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| For the longitudinal stream, it is recommended that you make wm.mgz edits to the base. That is, if you are not using your cross-sectional data. This is because even though the long copies the wm.mgz from the cross, it takes the surfaces from the base, and if the base surfaces did not improve, neither will the long. The only way to make correction to the base surfaces themselves is to edit wm.mgz on the base. Therefore, making wm.mgz right on the base will save you a lot of time. So if you are using your cross-sectional data, then you should make edits to both stages (all cross time points and base) in order for the surfaces to improve in the long. | For the longitudinal stream, it is recommended that you make wm.mgz edits to the base. This is because even though the long transfers manual wm edits from the cross, it still takes the surfaces from the base, and if the base surfaces did not improve, neither will the long. The only way to make corrections to the base surfaces themselves is to edit wm.mgz on the base. Therefore, making wm.mgz right on the base can save you a lot of time. Of course it is best to edit all stages (all cross time points and base), but often it is sufficient to edit only the base. |
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Alternatively you could fix such problems in the cross and your edits will get automatically transferred into the long runs. |
Making white matter edits
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.
For the longitudinal stream, it is recommended that you make wm.mgz edits to the base. This is because even though the long transfers manual wm edits from the cross, it still takes the surfaces from the base, and if the base surfaces did not improve, neither will the long. The only way to make corrections to the base surfaces themselves is to edit wm.mgz on the base. Therefore, making wm.mgz right on the base can save you a lot of time. Of course it is best to edit all stages (all cross time points and base), but often it is sufficient to edit only the base.
Were you able to find the area that needs intervention? Here is what we found. You can see below on the brainmask.mgz (left) that the pial surface is cutting through the wm. If you toggle to the wm.mgz (right), you can see that there are a few wm voxels missing.
This happens also at the tip of the lh temporal lobe several slices away.
Add wm voxels to connect the wm together in all the slices that need it. Here is what we did.
After you are satisfied with your edits, save the aux volume and rerun the base.
recon-all -base OAS2_0185 -autorecon2-wm -autorecon3
After that is done, check the surfaces on base using tkmedit.
tkmedit OAS2_0185_fixed brainmask.mgz -aux wm.mgz -surfs
This is what it should look like, slice 168 (left) and slice 163 (right).
When the surfaces are all corrected, you can recreate the long (make sure you remove the long directories before the rerun - or at the very least, remove the wm.mgz files in all the mri directories).
recon-all -long OAS2_0185_MR1 OAS2_0185 -all recon-all -long OAS2_0185_MR2 OAS2_0185 -all
Inspect your output in tkmedit.
tkmedit OAS2_0185_MR1.long.OAS2_0185_fixed brainmask.mgz -aux wm.mgz -surfs tkmedit OAS2_0185_MR2.long.OAS2_0185_fixed brainmask.mgz -aux wm.mgz -surfs
See here that the improved surfaces in the base also correct the surfaces in the long. Compare MR1.long slice 164 in the before (left) and after (right) images below.
The same improvement should have occurred with MR2.long.
Notice that the long isn't perfect. Around slice 166-169 for both MR1 and MR2, the wm is disconnected again. Here, you can just connect those voxels the same way you did with the base. Correct any other errors you see in the long, then run the following commands.
recon-all -long OAS2_0185_MR1 OAS2_0185 -autorecon2-wm -autorecon3 recon-all -long OAS2_0185_MR2 OAS2_0185 -autorecon2-wm -autorecon3
Alternatively you could fix such problems in the cross and your edits will get automatically transferred into the long runs.