Hello, We are using freesurfer to skull strip T1 images on a high-motion pediatric sample. We want to use freesurfer to get brain-only images and then do further analysis using FSL. The problem is that, in freesurfer, the images are in a different orientation than those in FSL. For example, the same brain extracted image in freesurfer seems to be rotated a bit more to the left than the image extracted in FSL.
QUESTION: Does anyone with freesurfer or FSL knowledge know how to convert the freesurfer’s brain-only images so that we can use them in FSL for ICA (both group and individual) as well as TBSS and Tractography ( back on freesurfer)? Thank you for your time and expertise. Cheers, Sara
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