Re: [Freesurfer] Freesurfer flips brains?

Hi Frank, we'll need a lot more detail. Are you doing all of this in FreeSurfer? What are your command lines? How are you evaluating whether volumes are flipped? doug

Léoné wrote:

Dear all,

I must be missing something really obvious, but it seems my brains are flipped. What I do:

• I have a highres structural scan, nii file format
• I convert it to a surface using recon-all
• Coregister the highres structural to the functional scan, so it is in the voxel size and orientation as the functional scans
• I try to bbregister the coregistered and resliced T1 with the surface

But then: hey, it doesn't fit, my low-res T1 is flipped compared to my y surface, hence to my original T1. So is it indeed true that my T1 might have been flipped? If so, does it make a wrong assumption on neurological vs radiological convention, or what is going on?

Thanks in advance,

   best,

         Frank

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer