| Deletions are marked like this. | Additions are marked like this. |
| Line 20: | Line 20: |
| Scroll through this subject and find the location where the white matter is being excluded from the surface. In subject 4 this happens around coronal slice 161. | Scroll through this subject and find the location where the white matter is being excluded from the surface. In subject 4 this happens around coronal slice 149. |
| Line 34: | Line 34: |
| After adding the control points, go to '''File -> Save Control Points'''; this will create a file called <subject name>/tmp/control.dat. With your control points saved you can re-run with the following command: | After adding the control points, go to '''File -> Save Control Points'''; this will create a file called <subject name>/tmp/control.dat. Using the added control points the subject should now look like this: |
| Line 36: | Line 36: |
|
attachment:subject4_afterCPs.jpg Once your control points saved you can re-run with the following command: |
|
| Line 41: | Line 44: |
|
You can compare the temporal lobe of this subject on coronal slice 149 before (left) and after (right) control points. The before image shows large amounts of white matter being left out of the lh.white surface (yellow line). The after image shows the placement of two control points (green crosshairs) along this temporal lobe strand and the inclusion of the white matter in the lh.white surface. |
[wiki:FsTutorial top] | [wiki:FsTutorial/MorphAndRecon previous]
To follow this exercise exactly be sure you've downloaded the [wiki:FsTutorial/Data tutorial data set] before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.
Using Control Points to Fix Intensity Normalization
Sometimes the intensity normalization step will fail because it cannot determine the proper intensity for white matter. The result is an erroneous white matter segmentation. A control point is a manually selected location in the volume that the user feels sure is inside the white matter boundary, and subsequently should be normalized to 110.
Manually Selecting Control Points
Subject 4 is an example of a subject that needs some control points in order to ensure that the voxels are normalized correctly and then included in the wm.mgz volume. This page will walk you through setting control points to fix this type of problem.
First, make sure you have subject4_before loaded into tkmedit:
tkmedit subject4_before brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white
Scroll through this subject and find the location where the white matter is being excluded from the surface. In subject 4 this happens around coronal slice 149.
attachment:subject4_beforeCPs.jpg
To add control points you will first need to select the Edit Control Points tool attachment:icon_control_points.gif. Middle-clicking will create a control point; right-clicking will delete a control point. As you select control points, they will appear as small green crosshairs. Select a few control points around your trouble areas, space them out throughout the brain and on different slices. You want to pick points in a region where the wm intensity is lower than it should be (that is, less than 110).
Some general tips for adding control points:
- Control points should only be added in regions that are definitely white matter (i.e., not in the cortex, cerebelum, brainstem, or outside of the skull).
- Control points should also only be added to regions that are NOT 110, a control point in a region that is already normalized to 110 will be useless.
Control points should NOT be used to try and normalize a brain lesion to 110. These defect should be fixed with [wiki:FsTutorial/WhiteMatterEdits white matter edits]
- Control points can help recover thin wm strands that are dark by putting some at the base of the strand.
- Control points are also useful in areas of very bright intensity.
- Start off with a few control points spread out in your trouble area. You may need to add more. With experience you will be able to determine how many is appropriate given your specific subject.
After adding the control points, go to File -> Save Control Points; this will create a file called <subject name>/tmp/control.dat. Using the added control points the subject should now look like this:
attachment:subject4_afterCPs.jpg
Once your control points saved you can re-run with the following command:
recon-all -autorecon2-cp -autorecon3 -subjid subject4_before
This step will take a long time so there is no need to run it for the purposes of this tutorial.