Hi, everone. The skull strip quailtiy from the reconall freesurfer was bad. I know I can manually revise the watershed parameters, but it will take a whil since I had over 30 patients. Therefore, is it possible to use the good quaility of brian mask in the recon-all process so that I can skilp the skull strip process?
At least in recent versions, you can pass
-noskullstrip -xmask /path/to/good/mask.nii.gz.
Thanks for your reply. Then If I use my own mask.nii.gz with using
-noskullstrip -xmask /path/to/good/mask.nii.gz , then will the reconall starts the first step of segmentation (autorecon1) using the brain mask I gave?
You need to pass
-noskullstrip when you run
-autorecon1. If you usually do:
recon-all -s sub-01 -i sub-01/anat/sub-01_T1w.nii.gz -all
Then you would instead write:
recon-all -s sub-01 -i sub-01/anat/sub-01_T1w.nii.gz \
-xmask sub-01/anat/sub-01_mask.nii.gz -all -noskullstrip
-noskullstrip needs to come after
-xmask can come anywhere.)
Thanks for your suggestion!
I’m using the freesurfer (7.4). And my main goal is to get a good segmentation quality for brainstem, cerebellum and thalamus.
With the freeusrfer using -xamsk option, I found an issue where
recon-all expects my brain mask placed to the result directory I set.
So, if I place my brain mask to the result directory before run the recon -all, the script won’ t run since my customize brain mask already existed in the result directory. It seems like the
recon-all pipeline is having trouble with a pre-existing
brainmask.mgz which I placed before running the recon -all.
In this case, would you recommend to run only autoren1 stage first, and replace the brain.mgz file with my customize brain mask. And the, run the rest of stage 2 and 3?
That would make sense, yes.