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.
Viewing using tkmedit
Very rarely, you will see FreeSurfer fail completely in the skullstrip step (usually associated with many other errors) as is clearly the case in the following example. For the purpose of this tutorial we will only focus on and fix the skull strip error.
Please take a look at subject OAS2_0004 in tkmedit, examine all cross, longs, and base (in separate terminals):
tkmedit OAS2_0004 brainmask.mgz -aux T1.mgz -surfs tkmedit OAS2_0004_MR1 brainmask.mgz -aux T1.mgz -surfs tkmedit OAS2_0004_MR2 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
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. Don't be overwhelmed by other problems presented in this case. You should always find out if there is a skullstrip error first, fix that, then attack the rest of the problems. You'll be surprised how much less you'll have to go through in the end.
Take it one step at a time. First, take a look at the coronal slice 125 for OAS2_0004_MR1, you can see that the entire neck is still present.
Now look at OAS2_0004_MR2. This timepoint looks even worse with parts of the skull still present and parts of the brain stripped off. If you scroll to slice 66, you will see that a great part of the brain is missing. Below is the comparison between the brainmask.mgz and T1.mgz for slice 66.
Fixing the problem
The best way to fix a problem like this is to adjust the watershed parameters. As mentioned earlier, this can only be done on the cross-sectionals, and you'll have to use the edited cross-sectionals to recreate the base and the longitudinals afterwards.
Adjust the watershed parameters for both MR1 and MR2 using the following commands. Feel free to run these commands (separately) since this step is fairly quick.
recon-all -subjid OAS2_0004_MR1 -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas recon-all -subjid OAS2_0004_MR2 -skullstrip -wsthresh 55 -clean-bm -no-wsgcaatlas
If you ran the commands, take a look at your output volumes (directory w/o _fixed), or simply check our edited volumes, and verify that the result of the new skull stripping is correct:
tkmedit OAS2_0004_MR1_fixed brainmask.mgz -aux T1.mgz -surfs tkmedit OAS2_0004_MR2_fixed brainmask.mgz -aux T1.mgz -surfs
After you are satisfied with the results, remember to run the rest of the cross sectional recon-all steps for all timepoints that you made an adjustment to:
recon-all -subjid OAS2_0004_MR1 -autorecon2 -autorecon3 recon-all -subjid OAS2_0004_MR2 -autorecon2 -autorecon3
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 (remove/rename the base dir if it existed, e.g. mv OAS2_0004 OAS2_0004_old, before running this):
Recreating base and longs
recon-all -base OAS2_0004 -tp OAS2_0004_MR1 -tp OAS2_0004_MR2 -all
Then, the final step is to recreate the longitudinals once base and cross sectional runs are complete:
recon-all -long OAS2_0004_MR1 OAS2_0004 -all recon-all -long OAS2_0004_MR2 OAS2_0004 -all
**NOTE: When recreating the base and longitudinals, it is recommended to remove or rename the existing base and longitudinal directories and start those processes from scratch, if possible.
Viewing final results
You can examine the corrected version of the 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_fixed brainmask.mgz -aux T1.mgz -surfs tkmedit OAS2_0004_MR2.long.OAS2_0004_fixed brainmask.mgz -aux T1.mgz -surfs
You should see the same improvement in the skull strip for OAS2_0004_MR2.long.OAS2_0004 as well. Note that, although much has been fixed, there are still problems here that need special treatment (e.g. inclusion of dura in the surfaces).
For more details on skull strip errors and the different ways to fix them, refer back to the Troubleshooting Skull Strip Tutorial.