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Fixing a bad skull strip
*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.
As you can see, the skull strip for this subject is very poor for both timepoints MR1 and MR2, therefore affecting the results of the base and the longitudinals downstream.
If you look at the coronal slice 158 for OAS2_0004_MR1_before, you can see that the entire neck is still present. If you scroll down to slice 45, you can see that part of the right hemisphere is missing, but is present in T1.mgz
The similar thing happened to OAS2_0004_MR2_before. At slice 170, a large part of the brain is missing while the neck is still present.
The best way to fix a problem like this is to adjust the watershed parameters. This can only be done on the cross-sectionals, and you can use the edited cross-sectionals to recreate the base and the longitudinals afterward.
First, adjust the watershed parameters for both MR1 and MR2 using the following command.
recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid OAS2_0004_MR1_before and recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid OAS2_0004_MR2_before
Take a look at your output volume (brainmask.mgz has been changed) along with the original T1 volume (T1.mgz), and verify the result of the new skull stripping is correct.
tkmedit OAS2_0004_MR1_before brainmask.mgz -aux T1.mgz -surfs tkmedit OAS2_0004_MR2_before brainmask.mgz -aux T1.mgz -surfs
The output for both should look like this:
After you are satisfied with the results, remember to run the rest of the recon-all steps for all timepoints that you made an adjustment to.
recon-all -autorecon2 -autorecon3 -subjid OAS2_0004_MR1_before recon-all -autorecon2 -autorecon3 -subjid OAS2_0004_MR2_before
To save time, you can check in with the recon-all-status.log in the scripts directory of these subjects to see if the normalization step is complete. Once that step is complete, you can start recreating your base.
recon-all -base OAS2_0004 -tp OAS2_0004_MR1_before -tp OAS2_0004_MR2_before -all
Then, the final step is to recreate the longitudinals.
recon-all -long OAS2_0004_MR1_before OAS2_0004 -all recon-all -long OAS2_0004_MR2_before OAS2_0004 -all
**NOTE: When recreating the base and longitudinals, it is better if you remove the existing base and longitudinal directories or rename them to something else and remove them.
You can examine the corrected version of base and longitudinals by using the following commands in separate terminals.
tkmedit OAS2_0004 brainmask.mgz -aux T1.mgz -surfs tkmedit OAS2_0004_MR1.long.OAS2_0004 brainmask.mgz -aux T1.mgz -surfs tkmedit OAS2_0004_MR2.long.OAS2_0004 brainmask.mgz -aux T1.mgz -surfs
This is only one example of a skull strip error, for more details on this type of error, you can read about it here.