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Thanks Chaogan. I tried 'new segment'+dartel but some subjects have bad segmentation results. Will try DPABI if no alternatives are available. Any one knows how to combine rigid deformation and DARTEL flow field? I'm trying the deformations utility from SPM8, but it seems to accept only _sn.mat format affine deformation. Or is it possible to convert DARTEL flow field to deformation, in SPM or FSL compatible format? Thanks again. Shengwei On Wed, Nov 5, 2014 at 10:22 AM, YAN Chao-Gan <[log in to unmask]> wrote: > Hi Shengwei, > > Possibly, you can try DPABI (http://dpabi.org) VBM analysis, it has a > step called "Reorient T1 Interactively". > > Also, the following New Segment + DARTEL happens automatically. > > Best, > > Chao-Gan > > On Wed, Nov 5, 2014 at 10:59 AM, Shengwei Zhang <[log in to unmask]> wrote: > >> Hi SPM experts, >> >> I'm using DARTEL in SPM8 for VBM study, and it is suggested that the >> input images should be roughly aligned to MNI space first before DARTEL >> processing. >> To avoid interpolation, I'm trying to first rigidly register all subjects >> to MNI space, run DARTEL on the aligned images, and then combine the rigid >> and DARTEL transformations and apply them to the raw space images. >> Does anyone have experience on how to implement this, in command-line or >> GUI mode? >> >> I'm thinking of using spm_coreg first to do the rigid registration, but >> how can I extract the rigid transformation from this step? Do I need to >> invert this rigid transformation first before combining it to the DARTEL >> transformation? >> >> Any help is appreciated. >> >> >> Shengwei >> > >