Hi,
I don't know this MIPAV, but have you loaded your 2 problematic original *struc.nii.gz images in FSLview to check that they have indeed the same orientation than the others? I still strongly suspect that this is the problem. If so, you need to use the fslswapdim command.
Hope this helps,
Gwenaelle
> De: Cibu Thomas <[log in to unmask]>
> Objet: [FSL] Warped Segmentation in VBM
> À: [log in to unmask]
> Date: Jeudi 9 juin 2011, 16h07
> Hello
> I ran the fslvbm_2_template -n command to create the GM
> template and upon
> checking the segmentation for each subject I found that 2
> of the 13 were
> warped (click on link 1 to see the incorrectly and link 2
> for correctly
> processed volumes ). I used MIPAV to check the orientation
> and image
> attributes of the individual brain volumes and did not find
> anything
> unusual between the correctly processed and incorrectly
> processed volumes.
> I would greatly appreciate your help resolving this issue.
>
> Many thanks in advance
> Cibu Thomas
>
> https://picasaweb.google.com/lh/photo/YAE83Nip-YhTTipzvQyQ8Ih-jtAukQASeqOsXlzi7nI?feat=directlink
>
> https://picasaweb.google.com/lh/photo/OVF2VJgnUR-AxHut6jeB8Ih-jtAukQASeqOsXlzi7nI?feat=directlink
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Gwenaëlle Douaud, PhD
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/~douaud
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