Thank you for your reply. What I fail to understand is why this would happen. Since, you only flip the orientation (and if I understand correctly freesurfer uses its “own” orientation LIA). The program should start at the same point.

 

If I apply mri_convert to both input image,s in this case “001.mgz”, and reorientate these to the LIA convention, they are exactly the same.  

I would therefore expect the output to be the same as well. Why would the starting point differ?

 

Best,

David

 

 

Yes, this can happen  (and happens to almost all neuroimaging packages).  As with any optimization program, where it ends up depends a little on where it starts.

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Hi,

 

I ran recon-all twice, once on a T1w image (nifti) with RAS orientation, and once on this image converted to LAS orientation

I would expect the output (especially in volume) to be equal, because freesurfer reconverts it to its own orientation if I understood correctly. However, I found that the segmentation and output volumes differed depending on the input orientation.

 

So while in fact both images are actually the same, the output differs. What would be the reason for this difference in output?

 

Any help would be much appreciated

 

Kind regards,

 

 

 

David van Nederpelt, MSc.  | PhD Candidate

Radiology and Nuclear Medicine

Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ Amsterdam, the Netherlands

E: d.vannederpelt@amsterdamumc.nl

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