Download I. Appendix of Specific Techniques

I. APPENDIX OF SPECIFIC TECHNIQUES
A. 10 SUGGESTED TAG POINTS
The image can be enlarged by holding shift + the middle mouse button, and it can be moved by holding
shift + the left mouse button
TAG points:
Be sure to always pick the points with the "record tags" icon located on the left of the screen. Never use
the right mouse button, otherwise the tag points will not stay in order, and order is critical. This is
especially important if you decide to re-pick a point. For example, if you decide to re-pick the first point,
go back to the first point by moving the highlighted number up to 1 using the up arrow. Then when you
re-pick the point, click the record tag icon. This will move your tag point while maintaining the order.
NOTE: The very center pixel of the cross hair is the actual location of the tag point.
A. Left and Right Cerebellum (1 & 2)
Scroll through the sagittal view. Keep an eye on the cerebellum, and watch for when it becomes so small
that you can no longer see the horizontal striations. Then in the sagittal view, click on the very center of
the cerebellum, seen as an oval shape, with the left mouse button (Fig 1, Fig 2). In the coronal view you
should be able to see a rough triangle formed by the transverse sinus (Fig 1, Fig 3). Look at the coronal
view, and select the tag by choosing the apex of the triangle formed by the transverse sinus, cerebrum,
and cerebellum (Fig 2, Fig 4). Double check through the axial view that the tag point chosen is in
approximately the same area as the average brain.
B. Corpus Callosum (3 & 4)
Most Anterior Point:
In the sagittal view, scroll to the mid sagittal slice until you're at the most anterior point of the corpus
callosum (Fig 5). Click on the most anterior point at which the corpus callosum curves. Be sure to look in
all views of the raw scan and compare them to see how similar the image is with the averaged brains.
Make sure you are in the very middle by checking in the coronal view that you are between the two
hemispheres (Fig 5).
Most Posterior Point:
Again, go to the sagittal view. You must scroll through again because sometimes the head can be tilted to
the left or right (which is visible in the axial view), and find the most posterior point of the corpus
callosum (Fig 6). Click on the corpus callosum right before the point at which it starts to curve in, but
after the round peak (Fig 6). Check in all views and compare your image with the sample images to
double check. NOTE: be cautious of what you think the most posterior point is because sometimes the
head can be tilted forward.
C. Left and Right Eye Sockets (5 & 6)
Scroll through the axial view until you can see the cornea quite distinctly. Pick the center of the eye
socket (Fig 7, Fig 8). Scroll through the coronal view to make sure you are at the point where the
diameter of the eye socket bones are the largest. Also make sure you are in the middle of the socket. Be
sure to check all views, and make sure the tag point is centered in all the views (Fig 7, Fig 8).
D. Fourth Ventricle (7)
Scroll in the mid sagittal view until you are at the very corner of the fourth ventricle (Fig 9). Look at the
axial view to be sure you are in the middle and at the most posterior point of the fourth ventricle. If not
just scroll through the sagittal view, while looking at the axial view, until you are at the most anterior
point. Then pick the tag point (Fig 9).
E. Left and Right Temporal Lobe (8 & 9)
Scroll through the coronal view until you are at the most anterior point of the left temporal lobe. NOTE:
be aware of bone and fats that are right below the temporal lobe. Do not confuse the fats and bone with
the temporal lobe. Click on the very center of the most anterior point of the temporal lobe. Be sure to pick
in the slice right before it is no longer visible (Fig 10, Fig 11). Look at all views, and scroll through to be
sure you are at the most anterior point. Again be cautious of fatty tissue and deposits. Scroll through and
enlarge the image to be sure that you have picked the most anterior point (Fig 10, Fig 11). NOTE: be
cautious of what you think is the most anterior point. You must account for the possibility of the head
being tilted forward or backwards.
F.Mammillary Bodies (10)
Go to the mid sagittal slice by scrolling through the sagittal view. Use the left and right arrows to go
through slice by slice. Tag the mammillary body at the point where the body looks very round and clear.
Another reference is to be able to see the brainstem, especially the pons, very clearly (Fig 12). NOTE:
clear, meaning the structures look well defined, and have a very clear and rigid edge or boundary.
A. Left and Right Cerebellum (1 & 2)
Scroll through the sagittal view. Keep an eye on the cerebellum, and watch for when it becomes so small
that you can no longer see the horizontal striations. Then in the sagittal view, click on the very center of
the cerebellum, seen as an oval shape, with the left mouse button (Fig 1, Fig 2). In the coronal view you
should be able to see a rough triangle formed by the transverse sinus (Fig 1, Fig 3). Look at the coronal
view, and select the tag by choosing the apex of the triangle formed by the transverse sinus, cerebrum,
and cerebellum (Fig 2, Fig 4). Double check through the axial view that the tag point chosen is in
approximately the same area as the average brain.
B. Corpus Callosum (3 & 4)
Most Anterior Point:
In the sagittal view, scroll to the mid sagittal slice until you're at the most anterior point of the corpus
callosum (Fig 5). Click on the most anterior point at which the corpus callosum curves. Be sure to look in
all views of the raw scan and compare them to see how similar the image is with the averaged brains.
Make sure you are in the very middle by checking in the coronal view that you are between the two
hemispheres (Fig 5).
Most Posterior Point:
Again, go to the sagittal view. You must scroll through again because sometimes the head can be tilted to
the left or right (which is visible in the axial view), and find the most posterior point of the corpus
callosum (Fig 6). Click on the corpus callosum right before the point at which it starts to curve in, but
after the round peak (Fig 6). Check in all views and compare your image with the sample images to
double check. NOTE: be cautious of what you think the most posterior point is because sometimes the
head can be tilted forward.
C. Left and Right Eye Sockets (5 & 6)
Scroll through the axial view until you can see the cornea quite distinctly. Pick the center of the eye
socket (Fig 7, Fig 8). Scroll through the coronal view to make sure you are at the point where the diameter
of the eye socket bones are the largest. Also make sure you are in the middle of the socket. Be sure to
check all views, and make sure the tag point is centered in all the views (Fig 7, Fig 8).
D. Fourth Ventricle (7)
Scroll in the mid sagittal view until you are at the very corner of the fourth ventricle (Fig 9). Look at the
axial view to be sure you are in the middle and at the most posterior point of the fourth ventricle. If not
just scroll through the sagittal view, while looking at the axial view, until you are at the most anterior
point. Then pick the tag point (Fig 9).
E. Left and Right Temporal Lobe (8 & 9)
Scroll through the coronal view until you are at the most anterior point of the left temporal lobe. NOTE:
be aware of bone and fats that are right below the temporal lobe. Do not confuse the fats and bone with
the temporal lobe. Click on the very center of the most anterior point of the temporal lobe. Be sure to pick
in the slice right before it is no longer visible (Fig 10, Fig 11). Look at all views, and scroll through to be
sure you are at the most anterior point. Again be cautious of fatty tissue and deposits. Scroll through and
enlarge the image to be sure that you have picked the most anterior point (Fig 10, Fig 11). NOTE: be
cautious of what you think is the most anterior point. You must account for the possibility of the head
being tilted forward or backwards.
F.Mammillary Bodies (10)
Go to the mid sagittal slice by scrolling through the sagittal view. Use the left and right arrows to go
through slice by slice. Tag the mammillary body at the point where the body looks very round and clear.
Another reference is to be able to see the brainstem, especially the pons, very clearly (Fig 12). NOTE:
clear, meaning the structures look well defined, and have a very clear and rigid edge or boundary.
B. CREATING 3D PROJECTIONS OF BRAIN SURFACE
1. AD GROUP WEB-SITE
In order to create the cortical object files, an intensity threshold needs to be given to tell the template
object where to start. To determine this intensity threshold, open the mnc in Display.
Display input_file.mnc
Zoom into the cortex. Move the mouse around the border between the CSF and the gray matter. Note the
intensities that appear under the heading Vl. It is important for you to do this at both the frontal and
occipital poles, as well as in the parietal and temporal lobes because they have different intensities.
