Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
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.