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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