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Well, if you want to do the higher level analysis easily within the context of FEAT, then you need to do the differencing within FEAT as well, so that the necessary other files (e.g., varcopes) are created. Plus, doing the differencing within FEAT will allow you to bring the lower level variances up to the next level. cheers, -MH On Wed, 2012-02-15 at 13:58 -0500, MCLAREN, Donald wrote: > There are two ways to do this, depending on what you want to do: > > For every subject (if you have N subjects repeat the chosen option for > each of the N subjects) > Option 1: > fslmaths image1 -subtract image2 differenceimage > > Option 2: Use FEAT (I just emailed the list/Eugene asking if FEAT > would have any benefits) to create a difference contrast. > > Then you take the difference images or difference contrasts and use > them in the group test. > > 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 Wed, Feb 15, 2012 at 1:41 PM, Gautam, Prapti <[log in to unmask]> > wrote: > Hi Donald, > > I have a brief question. To analyze my longitudinal data, I am > trying to > obtain a difference image between two time points (2 years > apart) for both > controls and patients. My question is, do I use fslmaths to > obtain the > difference between the two images directly for all the > controls and > patients in the group, or do I use first level analyses and > use the two > different time points as two groups (separately for controls > and patients) > to obtain group level differences? Sorry if this is a really > basic > question, but I am really new to FSL. > > Thank you, > Prapti > > > > On 2/10/12 3:27 PM, "MCLAREN, Donald" > <[log in to unmask]> wrote: > > > >I would run 4 models. Each model will have 7 subjects and 1 > image per > >subject. It will be a two-sample t-test. > > > >Each image will be the difference of time1 and time2 for each > of your > >four conditions, hence the four models. > > > >In setting up the model for each condition and using the > difference > >images, you can use FEAT and randomise. > > > >If you were to setup a big model with all conditions, two > groups, and > >two timepoints, you'd have at least two problems: > >(1) you'd have poor estimates of the effects since you have > multiple > >within-subject factors that increase the probability of > violations of > >sphericity, which are not corrected in FSL; and (2) you > wouldn't be > >able to use randomise. Thus, simplifying the model to a > series of > >paired t-tests since your not looking at the > group*time*condition > >interactions is probably your best option for the group > models. > > > > > >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, Feb 10, 2012 at 6:10 PM, Gautam, Prapti > <[log in to unmask]> > >wrote: > >> > >> The 4 copes are each different conditions in a task and I > want to look > >>at > >> them separately. Yes, there are two time points. > >> > >> Prapti > >> > >> From: Jeanette Mumford <[log in to unmask]> > >> Reply-To: FSL - FMRIB's Software Library > <[log in to unmask]> > >> Date: Fri, 10 Feb 2012 17:07:23 -0600 > >> > >> To: <[log in to unmask]> > >> Subject: Re: [FSL] help with design matrix-longitudinal > study > >> > >> What are your 4 copes? How many time points are there, > two? Are you > >>trying > >> to relate these 4 copes to each other or are you looking at > each one > >> separately? > >> > >> Jeanette > >> > >> On Fri, Feb 10, 2012 at 12:28 PM, Gautam, Prapti > <[log in to unmask]> > >> wrote: > >>> > >>> Hi Jeanette, > >>> > >>> Thank you for the link. However, I am really new at this, > and I still > >>>have > >>> a few more questions. > >>> The model in the example seems to refer to mean group > differences > >>>between > >>> the two groups. While I am interested in that, I would > also like to > >>> investigate differences between different task levels with > time for > >>>which I > >>> am currently using four copes in the first level analyses. > Do you know > >>>how I > >>> would accommodate these copes in the design matrix and > look for > >>>differences > >>> between the two groups as well as looking at change with > time ? Or > >>>should > >>> these be two different types for analyses? One for group > differences > >>>and one > >>> for time point differences? > >>> > >>> Thanks, > >>> > >>> Prapti > >>> > >>> > >>> From: Jeanette Mumford <[log in to unmask]> > >>> Reply-To: FSL - FMRIB's Software Library > <[log in to unmask]> > >>> Date: Thu, 9 Feb 2012 17:09:57 -0600 > >>> To: <[log in to unmask]> > >>> Subject: Re: [FSL] help with design matrix-longitudinal > study > >>> > >>> I think you'd follow the model described here: > >>> > >>> > >>>https://www.jiscmail.ac.uk/cgi-bin/webadmin? > A2=ind0809&L=fsl&P=R7901&1=f > >>>sl&9=A&J=on&K=2&d=No+Match%3BMatch%3BMatches&z=4 > >>> > >>> > >>> Hope that helps, > >>> Jeanette > >>> > >>> On Thu, Feb 9, 2012 at 4:44 PM, Gautam, Prapti > <[log in to unmask]> > >>> wrote: > >>>> > >>>> Dear all, > >>>> > >>>> I am trying to design a longitudinal experiment looking > at group > >>>> differences over 2 time points but I am having trouble > designing the > >>>> contrasts and the design matrices. > >>>> > >>>> For example, if I had 3 patients and 4 controls in the > study, I think > >>>> that I can conduct the first and second level analyses > separately for > >>>>the > >>>> two groups and then find group level differences in the > third level > >>>> analyses. For the analyses, I would have 4 copes for the > first level, > >>>>which > >>>> could then be fed into the second level, the results of > which would > >>>>then be > >>>> fed into the third level. > >>>> > >>>> However, I am not too sure whether this would be the best > way to do > >>>>the > >>>> analyses. I have looked at the examples in the FSL pages > for help with > >>>> higher level analyses, but I couldn't figure out if the > examples > >>>>applied to > >>>> my case. > >>>> > >>>> If I could get some advice on how to set up the design > matrices and > >>>>the > >>>> contrasts, that would be very helpful, > >>>> > >>>> Thanks, > >>>> > >>>> Prapti > >>>> > >>>> > >> > >> > >> > --------------------------------------------------------------------- > >> CONFIDENTIALITY NOTICE: This e-mail message, including any > attachments, > >> is for the sole use of the intended recipient(s) and may > contain > >> confidential > >> or legally privileged information. Any unauthorized review, > use, > >>disclosure > >> or distribution is prohibited. If you are not the intended > recipient, > >>please > >> contact the sender by reply e-mail and destroy all copies > of this > >>original > >> message. > >> > --------------------------------------------------------------------- > > > > > --------------------------------------------------------------------- > CONFIDENTIALITY NOTICE: This e-mail message, including any > attachments, > is for the sole use of the intended recipient(s) and may > contain confidential > or legally privileged information. Any unauthorized review, > use, disclosure > or distribution is prohibited. If you are not the intended > recipient, please > contact the sender by reply e-mail and destroy all copies of > this original message. > > --------------------------------------------------------------------- > >