Hi Doug,
Ah, I found the cause myself, which might be useful for others. It happens already in the first step, before the ones I listed: in mri_convert. I do:
mri_convert struct.nii 001.mgz
And it flips. This I can see because I converted the mgz back (mri_convert 001.mgz orig.nii) and then it's indeed reversed (and shifted, rotated, all rigid body transformations one can think of). Why does this happen? Is it normal for nii-files? I see that I can specify the orientation in mri_convert by doing mri_convert -in_orientation and then a three letter specification. I chose PSR and now the changes are far less severe (only a small shift still) and most importantly: no flip anymore. Do I now need to reconvert my all my surfaces? I don't hope, but I'm at least glad I have this one fixed.
best,
Frank
----- "Douglas N Greve" greve@nmr.mgh.harvard.edu schreef:
Van: "Douglas N Greve" greve@nmr.mgh.harvard.edu Aan: "Frank Leoné" f.leone@donders.ru.nl Cc: freesurfer@nmr.mgh.harvard.edu Verzonden: Woensdag 18 januari 2012 18:34:31 Onderwerp: 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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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