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I really appreciate for your help!!! 2011/12/3 MCLAREN, Donald <[log in to unmask]> > eps -- http://www.mathworks.com/help/techdoc/ref/eps.html > > Basically, it adds a tiny value. It prevents the denominator from being 0, > since X/0 would be Inf. and 0/0 would also be Inf. instead of 0. > > > 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 Fri, Dec 2, 2011 at 10:57 AM, Jeff Browndyke <[log in to unmask]>wrote: > >> What is "eps" specifying in the formulas below? >> >> Jeff >> >> >> On Dec 2, 2011, at 10:24 AM, MCLAREN, Donald wrote: >> >> You might also consider: >> >> sum(X)./(eps+sum(X>0) >> >> or >> >> (i1+i2+i3+i4...ix)/(eps+(i1>0+i2>0+i3>0+i4>0+...ix>0)) >> >> The advantage of these is that it will not include subjects whose value >> is 0 at a particular voxel. This is sometimes called a soft mean. The >> advantage is that if 0 is really not 0, but is missing data. For example, >> if you thresholded the image such that brain tissue has a value and >> non-brain is set to 0. Then you wouldn't want to average brain and >> non-brain because you'd average the artificial value of 0. >> >> >> 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 Fri, Dec 2, 2011 at 10:17 AM, Christian Lambert < >> [log in to unmask]> wrote: >> >>> Or in imcalc (again), but without i1+i2+i3+i......ad infinitum: >>> >>> - Set "read to data matrix" >>> - Select all your images >>> - Expression = sum(X)./n >>> ...where n=number of images >>> >>> - Chris >>> >>> On Fri, Dec 2, 2011 at 3:16 PM, S.F.W. Neggers <[log in to unmask]>wrote: >>> >>>> or do >>>> >>>> ---- >>>> imgs=spm_select; %select your T1s to average here >>>> N=size(imgs,1); >>>> >>>> V=spm_vol(imgs); >>>> data=spm_read_vols(V(1)); >>>> data_c=zeros(size(data)); >>>> >>>> for i=1:N, >>>> data=spm_read_vols(V(i)); >>>> data_c = data_c + data/N; >>>> end >>>> >>>> V(1).fname='/home/bokyung/**data/averageT1.nii' %or wherever you >>>> want your average image to go >>>> spm_write_vol(V(1),data_c); >>>> >>>> --- >>>> >>>> hope i didnt make any typos or mistakes.... >>>> >>>> Op 02-12-11 16:06, Jeff Browndyke schreef: >>>> >>>>> The SPM imCalc function is quite useful for this purpose. >>>>> >>>>> If you already have normalized T1 images, then you would simply >>>>> specify (i1+i2+i3+i4...ix)/x, where x is the total number of images. >>>>> >>>>> Jeff >>>>> >>>>> >>>>> On Dec 2, 2011, at 9:58 AM, BoKyung Park wrote: >>>>> >>>>> >>>>> >>>>>> Dear All, >>>>>> >>>>>> >>>>>> I'd like to average T1 anatomical images of all my subjects using >>>>>> spm8, but it's hard to find how to do this. >>>>>> >>>>>> >>>>>> As some previous works indicated, I coregistered T1 anatomy images to >>>>>> individual subjects' mean EPI then normalised the T1 images but I couldn't >>>>>> understand how I could average these normalised anatomical images... >>>>>> >>>>>> >>>>>> How can I do this and make average T1 image of all subjects? A little >>>>>> advice would be really appreciated. >>>>>> >>>>>> >>>>>> >>>>>> Thanks a lot in advance& Best Regards. >>>>>> >>>>>> >>>>> ------------------------------**------------------------------** >>>>> ----------- >>>>> Jeff Browndyke, Ph.D. >>>>> Clinical& Research Neuropsychologist >>>>> Durham VA& Duke University Medical Centers >>>>> >>>>> >>>>> [log in to unmask] / [log in to unmask] >>>>> office: (919) 286-0411 ext. 4656 >>>>> cell: (336) 264-4222 >>>>> >>>>> >>>> >>>> >>>> -- >>>> ------------------------------**-------------------- >>>> 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 B01.206, 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.neuromri.nl/people/**bas-neggers<http://www.neuromri.nl/people/bas-neggers> >>>> : http://www.neuralnavigator.com (CEO) >>>> ------------------------------**-------------------- >>>> >>>> >>>> ------------------------------**------------------------------** >>>> ------------------ >>>> >>>> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is >>>> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht >>>> onterecht >>>> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender >>>> direct >>>> te informeren door het bericht te retourneren. 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If you receive this message unintentionally, please >>>> do not >>>> use the contents but notify the sender immediately by return e-mail. >>>> University >>>> Medical Center Utrecht is a legal person by public law and is >>>> registered at >>>> the Chamber of Commerce for Midden-Nederland under no. 30244197. >>>> >>>> Please consider the environment before printing this e-mail. >>>> >>> >>> >> >> ----------------------------------------------------------------------- >> Jeff Browndyke, Ph.D. >> Clinical & Research Neuropsychologist >> Durham VA & Duke University Medical Centers >> >> [log in to unmask] / [log in to unmask] >> office: (919) 286-0411 ext. 4656 >> cell: (336) 264-4222 >> >> >