Now that the threshold has been selected, the cortical objects can be created. In addition to the threshold
value, two other thresholds will be run (generally higher than the one selected). They are usually five and
ten higher than the original threshold. Run these on autarch.
cortical_surface.pl case#_nu_ss_7p_Atlas.mnc case#_nu_ss_7p_Atlas_threshold#.obj threshold#
/data/ad/mass1/users/mega/cmAD_Atlas.dir/AD_Atlas_2_305.xfm &
cortical_surface.pl case#_nu_ss_7p_Atlas.mnc case#_nu_ss_7p_Atlas_threshold#+5.obj threshold#+5
/data/ad/mass1/users/mega/cmAD_Atlas.dir/AD_Atlas_2_305.xfm &
cortical_surface.pl case#_nu_ss_7p_Atlas.mnc case#_nu_ss_7p_Atlas_threshold#+10.obj threshold#+10
/data/ad/mass1/users/mega/cmAD_Atlas.dir/AD_Atlas_2_305.xfm &
Once the object files have been created, open them up one at a time, and see which one best captures the
cortical surface. Often times the parietal/temporal region is not as extracted as possible, so a higher
threshold becomes necessary. Also, because the cerebellum is still present, the inferior surface does not
come out crisp all the time, or the cerebellum is part of the object. If this is the case, do the following:
Create a mask of the minc file.
mincmath -ge -const 0.0001 case#_nu_ss_7p_Atlas.mnc case#_nu_ss_7p_Atlas_mask.mnc
Open the minc file and the mask.
Display case#_nu_ss_7p_Atlas.mnc -label case#_nu_ss_7p_Atlas_mask.mnc
Remove the cerebellum by going through the sagittal slices and deleting that part of the mask. When this
is done, save the mask.
Remove the cerebellum from the minc file.
mincmask case#_nu_ss_7p_Atlas.mnc case#_nu_ss_7p_Atlas_mask.mnc case#_nu_cs_7p_Atlas.mnc
Run the cortical surface commands again, this time with the _cs_ file.
When one object file is determined to be a good representation of the cortex, delete the others. Drawing
the sulci is the next step.
2. SOWELL WEB-SITE
*NOTE: Sometimes the dilate and blur in the first step does not dilate far enough at the edge of the mask,
and CSF gets missed. Before creating csfonly mincs, it is necessary to fill in the areas inside the dura
that segment as CSF. To do this, open the rf-corrected segmented image and the blur_label.
Display case#_reslice_seg_rf.mnc.gz -label case#_reslice_mask_1mm_blur_label.mnc.gz
case#_reslice_mr_rf.mnc.gz
Adjust the color of the segmented image so that each tissue type is a different color and missed csf is easy
to see. Usually it is adequate to leave the image in "hot metal" and to raise the top line of the color bar to
the top (4) and leave the bottom on 1. Increase the brush size to 3 ("F" Segmenting Menu & "F" XY
Radius). Set the threshold so as to only paint csf and background pixels ("F" Segmenting Menu & "Y" Set
Threshold Type "2.9 4.1" for the new threshold) Progress slice-by-slice from anterior to posterior filling
in CSF at the outer edge of the brain, inside the dura. Missing CSF: Figure 5a, Figure 5b Filled in:
Figure 6a, Figure 6b
When the label is done, save the brain mask with addcsf in the filename. To do this, type:
"Space bar"-to go to the main menu
"T"-to open the File menu
"1"-to turn Crop Save Labels: OFF
"W"-to Save Labels (brain mask) as a mnc
case#_reslice_mask_1mm_blur_label_addcsf.mnc
C. ADDITIONAL INFORMATION ON CORTICAL
MODELS, WARPING, AND FLATMAPPING
1. OTHER TIPS OR TROUBLESHOOTING:
It is not uncommon for problems to come up during the process of following this protocol. The most
frequent sign that something is wrong is warped flatmaps with holes or excessive swirling. The following
tips might help to determine the source of the problem.
# Flatmapping and warping depend upon only the sulcal lines that were drawn and the object model on
which they were drawn. If there is a problem with one of these step, these are the files to check.
# If a particular line is suspected to be a problem, re-run the warping script without that line. If the
flatmap is fixed, it is likely that that line was drawn or flattened incorrectly; if not, another issue exists.
# If a line is called on in the script that was not drawn for that subject, there will be warping problems as
the script tries to warp the target from the missing line to the next line that was drawn for the subject,
even though the anatomy might be way off. If this is the problem, there will be a "No match" error
following the echoed lines "DOING LEFT Hem first...setting filenames" or "DOING RIGHT Hem
next...setting filenames" in the UNIX window.
# Warping problems can occur if the filenames or paths given in warping script are incorrect. The
reference ucfs (the lines for each subject) should come from the directory pointed to in lines 30 and 37 of
the warping script and the target ucfs (the average lines) should come from the directory pointed to in
lines 43 and 49. Check to be sure these directories exist and hold the files they're expected to. In lines 54
through 63, the files are renamed from their original names to simplified names. Check to be sure that the
correct file is targeted and moved. If a problem is occurring with copying the lines, the window in which
the script was run should show "no match" errors after the echo information about copying the ucfs
("Copying REFERENCE ucfs- Left hemisphere", "Copying REFERENCE ucfs- Right hemisphere",
"Copying target ucfs- RSP files - Left hemisphere", or "Copying target ucfs - RSP files - Right
hemisphere"). If the filenames are incorrect, there will be a string of "No match" errors following the
echoed lines "DOING LEFT Hem first...setting filenames" or "DOING RIGHT Hem next...setting
filenames" .
# A problem in warping can occur any time that target lines and reference lines are not matched properly.
To determine if this is the problem, list the lines that are used in warping into a text file. Once the
warping script has been run, go into the directory of the problem subject. Open the files in nedit to see
that they are paired properly (that a target and reference exist for each line).
ls ??L.ucf ???L.ucf > Left_match.txt
ls ??R.ucf ???R.ucf > Right_match.txt
# nedit Left_match.txt Right_match.txt Lines must fall correctly on the object model. The lines and
objects must be in the same space. If the object model has been recreated and lines have not been
withdrawn, they may fall underneath the surface or hover above it. While the commands have a built-in
step which sucks the lines onto the surface, an extreme case might still cause problems. To check for this,
load the lines and surfaces in Display. Redraw lines as necessary.
# Lines must not cross. When lines cross, it means that the same point is labeled as two separate pieces of
anatomy. When warping occurs and the anatomy is directed in separate ways, the map can be torn.
Check for crossing lines in Display. Even if lines do not cross on the object model, they may cross when
flattened. Pull up the flattened lines over the non-warped flatmap to check for this. If two lines are
suspected of crossing, try re-warping using only one of the lines. If the problem is fixed, redraw the lines
and warp again using all the lines.
# Lines must not be drawn backwards. If a line is drawn backward, the first point of that subject's line is
directed to the last point of the average line, and the violence of that movement can cause swirling or
holes. To check for backward lines, create markers out of the starting point of each line by running the
script make_markers_at_start.csh. Open the lines and markers for all objects, one line at a time. If lines
have been drawn backwards, the green markers at their starting points will be at the opposite end of the
mass of lines from the rest of the markers. The exact lines which have been drawn backward can be
determined by making each subject's marker invisible and noting which subject was different.
# Ucfs can be viewed with either ~thompson/vu or ctrview. The flattened target and reference lines for a
subject can be shown this way. For a given sulcus, the target and reference UCF should be fairly close to
each other. The re-inflated ucf representing the whole brain can also be shown using vu or ctrview. A
hole in the flatmap will frequently show up as lines extending from the surface of the brain in the UCF,
like Fig 3.
# Gray matter maps depend on the lines, the object, and the binary gray image. If the warped flatmap
looks correct, but a problem exists with the gray matter maps, the binary gray image is likely the problem.
To check to make sure that the binary gray image is in the same space, pull up the object model and
binary gray image in Display. Select R (Objects) then W (Scan Object to Vol). A red line should appear
on the gray image. The line shows how the object model falls on the surface. It should follow the outside
border of the gray matter fairly closely, like Fig 4.
# The first 3 numbers in each line of the gray matter ucf for each subject should match the numbers in the
same line in 0prEw_hem_R.ucf or 0prEw_hem_L.ucf . If the numbers do not match, the eat volume
script is grabbing the wrong input.
2. CLEANING
The process of flatmapping creates many files in each subject's CORT and WARP directories which are
duplicates of files that exist elsewhere. To conserve space, these duplicated files are removed.
