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Hi Haakon, Your strategy may work (although I think you meant to say coregister the original T1 to the stripped T1), but there's an easier way. Just do unified segmentation with the VBM toolbox, and go into 'Writing Options' and change 'Skull Cleanup' to 'Yes' and 'Native Space' to 'Yes'. Then you can normalize, skull-strip, and bias-correct your T1 image all in one step. There's another advantage to doing it this way. Your proposal has you coregistering the T1 to the T2, and then segmenting. This means the T1 is lined up with the T2 before segmenting, but when segmenting you should have the T1 lined up so that its AC-PC is correctly positioned. I had similar problems with coregistration, and this is the method I use. It seems to work well so far... 1) Position AC-PC on T1 2) Segment T1 using VBM toolbox (also changing options to use origin from header because of step 1) 3) Coregister mean T2 to bias-corrected, skull-stripped T1 and select remaining T2 images as 'Other Images' 4) Apply seg_sn normalization matrix If you would like to continue using the other skull-stripping toolbox, then I would suggest the following. 1) Position AC-PC on T1 2) Segment 3) skull-strip T1 4) Coreg mean T2 (+others) to skull stripped T1 5) Coreg skull-stripped T1 (+T2 images) to original T1 6) Apply normalization matrix I hope this helps. Regards, Neil Neil Chatterjee Research Assistant Stanford Systems Neuroscience and Pain Laboratory [log in to unmask] 650-724-0522 On Mon, 19 Jan 2009 17:13:21 +0100, Neggers, S.F.W. <[log in to unmask]> wrote: >Skull stripping of course could further minimize mismatch beteen EPI and T1. > >However, EPI specific distortion can never be modelled with a rigid body registration (as in coregistration), you would not get around that problem by skull stripping. That is, in case your EPIs are spatially distorted considerably. They always are to some extent. > >When you minimized EPI distortion during acquision your strategy sounds fine to me. > >Cheers, > >Bas > >-------------------------------------------------- >Dr. S.F.W. Neggers >Division of Brain Research >Rudolf Magnus Institute for Neuroscience >Utrecht University Medical Center > >Visiting : Heidelberglaan 100, 3584 CX Utrecht > Room B.01.1.03 >Mail : Huispost B.01.206, P.O. Box 85500 > 3508 GA Utrecht, the Netherlands >Tel : +31 (0)88 7559609 >Fax : +31 (0)88 7555443 >E-mail : [log in to unmask] >Web : http://www.linkedin.com/pub/3/774/590 >-------------------------------------------------- > > >-----Oorspronkelijk bericht----- >Van: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] Namens Haakon Engen >Verzonden: maandag 19 januari 2009 16:53 >Aan: [log in to unmask] >Onderwerp: Re: [SPM] Coreg problems > > Hi Marko and Bas, > > Unfortunately neither of your solutions worked, but I did get a workaround tip off- list by Jimmy Jensen which seems to have done the trick. I used the nordic Image Control and Evaluation toolbox to skull strip the T1 image, and when I coregistered the stripped T1 to the T2 they were in aligment. > > Now, if I am correct, coregistering the stripped T1 to the T2, and then registering the original T1 to the T2 should allow me to use the unified segmentation procedure to calculate the normalization parameters which then can be applied to the T2 images. > > > Am I correct in thinking that this is a methodologically sound approach to fixing my problem? > > > Thank you for your help, > > h. > >> Hi Haakon, >> >> just a hunch as your images even by visual inspection seem rather >> inhomogeneous: try writing out the bias-corrected images during >> segmentation and use these as the target for your EPI. Perhaps the >> coregistration gets caught up on the inhomogeneity gradients (which >> would explain the shift in one direction only). I had similar problems >> several years ago with high-field data and using the bias-corrected >> images helped. >> >> Good luck, >> Marko >> >> Haakon Engen schrieb: >>> Dear SPM'ers, >>> >>> I realize questions as basic as how to get coregistration to work >>> are a few notches below what usually gets answered on this list, but >>> I'm really at my wits end here. >>> >>> The problem is that 4 (out of 27) of my subjects plainly refuses to >>> have their T1 images coregistered to the mean EPI image, or any other >>> EPI image for that matter. The experiment totals 4 runs, and I've >>> tried to coregister the T1 to all of the mean images post- >>> realignment, as well as multiple ordinary, realigned, images. I've >>> also tried to coregister the EPI's to the T1, once again without >>> success. >>> >>> I've attached the coreg output files for all 4 subjects. As you can >>> see they all seem to be out of alignment in the Z- dimension, with >>> the T1 consisently lower than the EPI's, while otherwise seemingly in >>> OK registration. >>> >>> I've tried fiddling around with the settings, changing objective >>> functions, seperation and tolerances without much success. I've also >>> tried using the coregister and reslice function, with interpolations >>> from trilinear up to 7th degree spline- again without success. This >>> is rather troublesome as this means that the normalization parameters >>> calculated by the unified segementation procedure are similarly >>> shifted, which results in "extracranial" activations, when overlaid >>> on the glassbrain. >>> >>> Can anyone give me a clue as to why this happens, and how to fix or >>> work around it? >>> >>> I'm on a Vista x64 workstation using Matlab R2007b, and SPM 8b r2598. >>> >>> Kind regards, >>> >>> Haakon G. Engen >>> Research assistant >>> University of Oslo >>> >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> >>> --------------------------------------------------------------------- >>> --- >>> >> >> -- >> ========================================================== =========== >> Marko Wilke (Dr.med./M.D.) >> [log in to unmask] >> >> Universitäts-Kinderklinik University Children's Hospital >> Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology) >> Hoppe-Seyler-Str. 1, D - 72076 Tübingen >> Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473 >> ========================================================== =========== >>