Can you be more specific about what abnormality you are seeing? The Screenshot2 does not look so bad to me. I'm assuming that this is the talairach.xfm transform you are talking about? If so, that is hardly used in the stream (and certainly not for placing surfaces), so it is no surprise that the results look ok even if the xfm is off a little

On 3/6/2024 5:08 AM, GOFFINET Sara wrote:

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Hello,

I ran freesurfer recon_all on a T1 MRI sequence (you can find the orig T1 in Screenshtot1) and my participant's brain warped to MNI (worig.nii) looks deformed (Screenshot2). Do you know why is there a bump (the worig file does not overlay well on MNI) while the reconstruction of the pial surface (lh.pial, rh.pial) shows no abnormality?

Thanks in advance,

Sara Goffinet
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