1) The script 8_clean_script.csh removes files from each subject's CORT and WARP directories which
exist elsewhere. The shortened UCFs are removed from the CORT directory, but they remain in the RSPs
directory under the directory holding all the lines. The object is removed from the CORT directory, but it
remains in the CLRD directory under the directory holding all the lines. The flattened lines are removed
from the WARP directory, but they remain in the AVG_FLAT directory.
D. DETAILED INFORMATION ABOUT HOW TO DRAW
THE LINES FOR SULCAL ANATOMY
1. LATERAL
a) The Sulci
16. Sylvian Fissure
Starting Point: Point on object where temporal lobe separates from frontal lobe
Direction: Anterior to Posterior
Ending Point: Nestled inside the supramarginal gyrus
Notes: Follow the natural course, do not pass over any gyri. You will not need to rotate the object.
Sylvian moves superior as it moves posterior. The anterior end almost always starts anterior to, or directly
at, the inferior extent of the precentral Sulcus. Always confirm your sulcus choice in the coronal slice
view. Occasionally, Sylvian moves dramatically superior, sometimes interfering with the designation of
the postcentral sulcus. In these cases (for example, case?), follow the Sylvian Fissure, but do not draw
superior to Intraparietal sulcus. Then draw postcentral ending at superior extent of the Sylvian. Use axial
and saggital reslice views for assistance, but ultimately use the object view for decision. When there are
two paths to choose from at the posterior extent, always take the more superior route (as seen in case
102812).
References: Figure 16
1. Central Sulcus
Starting Point: Top view, close to midline.
Direction: Superior to Inferior
Ending Point: Side view, superior to Sylvian fissure
Notes: Generally unambiguous. The axial view can be helpful because the sulcus has a characteristic bend
(moving lateral bends to the anterior. See Figure 1a). Do not cross over any gyri as you move inferior.
The superior extent tends to curve posterior as it moves towards midline.
References: Figure 1
3. Postcentral Sulcus
Starting Point: Top view, just behind the Central sulcus, near midline
Direction: Superior to Inferior
Ending Point: Superior to the Sylvian fissure
Notes: Always first identify the postcentral sulcus in superior axial view, as it is always the sulcus just
behind the central sulcus at the superior extent. There is often a small extra sulcus between the central and
the postcentral near the Sylvian at the inferior extent of the sulcus (see case 10792, 2137, 102812). If this
extra sulcus is present, take the posterior route (tends to intersect directly into Sylvian Fissure in these
cases). If the superior extent of the sulcus is not continuous up to the midline, always choose the posterior
extent (e.g., not anterior towards the central sulcus) using the following guidelines: move posterior when
you reach the most superior bifurcation from the midline. Almost always ends in an insular type sulcus.
Do not jump sulci, unless you have no other options.
References: Figure 3
19. Precentral Sulcus
Starting Point: Near midline, in top view
Direction: Superior to Inferior
Ending Point: At or near Sylvian fissure
Notes: Frequently discontinuous in the middle of the sulcus. This sulcus should be just anterior to the
central sulcus. The middle frontal terminates on the precentral, which can give you a clue. The most
superior extent ends towards the midline and it runs generally parallel to the central sulcus. If there is a
superior fork, take the anterior route, staying relatively parallel to the central sulcus. Staying parallel
should take priority over sulcal continuity if it veers dramatically anterior (rough guideline: if the sulcus
angles > 45 degrees anterior, then don’t go that way). If there is a choice between two different routes at
the inferior aspect, always take the more anterior path unless the other is clearly more continuous.
References: Figure 19
2a. Superior Temporal Sulcus Main Body
Starting Point: Furthest anterior high-contrast point in temporal pole
Direction: Anterior to posterior
Ending Point: Temporal-Occipital Notch, or the anterior occipital sulcus, which ever is more anterior
(see Duvernoy, p9, #23).
Notes: Coronal slice view can be helpful in determining the pathway. As a general rule, the Superior
Temporal sulcus tends to parallel the Sylvian Fissure and the inferior temporal (but not in all cases). The
anterior termination point of the inferior frontal sulcus (as seen in the axial view) is always near the
junction with the superior temporal gyrus. Do not interfere with the drawing of 2b. Note that if there is no
occipital temporal sulcus available for a stopping point, use cross hair from temporo-occipital notch for a
guide.
References: Figure 2a
2b. Superior Temporal Sulcus Ascending Branch
Starting Point: Superior Temporal sulcus main body bifurcation
Direction: Inferior to Superior
Ending Point: Inside the angular gyrus
Notes: Do not draw the sulcus higher than the most superior aspect of the supermarginal gyrus. You
might have to cross over a gyrus to complete the sulcus. It will often run very close to the Sylvian, but can
also move back towards the occipital lobe. Runs between the secondary intermediate and the primary
intermediate sulcus. Do not interfere with 22.
References: Figure 2b
2c. Superior Temporal Sulcus Posterior Branch (horizontal posterior segment of the parallel sulcus,
Duvernoy, p8 #19)
Starting Point: Posterior extent of superior temporal sulcus, main body
Direction: Anterior to Posterior
Ending Point: Most posterior high contrast point closest to the junction of the Intraparietal and transverse
occipital sulci.
Notes: This sulcus may not always be present, but when it is make sure to draw it along the path of least
resistance. Occasionally this sulcus runs into the temporo-occipital sulcus, if so, stop there.
References: Figure 2c
15. Intraparietal Sulcus
Starting Point: Post central sulcus
Direction: Anterior to Posterior
Ending Point: Transverse-occipital sulcus
Notes: Always a T-intersection at the anterior extent with Post Central (when it requires jumping a gyrus,
take the path closest to the apex of the supramarginal gyrus). When the posterior/inferior extent is
ambiguous, take the inferior extension (not part of post central sulcus). The Intraparietal sulcus always
has a ½ Y shape relative to the midline.
References: Figure 15
22. Primary Intermediate Sulcus
Starting Point: Apex of supramarginal gyrus at the intraparietal, or occasionally at the postcentral sulcus
Direction: Superior to Inferior
Ending Point: End of the sulcus or far enough down to contain the supramarginal gyrus. If it forks at the
inferior extent, stop at the intersection.
Notes: It will hug the posterior border of the supramarginal gyrus. Never continue the sulcus all the way
to the superior temporal. It is all right to jump a gyrus to get to the primary intermediate sulcus. If, at the
inferior portion of the sulcus, you have a choice between moving inferior and moving anterior, move in
the anterior direction. If the only way to draw the sulcus is off the post central, then do so. This sulcus
may not always be present.
References: Figure 22
20. Secondary Intermediate Sulcus
Starting Point: Intraparietal sulcus
Direction: Superior to Inferior
Ending Point: End of sulcus
Notes: Offshoot from nearby the middle of the Intraparietal sulcus. It is always the posterior border of the
angular gyrus. Never let it interfere with the posterior branch of the post central. Should resemble a "T" as
it comes down from the top of the Intraparietal sulcus into the depths of the angular gyrus.
References: Figure 20
21. Transverse Occipital Sulcus
Starting Point: On midline or highest contrast point nearest midline on medial surface of hemisphere.
Sulcus frequently branches (y or t intersection) at the midline, stop at the intersection.
Direction: Medial to Lateral
Ending Point: Follow all branches that extend posterior/inferior; insular type sulcus. Stop if you intersect
the sulcus lunatus (see Duvernoy, p 16, #11)
Notes: Intraparietal sulcus runs into TOS more than 90 percent of the time. Should start at the most
posterior branch at the medial surface (it often forms a Y-intersection with the medial surface of the
hemisphere). The sulcus should be continuous and follow all branches that extend posterior/inferior (even
if it requires turning medially).
References: Figure 21
9. Inferior Temporal Sulcus
Starting Point: Farthest anterior high contrast point visible in the side object view
Direction: Anterior to Posterior
Ending Point: Temporal-Occipital Notch or insular gyrus if it ends more anterior than the temporooccipital notch, or end of sulcus intersecting at anterior occipital sulcus.
