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... > The key to choosing EPI-->MNI EPI Template or using the segmentation > parameters is whether the EPI and T1 are properly aligned. Poor alignment > between EPI and T1 will lead to problems in the normalization. Could you please clarify your thought here? Jonathan argued that the advantage of using the EPI template would be due to the fact that the shape of EPI and T1 volumes are different. That appears to point to the role of the nonlinear part of the warp rather than affine alignment. Best wishes, Roberto Viviani University of Ulm, Germany > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Postdoctoral Research Fellow, GRECC, Bedford VA > Research Fellow, Department of Neurology, Massachusetts General Hospital > and > Harvard Medical School > 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. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773) > 406-2464 or email. > > > > On Thu, Dec 15, 2011 at 6:11 PM, Christine Zakrzewski < > [log in to unmask]> wrote: > >> Hi. Just to contribute to this conversation...In our lab, we align the >> anatomical image to the epi data, rather than epi data to the anatomical >> image. This approach avoids an additional resampling, or interpolation of >> the epi data--thereby, increasing the power of your results. >> Hope this is helpful. >> Christine >> ________________________________________ >> From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf >> of Jonathan Peelle [[log in to unmask]] >> Sent: Thursday, December 15, 2011 7:57 AM >> To: [log in to unmask] >> Subject: Re: [SPM] Difference between two normalization approaches >> >> Dear Shilpi Modi, >> >> > This might sound to be a very basic question but I would like to know >> what >> > is the difference between 'normalization to EPI template' and >> 'normalization >> > with the parameter file generated after segmentation step (as given in >> > example data set of SPM8 manual)' ? >> > >> > Which option should be used? >> > >> > If I use the later option doesn't it mean that, I am actually not >> > normalizing all the subjects to a common template? >> >> In both cases you are normalizing subjects to a common space (MNI >> space). The difference is whether you use the functional (EPI) images >> to do so, or the structural image (via segmentation). >> >> I would guess that most people use the parameter files generated >> during segmentation. However, in some cases?particularly if your EPI >> images are fairly distorted?directly normalizing to the EPI template >> may work better. I'm not aware of any systematic comparison between >> the two, so it's hard to say which is "best" (and that probably >> depends on the situation). >> >> Hope this helps! >> >> Best regards, >> >> Jonathan >> >> -- >> Dr. Jonathan Peelle >> Department of Neurology >> University of Pennsylvania >> 3 West Gates >> 3400 Spruce Street >> Philadelphia, PA 19104 >> USA >> http://jonathanpeelle.net/ >> >> The information in this transmission is intended for official use of the >> Kessler Foundation. It is intended for the exclusive use of the persons or >> entities to which it is addressed. If you are not an intended recipient or >> the employee or agent responsible for delivering this transmission to an >> intended recipient, be aware that any disclosure, dissemination, >> distribution or copying of this communication, or the use of its contents, >> is strictly prohibited. If you received this transmission in error, please >> notify the sender by return e-mail and delete the material from any >> computer. >> >