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Hello Donald, Following your response below: When I binarise the images as you suggested with the threshold 3 (-thr 3 bin BImg1) the final summedigame is only composed of regions with intensity 0 or 1 (and 1s are awfully extensive). But when I binarise without using -thr 3 (eg. fslmaths img1 -nan -bin Bimg1) the final summedimage is composed of regions with the intensity 0, 1, 2 or 3. Do you think this might actually be the correct way to do this ? I couldnt understand the rationale of thresholding the statistical images at 3. Sorry for asking about this again. Thank you very much for your help Cagri 2012/1/16 MCLAREN, Donald <[log in to unmask]> > > On Mon, Jan 16, 2012 at 5:25 AM, cc yy <[log in to unmask]> wrote: > >> >> Thank you very much for this detailed information Donald. I apologise for >> the late response, I have been busy finalising my thesis. I think I will go >> with 2-b, which was what Michael had suggested too. >> >> Can I kindly ask how to convert test results to binary and add them up? >> > > There are a number of programs that would add them up (FSL, SPM, MATLAB, > etc.). I prefer MATLAB (load the statistical image (img1); then convert to > 1s and 0s by creating a second matrix (Bimg1) of zeros using the equation > Bimg1=zeros(size(img1)); and then Bimg1(img1>0)=1; repeat for the other > three; then IMG=Bimg1+Bimg2+Bimg3, then save the image). SPM has several > commands for reading and writing nifti files in MATLAB. In FSL (since this > is the FSL list): > > fslmaths img1 -nan -thr 3 -bin Bimg1 > fslmaths img2 -nan -thr 3 -bin Bimg2 > fslmaths img3 -nan -thr 3 -bin Bimg3 > fslmaths Bimg1 -add Bimg2 summedimage > fslmaths Bimg3 -add summedimaged summedimage > > > And would the number of subjects make any difference in choosing the >> alternatives you suggested i.e 2-a vs.2-b. My numbers are low for a t-test >> (i.e. 31, 21, 42, 28 ). >> >> > Nope. The difference between 2a and 2b is in the interpretation. > > > >> >> Thanks a lot again. >> >> Cagri >> >> >> 2012/1/9 MCLAREN, Donald <[log in to unmask]> >> >> Cagri, >>> >>> There are two approaches: >>> (1) Linear Regression where you have a grouping variable that takes >>> values 1-4. Then you evaluate the slope of the grouping variable. This >>> doesn't allow for different variances in each group unless you tell FSL to >>> allow different variances, but usually doesn't because group is now a >>> single continuous variable. >>> (2) Multiple Linear Regression where you have one EV for each group. >>> There are two potential tests you can use to evaluate this model: (a) 1.5 >>> 0.5 -0.5 -1.5; (b1) 1 -1 0 0; (b2) 0 1 -1 0; (b3) 0 0 1 -1. The variance >>> for each group can be modelled separately and should be modelled >>> separately. Test (a) will be very similar to (1) and has the disadvantage >>> that group 2 and 3 don't have to be less than group 1 to get a >>> significantly positive result if group 4 is really lower than group 1 (e.g >>> GM estimate in the four groups are .75 1 1 .25. Tests (b), are what Michael >>> suggested, will test if each successive group is different. Then using a >>> conjunction (I like logical AND), you can assess whether you have the >>> ordered pattern based on successive differences in all 3 b tests. For the >>> logical AND, threshold each (b) test and convert to binary (1 for >>> significant, 0 otherwise); then add them up. Any voxel with a value of 3 >>> has the continuum pattern, otherwise it doesn't. There are other forms of >>> conjunctions that are less conservative that have been described previously. >>> >>> Hope this helps. >>> >>> >>> 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 Sat, Jan 7, 2012 at 10:49 AM, Cagri Yuksel <[log in to unmask]> wrote: >>> >>>> I see, thank you very much anyways. >>>> I am wondering if it's my misinterpretation of the reviewers comment, >>>> so I am copying the exact words of the reviewer to give a better idea about >>>> what is asked from us (I just changed the group names): >>>> >>>> " the examination of a potential continuum of abnormalities between >>>> these groups is likely the more adequate approach. Given the limited >>>> statistical power of this study this is probably best examined in the >>>> context of a multiple regression model with a group variable (e.g., Group X >>>> = 4, Group Y = 3, Group Z = 2, healthy volunteers = 1) and an independent >>>> estimation of (potentially unequal) group variances. Given the strong a >>>> priori evidence for a continuous increase in gray matter deficits in >>>> prefrontal and temporal cortices over groups, one-sided testing of such a >>>> model appears legitimate." >>>> >>>> Many thanks >>>> >>>> Cagri >>>> >>>> >>>> On Fri, 6 Jan 2012 08:07:23 -0600, Michael Harms < >>>> [log in to unmask]> wrote: >>>> >>>> >I've never had to test for an "ordered continuum" between groups, so >>>> >maybe others will chime in. Perhaps you could do the conjunction of >>>> the >>>> >regions that satisfy 1 > 2, 2 > 3, and 3 > 4 ? >>>> > >>>> >good luck, >>>> >-MH >>>> > >>>> >On Fri, 2012-01-06 at 12:34 +0000, Cagri Yuksel wrote: >>>> >> Thank you Michael, that was enlightening. The answer is no, we can >>>> not assume that there is a linear relationship between these diagnostic >>>> groups. >>>> >> >>>> >> So how should a model be testing a continuum of GM abnormalities >>>> between these 4 diagnostic groups using a multiple regression model ? I >>>> really can not think of anything at this point. >>>> >> >>>> >> Cheers >>>> >> >>>> >> Cagri >>>> >> >>>> >> On Thu, 5 Jan 2012 10:56:47 -0600, Michael Harms < >>>> [log in to unmask]> wrote: >>>> >> >>>> >> >Whether or not a linear model relating the groups makes sense >>>> depends on >>>> >> >on the specific groups, so I don't know whether it makes sense in >>>> your >>>> >> >context or not. I'll just note that modeling a linear relationship >>>> >> >between groups is a specific hypothesis that assumes that each step >>>> up >>>> >> >in the "group" variable yields an identical change in the dependent >>>> >> >variable (since all the groups were themselves spaced by a delta of >>>> 1 >>>> >> >unit). This is *not* the same as hypothesizing that there is >>>> merely a >>>> >> >continuum in the DV such that 1 > 2 > 3 > 4 (or 1 < 2 < 3 < 4). >>>> >> > >>>> >> >cheers, >>>> >> >-MH >>>> >> > >>>> >> >On Thu, 2012-01-05 at 16:38 +0000, Cagri Yuksel wrote: >>>> >> >> Hello Michael, >>>> >> >> >>>> >> >> Thank you for your answer. Yes, I realized my mistake about the >>>> interpretation of the results right after I sent the message. >>>> >> >> >>>> >> >> These diagnostic groups are related and this analysis is to test >>>> an a priori hypothesis about a possible continuum of GM abnormalities in >>>> these groups, that's why I was thinking a linear model. >>>> >> >> >>>> >> >> Do you think it makes sense ? Do you have other suggestions? >>>> >> >> >>>> >> >> Thank you again, >>>> >> >> >>>> >> >> Cagri >>>> >>> >>> >> >