Notes: Sulcus usually moves into parietal lobe, not occipital. The inferior view of the Inferior Temporal is
not much help. It should never exit temporal lobe at inferior surface. Inferior should never finish higher
up than Superior or cross it. When you lose the end of the sulcus on the surface view, jump to the closest
available sulcus that you can identify as that sulcus without exiting to the bottom of the brain. Note, in
this case, you must be able to see the inferior temporal sulcus below your line, or you might be exiting the
bottom of the brain. If you hit any intersection that requires you to move back in the anterior direction,
stop. It is often necessary to jump a large, ambiguous area to get back to the sulcus.
References: Figure 9
4. Inferior Frontal Sulcus
Starting Point: Most posterior segment of the lateral orbital sulcus
Direction: Anterior to Posterior
Ending Point: Pre Central sulcus
Notes: Frequently discontinuous. Always terminates ON Pre Central Sulcus on posterior end even if you
have to jump a sulcus that abuts the pre central. Makes an upside-down "Y" with the Pre Central. The
sulcus may be divided from Pre Central by pars opercularis and pars triangularis (see Duvernoy 1).
Posterior end determined by taking lowest continuous horizontal sulcus coming off the Pre Central.
Always take the inferior route at the most anterior intersection. Often terminates at an insular sulcus. Most
anterior extent always ends at most anterior vertically oriented sulcus, e.g. lateral orbital sulcus (see
Duvernoy 2). At the anterior end, never jump more than one vertically oriented gyrus before taking
intersection in the inferior direction (it is often necessary, however, to jump one gyrus). Note, do not
chose a sulcus that curves around the inferior surface of the frontal lobe. If it is ambiguous whether you
are actually jumping a gyrus, use the slice view to aid you. Anterior end frequently curves back around to
move almost posterior in direction.
References: 1-Duvernoy pg. 9 #12,13; 2-pg. 8, #8?; Figure 4
5. Superior Frontal Sulcus
Starting Point: Highest contrast point closest to midline of the most inferior frontal marginal gyrus
Direction: Anterior to Posterior
Ending Point: On or near the Pre Central
Notes: Do not start the curve at a point that lies on the mesial surface (don?t wrap around-use the axial
slice view to help). Choose the most inferior horizontally oriented frontal marginal sulcus even if this
requires jumping a gyrus. Further, do not choose a sulcus that appears to lie on the inferior surface of the
brain. The sulcus is usually continuous from this point on. If there is a question as to which path to take,
take the inferior lateral path. In the event that there appears to be 2 Frontal-Marginal Sulci, take the most
continuous route, while generally choosing the most inferior sulcus if possible. Sulcus may bend
frequently around small gyri. Use the coronal reslice view to help with ambiguities.
References: Figure 5
6. Olfactory Sulcus
Starting Point: Most anterior extent of sulcus, near the frontal pole.
Direction: Anterior to Posterior
Ending Point: Curve of the sulcus away from midline
Notes: Posterior extent always determined by most posterior extent of the olfactory sulcus as visualized in
saggital slice view, and tends to curve away from the midline. Use the inferior axial slice view to
determine the anterior extent.
References: Figure 6
7. Occipital-Temporal Sulcus
Starting Point: Most anterior high-contrast point before the temporal pole
Direction: Anterior to Posterior
Ending Point: In occipital pole; highest contrast point near midline
Notes: Is always lateral to the collateral sulcus, and generally runs parallel to it. Choose the highest
contrast point nearest the temporal pole regardless of continuity. May require jumping from high contrast
point to a definitive sulcus. Use the slice views to help you determine which path to take. Also, never start
at any point more mesial than the starting point of the collateral. For any bifurcations, take lateral extent
as long as it does not interfere with the inferior temporal. When the double parallel type occurs, always
choose the most lateral. May require a jump to the highest contrast point in occipital pole.
References: Figure 7
8. Collateral Sulcus
Starting Point: Level with the pons at its widest lateral extent
Direction: Anterior to Posterior
Ending Point: On midline
Notes: Move laterally from the pons until you reach the most mesial sulcus that can be followed to find
the starting point. Bifurcates frequently in more posterior extent; always take mesial route.
References: Figure 8
Guidelines for Drawing the Control Lines
Note, change line-weighting back to 0 before drawing control lines.
Imagine a plane bisecting the inter-hemispheric fissure. Generally, keep the control lines parallel to this
plane without veering too far laterally to accommodate gyrification.
Draw lines roughly at the location which best distinguishes the separation between the lateral and medial
surface of the hemisphere.
10. Olfactory Control Line
Starting Point: Beginning of olfactory sulcus
Direction: Anterior to Posterior
Ending Point: End of olfactory sulcus
Notes: Draw line just off of midline (about 5mm) on bottom view.
References: Figure 10
17. Olfactory-Middle Frontal Control Line
Starting Point: Most anterior point of olfactory sulcus
Direction: Inferior/anterior to Superior/posterior
Ending Point: Beginning of middle frontal sulcus
Notes: Drawn on front view
References: Figure 17
11. Middle Frontal-Precentral Control Line
Starting Point: Beginning of middle frontal sulcus
Direction: Anterior to Posterior
Ending Point: Precentral sulcus
Notes: Start drawing in front view, end drawing in top view.
References: Figure 11
18. Precentral-Central Control Line
Starting Point: Precentral sulcus
Direction: Anterior to Posterior
Ending Point: Central sulcus
References: Figure 18
12. Central-Postcentral Control Line
Starting Point: Central sulcus
Direction: Anterior to Posterior
Ending Point: Postcentral sulcus
References: Figure 12
13. Post Central-Transverse Occipital Control Line
Starting Point: Postcentral sulcus
Direction: Anterior to Posterior
Ending Point: Transverse occipital sulcus
References: Figure 13
14. Occipital Control Line
Starting Point: Transverse occipital sulcus
Direction: Anterior to Posterior
Ending Point: Termination of collateral sulcus
Notes: Start drawing in back view; end drawing in bottom view. Do not rotate.
References: Figure 14;
This protocol was created and tested by the following people (whom you can email with any questions or
concerns):
Elizabeth Sowell
Chris Lindshield
Michael Mega
David Rex
Paul Thomson
Chris Zoumalan
b) The Medial Sulci
30. Callosal Sulcus
Starting Point: Rostrum of the Corpus Callosum
Direction: Anterior to Posterior
Ending Point: Splenium of the Corpus Callosum
Notes: The actual sulcus may not appear on the model, so trace the outer boundary of the corpus
callosum. Start at the underside of the rostrum at its most posterior point and follow around the curve of
the splenium. End the line at the most inferior point of the splenium BEFORE curving upward again.
This will be defining the border of the cingulate gyrus. Also, magnify the callosal area to occupy most of
the computer screen to ensure accurate drawing around this structure.
References: Figure 30i Figure 30ii Figure 30iii Figure 30iiii
31. Inferior Callosal Outline Segment
Starting Point: Rostrum of the Corpus Callosum
Direction: Anterior to Posterior
Ending Point: Splenium of the Corpus Callosum
Notes: Change the curve weight level to 100 in order to get a good fit of the underlying callosum. Also
magnify the callosal area greatly to occupy most of the computer screen to ensure accurate drawing
around this structure. Start at the underside of the rostrum at the most posterior point and follow the
callosum until you reach the most inferior point of the splenium. Be sure to draw the line on the corpus
callosum, keeping an eye out for the line going into the ventricle. If it is drawn in the ventricle, the line
disappears and there will be a large distance recorded between points clicked. Another obstacle to look
out for is the fornix. When the fornix is present, stop drawing at the most anterior extent where the fornix
attaches to the corpus callosum and jump straight across to the most posterior extent where the two
structures are attached.
References: Figure 31i (fornix present) Figure 31ii Figure 31iii Figure 31iiii
34. Superior Rostral Sulcus
Starting Point: Inferior to Genu of the corpus callosum
Direction: Posterior to Anterior
Ending Point: Medial surface, close to boundary of the dorsolateral surface
Notes: The actual sulcus may begin posterior to the genu of the corpus callosum; however, do not start
posterior to the inner bend of the genu. Make sure to verify the correct starting point and sulcal path via
the mid-sagittal resliced view in Display. The superior rostral sulcus may connect with the cingulate
sulcus. If there is a bifurcation in the anterior aspect of the sulcus, take the superior path, unless the
superior path extends or curves superior to the most anterior point of the genu. In this case, take the
inferior path of the sulcus. Getting to the superior most exit point may require jumping a gyrus. This
takes precedence over continuity with a more inferior path. The posterior end of the superior rostral
sulcus, at times, abuts the para-olfactory sulcus.
