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, 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.
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.
First, 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 -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid OAS2_0004_MR1 recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid OAS2_0004_MR2
Take a look at your output volumes (w/o _fixed), or our edited volumes below, 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 -autorecon2 -autorecon3 -subjid OAS2_0004_MR1 recon-all -autorecon2 -autorecon3 -subjid OAS2_0004_MR2
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 -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.
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 longitudinal before (left) and after (right) images of OAS2_0004_MR2_long.OAS2_0004_fixed at slice 170.
For more details on skull strip errors and the different ways to fix them, refer back to the Troubleshooting Skull Strip Tutorial.