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Hi Pia, I'm not too sure of the details of how FSLview displays images, but in general, the coregistration in SPM is more robust if given reasonably good initial starting estimates. Sometimes though, even this does not help - particularly if the anatomical images were collected at high field and contain large intensity inhomogeneities. One thing that you could try is to segment the anatomical image first, so that a bias corrected version is generated. Coregistration can then be done with the bias corrected version. Note that if you do this, the coregistration should have the bias corrected anatomical as the target and the FA image as the source (with any other images that are in alignment with the FA specified as "other"). This should allow the original *_seg_sn.mat to be used for spatially normalising the FA. All the best, -John On Tuesday 07 October 2008 10:04, Pia Rotshtein wrote: > Hi Tom, > > Thanks for the reply, > > We exhausted few options, converting to *.nii, *.img, *.hdr > > It just seem like the origin register by SPM are different (spm_vol.m). > > We figure there is something else hidden in the hdr, that FSL reads and > write but SPM do not but could not find what. > > > > Will look at the discussion in the FSL list > > > > Cheers > > > > Pia > > > > > > > > ________________________________ > > From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] > On Behalf Of Thomas Nichols > Sent: 06 October 2008 22:43 > To: > Subject: Re: [SPM] FSL 2 SPM > > > > Hi Pia, > > Have you double-checked that all of the images are true NifTI images > (and not Analyze)? (fslinfo will tell you). If you've got a mix of > Analyze and NifTI you'll have trouble. > > OTW, you're might be having qform-sform nightmares. See a thread on the > FSL list "MNI Space in MRIcro and FSL" from 2007. > > -Tom > > On Mon, Oct 6, 2008 at 7:22 PM, Pia Rotshtein <[log in to unmask]> > wrote: > > Hi everyone, > > Our aim is to co-register FA maps to T1 images. > > > > We have tried with both SPM and FSL. > > FSL seem to be doing a good job, and when check with FSLview it is > perfect, but when checked with SPM5 check-reg it seems to be offset > (mostly on the y,z dimensions). > > Similarly, when SPM is co-registering, when we check with FSLview it is > perfect, but with SPM check-reg it is offset (mostly on the y,z > dimensions). > > > > We have read that the scales are different in FSL-nifti and SPM-nifti > but we could not understand how to go about it. > > We want to end up with both images co-registered in SPM so we could > apply the normalization parameters of the T1 to the FA images. > > > > Any advice would be appreciated > > > > Thanks > > > > Pia (& Magda) > > ____________________________________________ > Thomas Nichols, PhD > Director, Modelling & Genetics > GlaxoSmithKline Clinical Imaging Centre > > Senior Research Fellow > Oxford University FMRIB Centre