References: Figure 34i (end inferior to anterior most point of genu) Figure 34ii Figure 34iii (start level
with inner bend of genu) Figure 34iiii (take more superior branch)
35. Inferior Rostral Sulcus
Starting Point: Inferior to Genu of the corpus callosum
Direction: Posterior to Anterior
Ending Point: Medial surface, close to the boundary of the dorsolateral surface.
Notes: The inferior rostral sulcus will most likely parallel the superior rostral sulcus inferiorally. It may
be interrupted into two or more segments. Jump the interruptions. Make sure to verify the correct sulcal
path via the mid-sagittal resliced view in Display. Do not start the line posterior to the start of the superior
rostral (#34). If a bifurcation exists at the anterior end, stop at the bifurcation. The posterior end of the
inferior rostral sulcus abuts the para-olfactory sulcus.
References: Figure 35i Figure 35ii Figure 35iii Figure 35iiii
33. Paracentral Sulcus
Starting Point: Anterior portion of precentral gyrus
Direction: Superior to Inferior
Ending Point: Ending point of the Anterior Segment of the Cingulate Sulcus
Notes: This sulcus defines the anterior boundary of the paracentral lobule. The term "paracentral lobule"
refers to the continuation of the precentral gyrus of the frontal lobe and the postcentral gyrus of the
parietal lobe on the medial surface of the cerebrum. The paracentral sulcus defines the anterior border of
the paracentral lobule, which is bordered posteriorally by the marginal ramus of cingulate sulcus. If the
cingulate sulcus is interrupted, the interruption will most likely occur at or near the paracentral sulcus.
Since the lobule has, at times, several sulci that can resemble the paracentral sulcus, the best approach to
mapping this sulcus is to mark the anterior portion of the precentral gyrus from the "top view" under "3D
View" menu button in Display. The paracentral sulcus will lie near or often anterior to the anterior border
of the precentral gyrus on the medial surface. Do keep in mind the lobule's general "U" shape, which
houses two gyral regions. This visualization of the lobule will help when determining where the
paracentral sulcus should generally lie. The most common form of the paracentral sulcus is interrupted
into two segments as in Ono p.117 (B). In this instance, draw only the inferior portion that is connected
to the cingulate sulcus. If this form does not exist, look for the paracentral as a side branch extending
superiorally from the cingulate sulcus as in Ono p.117 (A&D). Finally, if neither of these options are
available, draw the paracentral that extends inferiorally from the lateral surface, bordering the lobule as in
Ono p.117 (C). Do not cross the midline superiorally to start the line, make sure by using the "top view"
under "3D View" menu button in Display.
References: Figure 33i (cursor on precentral gyrus)Figure 33ii (split paracentral) Figure 33iii (cursor on
precentral) Figure 33iiii (cursor on precentral)
Double Parallel Anterior Segment of the Cingulate Sulcus: is it there?
The anterior cingulate may be found as part of a double parallel series of anterior segments, or just by
itself.
To determine whether or not a double parallel exists, draw 32a first as the most continuous sulcus, then if
an outer segment exists, draw it as 32c.
32a is the inferior or the inner of the two segments and is always more continuous with the posterior
segment of the cingulate than 32c. If the outer sulcus is more continuous with 32b, there is no double
parallel. That sulcus is 32a.
The inner segment must begin level with or inferior to the plane at the most anterior point of the genu. In
the instance that it appears to begin superior to this plane, do not draw a double parallel. Begin on the
"outer segment" using the guidelines below to determine the starting point. Follow that segment to its end
and jump to the sulcus that is most continuous with the posterior segment of the cingulate (#32b).
The outer segment must begin level with or inferior to the most anterior point of the genu, may only jump
one gyrus (too many jumps), and must end level with or posterior to the most posterior point of the
rostrum in order to be drawn (too short). If these criteria are not met, DO NOT DRAW 32c.
32a. Cingulate Sulcus, Anterior Segment
Starting Point: Anterior to the genu of corpus callosum
Direction: Anterior to Posterior
Ending Point: Intersecting at the Inferior extent of the Paracentral Sulcus
Notes: This segment is present in all brains, just superior to the callosal gyrus. Refer to the rules above
on determining whether or not a double parallel exists. Identify 32a as the sulcus that is most continuous
with 32b. There are two different scenarios involving the starting point for the anterior cingulate sulcus.
In either case, begin by using a straight edged tool (ruler or sheet of paper) that spans over 10 inches in
length. With the 3D brain object in mid-saggital view, place the tool over the plane that passes through
the most inferior point of the splenium and the most posterior point of the rostrum of the corpus callosum.
Then begin the anterior segment of the cingulate sulcus at the intersection of this sulcus with the plane,
regardless of its curve inferiorally and posteriorally. The second scenario involves an anterior cingulate
sulcus that begins superior to the plane prescribed by the inferior splenium and posterior rostrum. In this
case, begin drawing at the beginning of the sulcus regardless of where it stands relative the the plane. Do
not make a jump in the cingulate inferior to the anterior most point of the genu. At the posterior extent, if
the paracentral sulcus meets the cingulate sulcus, end the anterior segment there. If the paracentral sulcus
comes off the dorsolateral surface or does not connect to the cingulate sulcus, end the anterior segment of
the cingulate sulcus at the inferior extent of the paracentral sulcus. The cingulate may be continuous or
interrupted; in either case, the ending point of the anterior segment is the same. NOTE: In the rare case of
a discontinuous anterior cingulate sulcus (ONLY FOR THIS LINE) jump later rather than sooner.
Follow each segment to its end, then make the most direct jump to the segment that is most continuous
with the posterior cingulate (#32b).
References: Figure 32ai (single anterior cingulate) Figure 32aii (starting point below anterior most point
of genu) Figure 32aiii Figure 32aiiii (double parallel anterior cingulate, inner segment: marker on
starting point)
32b. Cingulate Sulcus, Posterior Segment
Starting Point: Inferior to the paracentral sulcus or posterior to the ending point of the anterior segment of
the cingulate sulcus
Direction: Anterior to Posterior
Ending Point: Medial Surface near the dorsolateral surface
Notes: The marginal ramus of the cingulate sulcus defines the posterior border of the paracentral lobule,
a medial region of the cerebrum that spans from the precentral to postcentral gyrus. If the paracentral
sulcus meets the cingulate sulcus, begin the posterior segment there. If the paracentral sulcus comes off
the dorsolateral surface or does not connect to the cingulate sulcus, begin the posterior segment of the
cingulate sulcus at the inferior extent of the paracentral sulcus just posterior to the ending of the anterior
cingulate sulcus. Will frequently exit to the dorsolateral surface; DO NOT CROSS THE MIDLINE. End
the sulcus on the medial surface. Look at the top view to ensure that you have not crossed the midline. It
will frequently branch or bifurcate at the posterior end. If this is the case, take the segment that crosses the
dorsolateral surface between the central and postcentral sulci. If both segments exit between the central
and postcentral sulci, take the most anterior segment.
References: Figure 32bi Figure 32bii (cursor on postcentral sulcus) Figure 32biii Figure 32biiii
32c. Outer Segment of a Double Parallel Anterior Cingulate Sulcus (also referred to as the paracingulate
sulcus)
Starting Point: Anterior to the genu of the corpus callosum, the outer of two double anterior cingulate
sulci present
Direction: Anterior to Posterior
Ending Point: Adjacent or near the Paracentral Sulcus
Notes: This may not be present in all brains. A double parallel anterior cingulate sulcus is present when
there are two sulci that are present, either intersecting the superior rostral sulcus or curving inferiorally
and posteriorally near the genu of the corpus callosum. The outer segment must intersect the superior
rostral or curve inferior to the most anterior point on the genu to be considered the outer segment of a
double parallel anterior cingulate sulcus. It must extend posteriorally to, either level with the most
posterior point of the rostrum of the corpus callosum, or to the paracentral sulcus with only one jump
allowed. If these criteria are not satisfied, do not draw the double parallel. There are two different
scenarios involving the starting point. In either case, begin by using a straight edged tool (ruler or sheet
of paper) that spans over 10 inches in length. With the 3D brain object in mid-sagittal view, place the tool
over the plane that passes through the inferior part of the splenium and posterior rostrum of the corpus
callosum. Then begin the outer anterior cingulate sulcus at the intersection of this sulcus with the plane
regardless of its curve inferiorally and posteriorally. The second scenario involves an outer anterior
cingulate sulcus that begins superior to the plane prescribed by the inferior splenium and rostrum. In this
case, begin drawing at the beginning of the sulcus regardless of where it stands relative to the plane. If the
outer segment meets the paracentral sulcus, end it there. In the case of a discontinuous outer segment,
which occurs more than with the inferior anterior cingulate segment, choose the sulcal path that extends
to the paracentral sulcus, jumping only one gyrus. In the case where the double parallel segment does not
extend to the paracentral, end the segment where the sulcus ends accordingly.
