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Hi Michael and Donald, I think what professor Ashburner is saying is that it is always a good idea to use the best possible registration. Let's say we have some ROI that has been defined in a bunch of subjects that have been linearly transformed (FLIRTED) into standard space and then averaged and thresholded. If the number of subjects was big enough we would expect that ROI to be a quite good standard space representation of the region in question, much better than we would expect if we just drew one ROI in one subject. Let's now say we have some subject we want to apply that ROI to. I think it would make sense to use the best possible registration (non-linear, though maybe not SPM ;-) ) to register that subject to standard space. After all, using a linear registration is likely to achieve a worse matching of that subject to standard space, and hence to the ROI in question. Does this make sense? Jesper On 28 Nov 2012, at 20:46, Michael Harms wrote: > Hi Donald, > I don't see any way to just warp the data. What you really want to know > in your example is what the Harvard-Oxford labels would have been had they > been derived using registrations that involved FNIRT. That seems an > empirical question to me. Ideally, one would want to use a set of ROIs > derived using the same templates and algorithms as the study to which > those ROIs are going to be applied. But since that isn't always possible > you have a make a decision informed by the needs/questions of your > particular study. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [log in to unmask] > > > > > On 11/28/12 1:24 PM, "MCLAREN, Donald" <[log in to unmask]> wrote: > >> Michael, >> >> Excellent points. However, the underlying question still remains about >> using existing ROI with newer normalization approaches. >> >> For example, would using the Harvard-Oxford labels be bad if you use >> FSLs FNIRT as they were created with FLIRT? Or is there a way to warp >> the data? >> >> We are not using DARTEL, just SPM's regular non-linear warp. >> >> On Wed, Nov 28, 2012 at 1:50 PM, Michael Harms <[log in to unmask]> >> wrote: >>> I would think that you might raise some eyebrows using ROIs obtained >>> using >>> FSL's FLIRT in data normalized using SPM's non-linear (Dartel?) tool, >>> due >>> to the big potential difference between linear (affine) and non-linear >>> approaches. Of course, it would depend on the anatomical precision that >>> you want/need for your particular study and whether the ROIs involve >>> regions that are particularly sensitive to non-linear registration. >>> >>> cheers, >>> -MH >>> >>> -- >>> Michael Harms, Ph.D. >>> >>> ----------------------------------------------------------- >>> Conte Center for the Neuroscience of Mental Disorders >>> Washington University School of Medicine >>> Department of Psychiatry, Box 8134 >>> 660 South Euclid Ave. Tel: 314-747-6173 >>> St. Louis, MO 63110 Email: [log in to unmask] >>> >>> >>> >>> >>> On 11/28/12 11:43 AM, "MCLAREN, Donald" <[log in to unmask]> >>> wrote: >>> >>>> Dear SPM/FSL users, >>>> >>>> It seems that there are several templates (SPM v FSL) as well as >>>> different normalization routines that could result in slight >>>> variations of the localization of the results. Do I need to worry >>>> about these small differences between methods? >>>> >>>> In particular, I want to know if I can take regions defined in a study >>>> using FLIRT in FSL and use them in my study that has been processed >>>> with SPM's non-linear normalization tool. Can I use them as is or is >>>> there a transform that can I compute and/or apply to the ROIs to get >>>> them into the SPM normalized space. >>>> >>>> Thank you in advance for your input. >>>> >>>> Best Regards, Donald McLaren >>>> ================= >>>> D.G. McLaren, Ph.D. >>>> Research Fellow, Department of Neurology, Massachusetts General Hospital >>>> and >>>> Harvard Medical School >>>> Postdoctoral Research Fellow, GRECC, Bedford VA >>>> Website: http://www.martinos.org/~mclaren >>>> Office: (773) 406-2464 >>>> ===================== >>>> This e-mail contains CONFIDENTIAL INFORMATION which may contain >>>> PROTECTED >>>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>>> intended only for the use of the individual or entity named above. If >>>> the >>>> reader of the e-mail is not the intended recipient or the employee or >>>> agent >>>> responsible for delivering it to the intended recipient, you are hereby >>>> notified that you are in possession of confidential and privileged >>>> information. Any unauthorized use, disclosure, copying or the taking of >>>> any >>>> action in reliance on the contents of this information is strictly >>>> prohibited and may be unlawful. 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