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Fixing a bad skull strip

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 158 for OAS2_0004_MR1, 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 in brainmask.mgz, but is present in T1.mgz.

The same happened to OAS2_0004_MR2. At slice 170, a large part of the brain is missing while the neck is still present.

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):

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.

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

Compare the base in the before (left) image at slice 173 and after (right) image at the corresponding slice 180.

And here are the longitudinals for OAS2_0004_MR1.long.OAS2_0004. Before (left) at slice 164 and after (right) at the corresponding slice 171.

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.