References: Figure 32ci (double parallel cingulate, outer segment: one jump)
36. Parieto-occipital Sulcus
Starting Point: Medial surface, close to the boundary of the dorsolateral surface
Direction: Superior to Inferior
Ending Point: Superior to Calcarine Sulcus
Notes: This sulcus divides the parietal from the occipital lobe. Also demarcates the inferior portions of
parietal and occipital lobes from the temporal lobe. The parieto-occipital sulcus ends at its intersection
with the anterior and posterior portions of the calcarine sulcus. It is easier to visualize it as the anterior
segment of three that constitute a Y, with the remaining segments composed by the posterior calcarine
(posterior segment of Y) and anterior calcarine (stem or inferior segment of Y). It will usually cross to the
dorsolateral surface; to avoid this pick a starting point on the medial surface. If it bifurcates at its superior
end, take the most anterior path that crosses to the dorsolateral surface.
References: Figure 36i Figure 36ii (Y-intersection) Figure 36iii Figure 36iiii
37a. Calcarine Sulcus Anterior Segment
Starting Point: Parieto-occipital sulcus
Direction: Posterior to Anterior
Ending Point: Medial surface inferior to the splenium
Notes: The anterior calcarine continues to the posterior calcarine, yet both are separated by the
intersection of the parieto-occipital sulcus, hence the Y shape. Begin drawing at the Y intersection. The
sulcus may seem to extend in the medial surface of the temporal lobe, but do not extend further than the
inferior most point of the splenium.
References: Figure 37ai Figure 37aii Figure 37aiii Figure 37aiiii
37b. Calcarine Sulcus Posterior Segment
Starting Point: Medial surface near dorsolateral surface in the occipital pole
Direction: Posterior to Anterior
Ending Point: Parieto-occipital sulcus
Notes: The posterior segment will very frequently begin on the dorsolateral surface; pick a starting point
on the medial surface. Be careful not to cross the control line at the posterior extent. The posterior
segment of the calcarine may have an interruption requiring a jump. If the sulcus bifurcates in the
occipital pole, choose the starting point at the point of bifurcation unless it is on the dorsolateral surface.
Ends at the Y intersection.
References: Figure 37bi Figure 37bii (begin at bifurcation) Figure 37biii Figure 37biiii
38. Subparietal Sulcus
Starting Point: Posterior segment of the Cingulate Sulcus
Direction: Anterior to Posterior
Ending Point: At the Y intersection between the Anterior/Posterior Cingulate and Parieto-occipital sulci
Notes: This sulcus is meant to separate the precuneus from the cingulate gyrus. The precuneus is bordered
by the marginal ramus of the cingulate sulcus anteriorally and the parieto-occipital sulcus posteriorally.
The actual sulcus usually includes many branches and frequently resembles an H pattern: blue. Therefore,
it is important to maintain a focus on following the sulcal path that outlines the inferior portion of the
precuneus from the cingulate gyrus. The sulcus begins by intersecting at the point where the marginal
branch of the cingulate begins ascending most rapidly (Intersecting sulcus: red). If no intersection or
branches exist off the posterior cingulate, make the shortest direct jump from the cingulate to the
subparietal. It will frequently bifurcate at the posterior end. Follow the most direct inferior path of the
subparietal sulcus, taking the branches that get you closest to the Y intersection for the shortest jump to
this intersection. Do not draw the line inferior to the Y intersection. Always end the sulcus at the Y
intersection between the Anterior and Posterior Calcarine and Parieto-occipital sulci. If sulcus ends
naturally at parieto-occipital, follow the natural path, but then follow down the parieto-occipital sulcus to
end at the required Y intersection, being very careful not to overlap or cross the lines.
References: Figure 38i (inferior most path) Figure 38ii Figure 38iiiFigure 38iiii
Control Lines
Guidelines for Drawing the Control Lines
*Note: Change line weighting back to 0 before drawing control lines.
Imagine a plane bisecting the inter-hemispheric fissure. Generally, keep the control lines parallel to this
plane without veering too far laterally to accommodate gyrification. Draw lines roughly at the location
which best distinguishes the separation between the lateral and medial surface of the hemisphere. Always
draw control lines in orthogonal views, do not rotate the brain. Be sure to follow curves of the brain to
maintain the difference between the lateral and medial surface.
10m. Olfactory Control Line
Starting Point: Beginning of Olfactory Sulcus
Direction: Anterior to Posterior
Ending Point: End of Olfactory Sulcus
Notes: Draw line next to olfactory sulcus (#6) just off of midline on bottom view.
References: Figure 10mi (bottom view) Figure 10mii (side view)
17m. Olfactory-Superior Frontal Control Line
Starting Point: Most anterior point of Olfactory Sulcus
Direction: Inferior to Superior
Ending Point: Beginning of Middle Frontal/Superior Sulcus
Notes: Begin drawing on "bottom view", then switch to "front view" for remaining portions of segment.
References: Figure 17mi (front view) Figure 17mii (side view)
50m. Superior Frontal-PreCentral Control Line
Starting Point: Beginning of Superior Frontal sulcus
Direction: Anterior to Posterior
Ending Point: Precentral Sulcus
Notes: Start drawing in "front view", end drawing in "top view". Begin segment level with the start of the
Superior Frontal sulcus (#5).
References: Figure 50mi (front view) Figure 50mii (top view) Figure 50miii (side view)
51m. Precentral-Marginal Ramus of Posterior Cingulate Control Line
Starting Point: Precentral Sulcus
Direction: Anterior to Posterior
Ending Point: Marginal Ramus (Posterior Segment) of the Cingulate Sulcus
Notes: In mid-saggital view, create a marker for the point at which the marginal ramus of the posterior
Cingulate (#32b) exits the medial surface. This point demarcates the end of the segment.
References: Figure 51mi (top view) Figure 51mii (side view)
53m. Marginal Ramus of Posterior Cingulate - Parieto-Occipital Control Line
Starting Point: Marginal Ramus of Posterior Cingulate
Direction: Anterior to Posterior
Ending Point: Parieto-Occipital Sulcus
Notes: In mid-saggital view, create a marker for the point at which the Parieto-Occipital (#36) exits the
medial surface. This marks the end of the control line. Start drawing in "top view." End the line in "back
view."
References: Figure 53mi (top view) Figure 53mii (back view) Figure 53miii (side view)
54m. Parieto-Occipital - Calcarine Control Line
Starting Point: Parieto-Occipital Sulcus
Direction: Anterior to Posterior
Ending Point: Calcarine Sulcus
Notes: In mid-saggital view, create a marker for the point at which the Calcarine exits the medial surface.
If the Calcarine ends without exiting the medial surface or branches at its posterior-most extent before
reaching midline, create the marker level with the starting point of the posterior calcarine (#37b) at the
medial/lateral boundary. Start the segment at the marker previously created for the point at which the
Parieto-Occipital exits the medial surface. End the segment at the marker just created for the exit of the
Calcarine.
References: Figure 54mi (back view) Figure 54mii (side view)
55m. Occipital Control Line
Starting Point: Calcarine Sulcus
Direction: Anterior to Posterior
Ending Point: Termination of Collateral Sulcus
Notes: Start drawing in "back view," end drawing in "bottom view".
