Correcting Pial Surfaces
To follow this exercise exactly be sure you've downloaded the 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.
The pial surface is created by expanding the white matter surface so that it closely follows the gray-CSF intensity gradient as found in the brainmask.mgz volume. Once an accurate white surface is created then you can work on correcting the pial surface if needed. The pial surface boundary and white matter surface boundary should not cross. After the pial surface has been generated, it's a good idea to visually check it for defects that may have been created during automatic topology fixing. To check the pial surface, it may be loaded into tkmedit and viewed along with the brainmask.mgz volume. If the surface appears not to follow the gray-CSF boundary in the volume, edits may be required.
Editing the Volume
Subject pial_edits_before is an example of the pial surface including non-cortex within the boundaries. This page will take you through fixing this and other similar problems with the pial surface including non-cortex material.
First, make sure you have pial_edits_before loaded in tkmedit:
tkmedit pial_edits_before brainmask.mgz -surfs
Use the arrow keys to go through the volume slice by slice, and view the pial surface (red line) and white matter surface (yellow line). Notice the bright diagonal line in slice 157 that has caused the pial surface to expand past the actual pial boundary. This is the result of a bad segmentation incorporating a piece of the dura within the pial surface.
To fix this type of error you can simply edit away the offending voxels from the brainmask.mgz volume. To do this you will need to select the edit voxels tool and set the brush to a size and shape comfortable for you. A circle brush of radius 2 works well for this edit. In the tkmedit toolbar, go to Tools -> Configure Brush Info... Set Radius to 2, and Shape to "Circle". Close the configuration menu, and click the "Edit Voxels" button in tkmedit toolbar.
Find a place in the image where the dura is causing errors in the segmentation. Use the right mouse button to delete the voxels. It is not necessary to completely remove the dura to get an adequate pial surface, but it is good to do so until you are more familiar with manual editing. When you are finished removing the bright diagonal line in slice 157, it should look like this:
Continue on the other slices until the dura is removed.
Ctrl-z and Edit -> Undo Last Edit in tkmedit only allow you to go back one edit. If you remove too many voxels, you can use the clone tool to paint areas back in from the original T1 volume. Load T1 as aux volume. To paint voxels, go to Tools -> Configure Volume Brush... , in the tkmedit toolbar.
Set Mode to "Clone", and Clone Source to "Aux Volume". To change the size and shape of your brush, go to:
Tools -> Configure Brush Info...
Select a radius and shape of the brush. Click the "Edit Voxels" button in tkmedit toolbar and use the middle button on the mouse to paint in voxels from the auxiliary volume
At any time, you can save the changes you've made to the brainmask.mgz volume by selecting 'Save Volume' in tkmedit's 'File' menu, and clicking 'OK'
You can check your result by viewing the brainmask.mgz volume in the pial_edits_after directory.
Regenerating the Surface
When you are finished editing the voxels, you will need to regenerate the surfaces. Since the white matter hasn't been changed, you don't need to resegment the volume. You can regenerate the pial surface with:
recon-all -autorecon-pial -subjid pial_edits_before
Do not run this command if you are conducting the tutorial! This step will take a long time and there is no need to run it for the tutorial purposes.
Edits to correct pial surface extension into cerebellum
The brain.finalsurfs.manedit.mgz volume will allow for the correction of a particular type of problem involving pial surface misplacement whereby parts of the pial surface have extended into the cerebellum in certain areas. It is only in this case where the pial surface extends into cerebellum where the brain.finalsurfs.manedit.mgz volume should be edited. For all other non-cerebellum pial surface problems, brainmask.mgz should be edited. This cerebellum / pial surface problem can be fixed by removing those cerebellum voxels and other surrounding problematic voxels in the brain.finalsurfs.manedit.mgz volume such that upon running recon-all, the pial surface will be pulled in as desired, bordering only gray matter/ CSF boundary, and not jutting into the cerebellum. If only edits to this volume are made on a subject, it is sufficient to re-run recon-all from the point of these edits using the flag -autorecon3. Note that you must create brain.finalsurfs.manedit.mgz by copying it from brain.finalsurfs.mgz:
cd <subjid>/mri cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz
You do not need to do this for this tutorial. If you're interested, please refer to the brain.finalsurfs section on the Longitudinal Tutorial here.