Hi Lara,
this is quite odd. It would look like the affine registration is working well (*_struc_GM_to_T.nii.gz), while the non-linear one is not (*_struc_GM_to_T_init.nii.gz).
Could you please upload one subject's set of images for which you see this problem (
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi) and send us the reference number?
Cheers,
Gwenaëlle
De : Lara Foland-Ross <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Jeudi 14 février 2013 19h58
Objet : Re: [FSL] problem with VBM nonlinear registration (fslvbm_2_template) step
Hi Jake,
Subject###_struc_GM.nii.gz and subject###_struc_GM_to_T.nii.gz look fine for all subjects. However, subject###_struc_GM_to_T_init.nii.gz does show distortion for the same subjects showing problems in the "template_GM_4D" image. Thoughts?
Thanks so much,
Lara
On Thu, Feb 14, 2013 at 11:07 AM, John Kuster
<[log in to unmask]> wrote:
Hi Lara,
Does it look like it could be a problem with the segmentation, or the registration? For example, how do subject###_struc_GM.nii.gz and subject###_struc_GM_to_template_GM.nii.gz look in the struc directory for the distorted?
-Jake
On Feb 14, 2013, at 2:00 PM, Lara Foland-Ross wrote:
> Hello,
>
> I'm running a VBM analysis in FSL and am experiencing problems with the output of fslvbm_2_template. In checking the "template_GM_4D" image in the "struc" directory, I see that ~50% of my subjects show a great deal of distortion. Moreover, the distortions appear to result from improper orientation of the images of these subjects (e.g., where the sagittal slices are shown for well registered subjects, subjects with distorted registration show there to be axial slices).
>
> I've checked the orientation of my images prior to the fslvbm_2_template step. All of the orientations are consistent across my 60 subjects at the very start of my analyses (prior to, and immediately following fslvbm_1_bet).
>
> Any suggestions on a possible way to correct this would be greatly appreciated!
>
> Many thanks in advance,
> Lara
>
>
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