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Hello list, Just a couple of questions regarding the previous discussions: So... in other words, in dartel, the workflow for non-imported images (like dti) differs from imported images, and warps should be applied to them only after they have been put into alignment with non-rigidly aligned (white-matter) c2 (in the case for dti)? Would it matter if the voxel sizes differs between the FA/MD and c1/c2, or should I first reslice the FA images so that they match the 1.5x1.5x1.5 resolution of the c1/c2 and rc1/rc2 images? Would dartel warp the FA to the Template space directly, or would the wFA image differ in alignment still (because the qform matrix was not used)? Thanks in advance, Regards, Johan van der Meer dept. Clinical Neurophysiology Academic Medical Centre Amsterdam [log in to unmask] On Fri, Dec 11, 2009 at 3:38 PM, John Ashburner <[log in to unmask]> wrote: > There is a second matrix in the headers that is used to encode the > relationship between the imported and original scans. If you do a > check-reg between an original and an imported, then you don't see them > in register - whereas if you do the same with a couple of imported > scans, then you would see them in approximate alignment. This is > because most of the SPM routines use the "mform" information in the > headers, whereas the DARTEL code also uses the "qform" information, > which relates the original and native images with each other. > > To answer your question: Yes. DARTEL would not apply the combination of > flow fields and the affine matrices in the way that you'd hoped. > > With hindsight, I would probably have used the matrices the other way > around - but it is slightly too late now. At the time, it made writing > the code much easier. > > Best regards, > -John > > On Fri, 2009-12-11 at 12:13 +0000, Dr. Maximilian Wagner wrote: >> Dear John, >> >> thank you for the suggestion. Just to double check: If I understand this >> correctly, DARTEL applies the second matrix (used for the alignment of the >> scans during the import step) to allow for the application of the flow field >> (e.g. estimated on T1 scans) to non-imported scans (e.g. DTI, fMRI) in the >> native space for highdimensional normalization, under the assumption that >> the original T1 scans and DTI/fMRI scans were collected in the same subject >> specific native space. >> Thus, if we apply the DARTEL flow fields with the "Dartel-Normalize-to-MNI" >> tool (without specifying template_6.nii) to non-imported DTI scans that were >> coregistered with imported GM segments (rc1 scans) rather than the "native" >> c1 scans, DARTEL would wrongly apply the combination of flow fields and the >> affine matrix to the DTI scans that are actually in the "inter-subject" >> rigidly aligned native space rather than the individual native space? >> >> Best regards, >> Max >> >> >> >> > > > -- > John Ashburner <[log in to unmask]> >