Hello,
I ran @SSwarper on the two subjects with poor skull stripping.. I ran the following code and the program seemed to run successfully:
@SSwarper \
11916.anat+orig \
MNI152_2009_template_SSW.nii.gz \
11916
I was reading online that the two JPEG files should be inspected to ensure that the skull-stripping and non-linear warping worked. For these, do I just ensure (1) there is no skull remaining (2) no brain regions are removed due to aggressive skull stripping (3) the yellow line follows the outer edges of the brain. Is there anything else I should keep an eye out for or any flags I should watch for? I just want to ensure I am checking these accurately. I have attached one of my outputs.
Thank you in advance for your help,
Tamara