Hi Douglas,
Ah, makes sense, sorry for that.
I do most of the work in SPM, so:
- 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 (SPM) - I try to bbregister the coregistered and resliced T1 with the surface using something like: bbregister --s S7_FS --mov ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --init-spm --reg ~/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --t1 and view it with vglrun tkregister2 --mov /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/flipped_rmasked_str_S2_seler20090508.nii --reg /home/action/fraleo/Data/Exp1_Saccades_phase/S7_FS/mri/orig/register.partial.auto.dat --surf
Here you see that I already use a flipped structural scan. If I do it like this, bbregister converges to a nice and correct solution (everything aligns). If I don't, tkregister2 showms unregistered struc and func, while it is obvious it would be roughly aligned if you would flip either of them.
In addition/in general: What would be the recommended way to do the coregistration etc. if you do all you analyses in SPM? Would it for example be better to coregistrate and reslice all functionals with the structural, so they are automatically aligned with the surface? Now I have a structural which is coregistered with the funcional and I realign that one, but that makes for one extra step where it can go wrong. Don't think this is related to the flip, but I also have a few alignment problems for other subjects.
Thanks a lot in advance,
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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