Severe skull stripping errors post SSwarper

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Hi all,

My lab has run into an issue for two participants post SSwarper and are looking for some suggestions on adjusting this.

We are implementing SSwarper prior to the remaining of the recon-all pipeline in FreeSurfer 7.3 and have found for the majority of participants, this has improved skull stripping, particularly in the occipital lobe. There are two participants who have typical raw data out of the scanner but have an excess amount of brain that is being classified as non-brain and is removed. See the below images:

QC_anatSS.1032
QC_anatSS.10321920×638 131 KB

Our first possibility is "unifize_off", but are looking for any other suggestions the group may have.

Thanks all!

2

This is a similar post to another one, and my advice is the same:

How about trying the newer sswarper2, which is an update to @SSwarper? It is now distributed in the very latest version of AFNI if you update your local version. The syntax of it is essentially the same as with @SSwarper, as is its outputs.

Or, you can go to where your AFNI binaries are, and run:

curl -O https://raw.githubusercontent.com/afni/afni/master/src/scripts_install/sswarper2
chmod 755 sswarper2

The first line downloads the file, and the second makes it executable, so it will run like a normal program.

--pt