References: Figure 55mi (back view) Figure 55mii (bottom view) Figure 55miii (side view)
This protocol was created and tested by the following people (whom you can email with any questions or
concerns):
Michael Mega
Paul Thomson
Stephanie Dittmer
Kiralee Hayashi
Chris Zoumalan
*Revised by Elizabeth Sowell
Suzanne Welcome
Amy Henkenius
FOR SURFACE EXTRACTION, PAUL THOMPSON SCRIPT
cortical_surface.pl
#!/usr/local/bin/perl
#
# Script to create a cortical surface from an MRI, given an intensity threshold
#
# Usage: cortical_surface.pl volume.mnc output_file.obj threshold_value
#
[transform.xfm]
#
$arch = `hostype`; chomp($arch);
$dirprefix = "/usr/local/icbm/MNI";
$exec_dir = $dirprefix . "/bin.$arch";
require "$dirprefix/scripts/utils.pl";
#--- get the 3 arguments
$volume = shift;
$output_file = shift;
$threshold = shift;
$transform = shift;
#--- if not all 3 necessary arguments are present, quit with usage message
if( ! $threshold ) {
die( "\n" .
"Usage: $0 volume.mnc output_file.obj threshold_value \n" .
"
[transform.xfm]\n" .
"\n" .
" Creates a cortical surface from the specified volume and\n" .
" threshold. If the volume is not in Talairach space,\n" .
" a transform must be specified.\n\n" );
}
#--- if the output file does not have an ending, give it the ending ".obj"
if( ! ( $output_file =~ /\..*/ ) ) {
$output_file = $output_file . ".obj";
}
#--- setup the parameters of the deformation
$deform_dir = $dirprefix . "/Surface_deformation";
$model_file = $deform_dir. "/avg_model_64.obj";
$tight_model = "-1 .5 $model_file -.04 .04";
$loose_model = "-1 .5 $model_file -.08 .08";
$tight_elastic = "-1 .5 parametric -.08 .08";
$loose_elastic = "-1 .5 parametric -.15 .15";
$step
= ".1 .1 30 0 $threshold $threshold - 0 0 0";
#--- define the deformation schedule, each entry is 4 items consisting of:
#
#
box_filter_width
#
number of polygons in deforming surface
#
model constraints to use
#
number of iterations to run deformation
#
# When the number of polygons increases from one entry to the next
# the deforming surface will be subdivided.
#--@schedule = (
6 , 8192, $tight_model, 100,
4 , 8192, $tight_model, 100,
4 , 8192, $loose_model, 100,
4 , 32768, $tight_elastic, 100,
3 , 32768, $tight_elastic, 100,
3 , 131072, $tight_elastic, 20,
2 , 131072, $tight_elastic, 20,
2 , 131072, $loose_elastic, 20,
1.5, 131072, $loose_elastic, 20,
0 , 131072, $loose_elastic, 50,
0 , 131072, $loose_elastic, 100
);
$sched_size = 4;
#--- copy the initial model to the output file
if( $transform )
{
system( "$exec_dir/transform_objects $model_file $transform $output_file invert");
}
else
{
system( "cp $model_file $output_file" );
}
#--- the deforming surface starts with 8192 polygons
$n_polys = 8192;
#--- perform each component of the deformation schedule
for( $i = 0; $i < @schedule; $i += $sched_size )
{
#--- get the 4 components of the deformation schedule entry
( $filter, $size, $model, $iters ) = @schedule[$i,$i+1,$i+2,$i+3];
#--- if the schedule size is greater than the current number of
#--- polygons in the deforming surface, subdivide the deforming surface
while( $size > $n_polys )
{
&system_call( "$exec_dir/subdivide_polygons $output_file $output_file" );
$n_polys *= 4;
}
#--- if the scheduled size is not a multiple of 4 times the previous
#--- deforming surface size, then this is an error
if( $n_polys != $size )
{ die "invalid # polygons in deformation schedule"; }
#--- check if the volume needs to be blurred out first
if( $filter > 0 )
{
$tmp_volume = "/tmp/fit$$.mnc";
&system_call( "$exec_dir/box_filter_volume $volume $tmp_volume " .
" $filter $filter $filter world byte" );
$used_volume = $tmp_volume;
}
else
{
$used_volume = $volume;
}
#--- finally, deform the surface, using the schedule parameters
&system_call( "$exec_dir/deform_surface $used_volume none 0 0 0 ".
" $output_file $output_file none 0 1 " .
" $model $step $iters 0.01 0.0 " );
if( $filter > 0 )
{ unlink( "$tmp_volume" ); }
}
print( "Surface extraction finished.\n" );
E. SPECIFIC BRAIN LABELS
Anatomy
Ventricles
Caudal Anterior Cingulate
Subcallosal Cingulate
Post Central
(label value 1)
(label value 2)
(label value 3)
(label value 4)
Ant. Parahippocampal Gyrus
Rostral Anterior Cingulate
Lateral Orbital Frontal
Precuneus/Posterior Cingulate
Nucleus Accumbens
Cerebellum
Thalamus
Caudate
Temporal Pole
Lenticular Nuclei/Putaman
Hippocampus
Substania Nigra
Basalmedial Diencephalon
Occipital
Post Parahippocampal Gyrus
Amygdala
Midbrain
Pons
Medulla
Superior Parietal Lobule
Inferior Parietal Lobule
Superior Temporal
Middle Temporal
Inferior Temporal
Medial Orbital Frontal
Inferior Frontal
Middle Frontal
Precentral
Insula
Superior Frontal
(label value 5)
(label value 6)
(label value 7)
(label value 8)
(label value 9)
(label value 10)
(label value 11)
(label value 12)
(label value 14)
(label value 17)
(label value 18)
(label value 23)
(label value 24)
(label value 86)
(label value 88)
(label value 100)
(label value 110)
(label value 111)
(label value 112)
(label value 123)
(label value 126)
(label value 135)
(label value 138)
(label value 141)
(label value 150)
(label value 165)
(label value 168)
(label value 172)
(label value 175)
(label value 200)
Ventricle
• Bounded by Caudal Anterior Cingulate, Rostral Anterior Cingulate, and Posterior Cingulate
(subcortical)
Caudal Anterior Cingulate
• In between Precentral and Ventricles (subcortical)
Subcallosal Cingulate
• Below Rostral Anterior Cingulate and above Medial Orbital Frontal (subcortical)
Post Central
• Surface area; bounded by Central Sulcus, Postcentral Sulcus, and Sylvian Fissure
Anterior Parahippocampal Gyrus
• Below Hippocampus and Amygdala (subcortical)
Rostral Anterior Cingulate
• Below Superior Frontal and next to Caudal Anterior Cingulate (subcortical)
Lateral Orbital Frontal
• At the bottom of the brain, underneath Superior Frontal region, Middle Frontal region
Precuneus/Posterior Cingulate
• In between the Occipital and Caudal Anterior Cingulate (subcortical)
Nucleus Accumbens
• Below Caudate and above Medial Orbital Frontal (subcortical)
Cerebellum
• Below Occipital and posterior to Brain Stem
Thalamus
• Near the posterior part of Ventricle (subcortical)
Caudate
• Next to the anterior part of Ventricle (subcortical)
Temporal Pole
• At the tip of Temporal Lobe
Lenticular Nuclei/Putaman
• Embedded in Insula (subcortical)
Hippocampus
• Below Midbrain and above Anterior Parahippocampal Gyrus (subcortical)
Substania Nigra
• Within Midbrain (subcortical)
Basalmedial Diencephalon
• Below Ventricles; in the vicinity of Midbrain and Medial Orbital Frontal (subcortical)
Occipital
• At the anterior region of the brain (at the back)
Post Parahippocampal Gyrus
• In the vicinity of Anterior Parahippocampal Gyrus and Hippocampus (subcortical)
Amygdala
• Bounded by Anterior Parahippocampal Gyrus, Lateral Orbital Frontal, Midbrain, and Hippocampus
(subcortical)
Midbrain
• In between Thalamus and Pons (subcortical)
Pons
• Below Midbrain and next to Cerebellum (subcortical)
Medulla
• Below Pons and next to Cerebellum (subcortical)
Superior Parietal Lobule
• Bounded by Transverse Occipital Sulcus, Postcentral Sulcus, and Intraparietal Sulcus
Inferior Parietal Lobule
• Bounded by Postcentral Sulcus and Intraparietal Sulcus
Superior Temporal
• Approximately bounded by Superior Temporal Sulcus Main Body (In between Inferior Parietal Lobule
and Middle Temporal)
Middle Temporal
• Below Superior Temporal and above Inferior Temporal
Inferior Temporal
• Bounded by Inferior Temporal Sulcus
Medial Orbital Frontal
• Next to Subcallosal Cingulate and Lateral Orbital Frontal
Inferior Frontal
• In between Middle Frontal and Lateral Orbital Frontal
Middle Frontal
• In between Inferior Frontal and Superior Frontal
Precentral
• Bounded by Precentral Sulcus and Central Sulcus
Insula
• Bounded by White Matter, Middle Frontal, Superior Temporal, Precentral, and Post Central
Superior Frontal
• Next to Middle Frontal
F. SPECIALIZED AREA ANALYSIS FOR CORPUS
CALLOSUM USING PAUL THOMPSON’S SCRIPTS
In accordance with the traditional approach of performing regional analyses, the callosal renderings will
be reoriented to maximize callosal length and divided into five vertical partitions representing the (1)
splenium, (2) isthmus, (3) posterior midbody, (4) anterior midbody, and (5) anterior third. Callosal area
measures will be acquired in mm2 for each callosal segment.
