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Hi Jake and Gwenaëlle, I've found a solution to the problem. I just needed to orient my scans to that of the template prior to running the VBM scripts. fslreorient2std did the trick! Thanks, Lara On Fri, Feb 15, 2013 at 6:20 AM, Gwenaëlle DOUAUD <[log in to unmask]>wrote: > 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 > > -------------------------------------------------------------------- > 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 > -------------------------------------------------------------------- > ------------------------------ > *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 > > > > > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > >