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Dear Donald, Thanks for your comments. But my design was repetitions of 6 seconds ON followed by 15 seconds OFF. So TR=3s, I got only 7 bins... Best, Andy On Wed, May 7, 2014 at 11:21 AM, MCLAREN, Donald <[log in to unmask]>wrote: > FIR is best for event-related designs with short events (e.g. less than > 10s). What is important is that the time bins cover the entire HRF from > beginning to end of the response. If you create longer time bins, I think > you will get better HRF responses. By using a shorter window, you are not > capturing the entire response and this could be contributing to your > issues. > > Another issue, if you have a fixed ITI, this can make it harder to > accurately estimate the HRF. This can sometimes be helped by random trial > order. Without enough jittering/variable ITI, then you don't have enough > unique equations to estimate the bins. Take a look at: > > Ollinger, J. M., Shulman, G. L., & Corbetta, M. (2001). Separating > processes within a trial in event-related functional MRI. *NeuroImage*, > *13*(1), 210–217. doi:10.1006/nimg.2000.0710 > > Bin 1 is at T=0. > Bin 2 is at T=3. > Bin 3 is at T=6. > Bin 4 is at T=9. > Bin 5 is at T=12. > Bin 6 is at T=15. > Bin 7 is at T=18. > Bin 8 is at T=21. > ... > Bin 10 is at T=27. > > > 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. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773) > 406-2464 or email. > > > On Tue, May 6, 2014 at 9:42 PM, Andy Yeung <[log in to unmask]> wrote: > >> Dear all, >> >> Thanks for your advice! One important question I have is: should I add a >> data point for time bin=0 so that I can show the beta at t=0? Because my >> stimuli are ON for 6 seconds (ie at time bins1&2) then OFF for 15 seconds. >> Now the plot looks as if beta is already at max right at the beginning... >> >> I wish to reply to Donald here: >> (1) These FIR plots are averaged from 25 subjects. >> (2) Yes, I made all trials to begin at the same time relative to the >> beginning of the TR. >> (3) All trials are of the same duration. >> (4) If each trial is preferred to be 20-30 seconds, does it mean >> event-related designs are discouraged from using FIR? >> >> And to Colin, would you share with me more by explaining what you mean by >> noisy HRFs? >> >> Thanks a lot. >> Andy >> >> >> On Tue, May 6, 2014 at 1:34 AM, MCLAREN, Donald <[log in to unmask] >> > wrote: >> >>> A few comments (that may or may not explain the issue): >>> (1) Group effects can appear significant even if the amplitude for each >>> subject is very low. This may make it hard to see the FIR effects in some >>> subjects. >>> (2) FIR needs all trials to begin at the same time relative to the >>> beginning of the TR. If you have some trials that begin at the mid-point of >>> the TR and some the begin at the beginning, then they need to be coded as >>> separate conditions. >>> (3) FIR needs all trials to be the same duration. Differing durations >>> will hurt the FIR model as the FIR model cannot take duration as an input >>> like the canonical HRF analysis does. >>> (4) 7 time bins seems quite short. I'm not sure how MarsBar compute time >>> bins or what it recommends (that's a question to ask on the MarsBar >>> listserv). For FIR to work well, you want to model out to 20-30 second for >>> each trial. Thus, the window length should be set to 20-30 seconds, and the >>> order should be set to the number of TRs the occur in that time period. >>> Rather than plotting time bins, you should plot time after stimulus onsets. >>> Generally, if the FIR is setup correctly, it should give you results where >>> you can pick out the response - if the HRF amplitude is great enough. >>> >>> 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. If you have received this e-mail >>> unintentionally, please immediately notify the sender via telephone at >>> (773) >>> 406-2464 or email. >>> >>> >>> On Mon, May 5, 2014 at 1:17 PM, Colin Hawco <[log in to unmask]>wrote: >>> >>>> I have also observed that my attempts to derive estimated time courses >>>> often don't look much like HRFs when you average within a group. I think at >>>> least part of this is because of the rather high variability in HRFs. Some >>>> are large, some small, some short, some long, and some people peak very >>>> early or late (I can say based on some of my past work we saw peaks ranging >>>> from at least 3 to 9 seconds). >>>> >>>> I think these sources of variability contribute to difficulties in >>>> extracting a nice clean time-course. I had had some success in the past >>>> extracting person-specific HRFs (using a fourier basis set, and even then >>>> about 405 of the time the we rejected the HRFs as to noisy). But averaging >>>> together always makes a mess for me. Having lots and lots of participants >>>> might help. >>>> >>>> There may be other issues related to FIR which others can comment on, >>>> though I have never tried this. >>>> >>>> Colin >>>> >>>> >>>> On 5 May 2014 04:47, Andy Yeung <[log in to unmask]> wrote: >>>> >>>>> To supplement information, as a result of my steps, I extracted >>>>> timecourse from first level of every individual, then transfer to Excel and >>>>> plot average curves. >>>>> >>>>> >>>>> On Mon, May 5, 2014 at 4:44 PM, Andy Yeung <[log in to unmask]>wrote: >>>>> >>>>>> Dear all, >>>>>> >>>>>> I used canonical HRF model (the default way) to specify 1st level for >>>>>> every subject, then in 2nd level ROI analysis I used 1-sample t-test to >>>>>> test for significance for each of my conditions (condition1 & condition2). >>>>>> Results showed I got significant peak voxels (pFWE <.05) for >>>>>> condition2 (at ROI 1 & ROI 2) and for condition1 (at ROI 3). >>>>>> >>>>>> To further explore, I used FIR model to divide my timecourse into 14 >>>>>> bins, 7 bins for each condition (condition1 & condition2). I extract beta >>>>>> value with Marsbar by the following method: >>>>>> http://www.jessicagrahn.com/marsbar-extract-data.html >>>>>> >>>>>> Attached are my resulted plots. Shapes are not similar to classical >>>>>> HRF curves, could anyone explain why this is so? And if I want to plot a >>>>>> graph more conforming to the shape of a classical HRF curve, what can I do? >>>>>> Thanks. >>>>>> >>>>>> Best, >>>>>> Andy >>>>>> >>>>> >>>>> >>>> >>> >> >