The core 6 landmarks Registration Only Borders

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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_LANDMARK-measurements_11May05.xls).

  4. Distances are +/- 10%. If your individual's brain is sufficiently bigger or smaller than 711-2C ( 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 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.


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).

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.

    1. 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.


Atero-Lateral Inflated

  1. The landmark continues along the superior branch of the circular sulcus. In the screen captures above (blue dotted line in the surfaces above).

  2. 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.

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