Subdivide and measure the CC according to the Witelson Parcellation Sheme. This step takes the CC and
parcellates it according to a standard, which means it is redigitized to fit this standard so that it can now
be separated (like the standard) to fit the 5 Witelson-Pieces.
 First make sure, the CCs are in the right orientation, after saving your file in Multitracer, it will
save your file in the same space in which the MRI was recorded. (what do you mean by the right
orientation-just maximizing callosal length? How do you make sure they are or not?) before
proceeding
 If necessary, reorient the callosal outlines with reslice_ucf from the AIR package, if your data is
in 305 space, you can use the following script… and what is this original file?
/data/woods/AIR5.2.5/reslice_ucf AIR_File ORIG_CC_File NEW_CC_File)
 Split the CC into Witelson-Pieces by executing the script below (after modifying it for your file
names). This script first redigitizes the CC contour at a higher resolution so that when it divides
it, it does it more precisely (using the command redig_hi) and then breaks it into the 5
standardized Witelson-Pieces (using the command witelson2).
#!/bin/csh
#this is a file which chops the callosum in five pieces
mkdir contin_area_cc_pieces_2
foreach x (ab01 ab12 ac27 al93 at37)
foreach side ( _rigid_m _rigid_r _rigid_l )
echo $x$sidecce
/nethome/users/thompson/HIPPO/SGI/redig_hi 1 2 3 4 5 6 r_$x$side.ucf > redig_$x$side.ucf
/sig/woods/UCFtest/witelson2 1 redig_$x$side > ./contin_area_cc_pieces_2/wit_piece1_$x$side.ucf
/sig/woods/UCFtest/witelson2 2 redig_$x$side > ./contin_area_cc_pieces_2/wit_piece2_$x$side.ucf
/sig/woods/UCFtest/witelson2 3 redig_$x$side > ./contin_area_cc_pieces_2/wit_piece3_$x$side.ucf
/sig/woods/UCFtest/witelson2 4 redig_$x$side > ./contin_area_cc_pieces_2/wit_piece4_$x$side.ucf
/sig/woods/UCFtest/witelson2 5 redig_$x$side > ./contin_area_cc_pieces_2/wit_piece5_$x$side.ucf
end
end
Check if this processed correctly segmented the CC:
 Log in on autarch (ssh autarch…) (necessary?)
 View the UCF file using viewUCF
viewUCF SEGMENTED-CC_File or ~thompson/vu SEGMENTED-CC_File

Compare with figure , there should be 5 different segments per callosal outline:
o Wit1
(Splenium)
o Wit2
(Isthmus)
o Wit3
(Posterior
Body)
o Wit4
(Anterior
Body)
o Wit4
(Anterior
Third).
Measure the area of each callosal segment:
ucfmeasure –area SEGMENTED-CC_File
Other tips or troubleshooting:
Sometimes the code that splits the callosal outline automatically into Top and Bottom does not work. So
if you want to invest some extra time, do the splitting yourself by outlining callosal Top and Bottom in
MultiTracer (and save it as two files). Then you can skip these processing steps:
~thompson/HIPPO/SGI/cc_split_top_bottom 1 2 3 4 5 6 ${x} > TOP_${x}
~thompson/HIPPO/SGI/cc_split_top_bottom 2 2 3 4 5 6 ${x} > BOTTOM_${x}
G. LONI SKULL STRIPPING PROTOCOL

Work on the coronal view. Use the sagittal and horizontal views as references.

Starting from the posterior of the brain is easier. This is because you can use “Space” “F” “N” to
copy the previous slice (posterior) to the next one (anterior). You can; however, start from the
anterior of the brain. To change your slice in the coronal view, click on the sagittal view (i.e. to begin
at the back, the most posterior point, and to begin in the front, the most anterior point).
As a general rule of thumb, areas that are extremely bright are nerve tracts, which need to be
excluded.

1. CEREBELLUM INCLUDED
a) Posterior aspect of the brain
In the coronal view, use “+” and “-” to find the starting slice. Click on the region and use the sagittal and
horizontal views to verify.
Coronal view
Sagittal view
Horizontal view
b) Medial Aspect of Posterior Brain Regions
Sometimes the sagittal view may be confusing in this region. Use the other two views to make your
decision. Temporarily removing the label also helps.
c) Confluence of Sinuses
This area is located where the occipital lobe meets the cerebellum. Exclude this area before the two
cerebellar hemispheres meet.
Sagittal view
Coronal view
Once the two cerebellar hemispheres meet, include the medial confluence of sinuses for masking
convenience. Do not include the lateral confluence of sinuses.
Coronal view
d) Spinal Cord and Medulla
When the spinal cord appears in the coronal view, make the label level with the lobes of the cerebellum,
one of which may disappear earlier than the other in the due to asymmetry.
Coronal views
Maintain that level until the natural boundary appears.
Coronal views
e) Cerebellum area
As you move anteriorly, this area can look confusing. Here are some photos that show the boundary of the
cerebellum in three views. The cursor location indicates areas that need attention.
Sagittal view
Coronal view
Horizontal view
f) Trigeminal Nerve
Exclude this structure.
Sagittal view
Coronal view
g) End of Pons
This region contains three nerve tracts that need to be taken out.
Oculomotor nerve
Coronal view
Sagittal view
Corticobulbar and Corticospinal tracts
Coronal view
Sagittal view
h) Temporal lobe
The medial and inferior boundary can be confusing, but it is usually faintly visible. Try switching the
label on and off and using the other two views to make your decision. The arrows indicate the optic tract
and the optic chiasm, which need to be taken out. If the optic tract is barely visible or is not easily
accessible in the coronal view, leave it for convenience.
Sagittal views
Coronal views
When the temporal lobe begins to shrink in the coronal view, clean up the meninges and nerve tracts on
the edges as much as possible but leave those if they are deeply embedded between the temporal lobe and
the inferior frontal lobe. Arrows indicate structures that should not be labeled.
Horizontal view
Coronal view
When the temporal lobe starts to disappear from the coronal view, use the sagittal view to find the ending
point of the temporal lobe.
Coronal views
i) Anterior frontal lobe
The arrows indicate areas that need attention.
Coronal views
Sagittal view
j) Superior and lateral boundary
Switch the label on and off to better distinguish the gray matter, CSF, and the meninges. Here are some
examples; the cursors and arrows indicate areas that need attention.
Horizontal and Coronal views
2. CEREBELLUM EXCLUDED
In the coronal view, follow the natural boundary of the cerebellum and exclude the confluence of sinuses.
Arrows indicate areas that need attention.
Coronal view
Sagittal view
The arrows indicate a line that will start to fade. Exclude the brainstem until the line begins fading.
Then keep your horizontal cut off line above the cerebellum and above the trochlear IV nerve.
Coronal view
Sagittal view
When the midline starts to show in the pons region, use the end of the midline as your cut off boundary.
Coronal views
From this point on, label areas are the same as those in masks including the cerebellum.