15mm from each end.
ii
Changes from prior instructions: Before 10/5/2005, we identified this intersection as the "SF-SF2
intersection, where we named SF the Sylvian fissure's primary fundus and SF2 the main secondary
fundus. From 12/21/2004 until 5/11/2005, the guideline was 12mm posterior to the SF-SF2 intersection.
Before 12/21/2004, Donna Hanlon aimed for the SF-SF2 intersection, requiring rework of borders on
CSM and Amaral studies.
iii
Changes from prior instructions: Before 5/11/2005, the guideline was 27mm gap (28 mm on the left side, 20 mm on the right
side)
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