Dear Danai,
that sounds a bit odd, the number of slices should in that case have the same ratio between both sequences as your TRs. This is not the case now: 3/2 is not equal to 36/16. Unless you have dead time between volumes for one of the sequences, which wouldn't make much sense (but is possible indeed), this can't yield the same TE and bandwith.
Did you actually look up the TEs and acquision bandwiths? I would definately do that, it is the only way to know for sure.
I just recalled another potential problem: with different TRs but identical TE and bandwith, your flip angle is probably different. To get to 90 deg equilibrium signal for your excited protons, according to the Ernst formula your flip angle should depend on TR:
flip angle = arccos (exp (-TR/T1))
Some scanners adapt this automatically, on others you have to reset it yourself for different TRs (for 2DEPI only, for 3D this is really different).
This difference in flip angles might also leads to partially nonlinear changes in contrast between to groups, unfortunately. Your grey matter might be comparable, but due to smoothing and partial voluming you'll get unequal contasy into your voxels anyway.
I really think you will have to rescan one of the groups...
Cheers,
Bas
--------------------------------------------------
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 B.01.206, 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] <blocked::mailto:[log in to unmask]>
--------------------------------------------------
________________________________
Van: DANAY DIMA [mailto:[log in to unmask]]
Verzonden: donderdag 3 december 2009 16:04
Aan: Neggers, S.F.W.; [log in to unmask]
Onderwerp: RE: [SPM] Second level analysis with different TRs between groupsþþ
Dear Bas,
First of all thanks for your reply.
After more checking of the acquisition parameters for each group, I came across that the group with TR=3s has 36 slices and the group TR=2s has 16 slices, thus all the others parameters TE, voxel dimensions, interslice gap, matrix size and flip angle are identical.
As I understood from your message if this was the case I could be fine and perform second level analysis?
Best wishes,
Danai
> Subject: RE: [SPM] Second level analysis with different TRs between groupsþþ
> Date: Thu, 3 Dec 2009 15:47:20 +0100
> From: [log in to unmask]
> To: [log in to unmask]; [log in to unmask]
>
> Dear Danai,
>
> did both groups have the same number of slices per volume (but a different TR)? Did you use 2D acquisition (eg not 3D)? When the answer to both questions is yes (which seems likely gieven your message), it is hard to imagine that only your TR differs between the 2 acquisition schemes. With TR often your acquisition bandwith, TE and other parameters will change automatically or have to be changed to make the pulse sequence fit. This means you might have a different absolute intensity or even image contrast. You can ask your MR phycisist to check this for you or look at the pulse sequence yourself.
>
> With some acrobacy you can keep some of these other acquisition parameters constant with different TRs, but that would be highly unusual. Or when your parameters were the same per slice, but one group has more slices per volume than the other and hence a larger TR, you could also be fine (as acquisition parameters such as TE and bandwith per slice could be identical in that case).
>
> Having said that, fMRI contrasts between active and rest are relative and (at least) scaled for the session mean. So they might be comparable to some extent, providing all changes are linear with respect to each other (which of course they are in fact not, maybe only by approximation).
>
> When you actually compare 2 groups with eachother, and each group was scanned with a different TR (and probably other acquisition parameters as well), I would be highly suspicious of any statistical difference between groups as that might in fact have arisen due to differences in acquisition. When half of each group (eg, patients and controls or so) was scanned with one TR, and the other half of each group with the other TR, you might get away with it (but it will be harder to find anything as your 2nd level error term increases).
>
> In either way, the design you chose seems problematic I am afraid. Why didn’t you use the same acquisition in both groups if I may ask?
>
> The best solution would be to scan 1 group (the easiest group perhaps, eg controls?) again with the acquisition scheme from the other group, so that you can still use the data from the other group.
>
> All the best,
>
> Bas
>
> --------------------------------------------------
> 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 B.01.206, 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]
> --------------------------------------------------
>
>
>
> > -----Oorspronkelijk bericht-----
> > Van: SPM (Statistical Parametric Mapping)
> > [mailto:[log in to unmask]] Namens Danai Dima
> > Verzonden: donderdag 3 december 2009 14:15
> > Aan: [log in to unmask]
> > Onderwerp: [SPM] Second level analysis with different TRs
> > between groupsþþ
> >
> > Dear All,
> >
> > I have two groups that have performed exactly the same
> > experimental design and all the first level analysis was the
> > same for both groups.
> >
> > The difference though between the two groups is that one has
> > an fMRI acquisition TR of 2 sec and the other for 3 sec, all
> > the other parameters being the same. Thus one group has 270
> > T2 weighted images for each subject and the other group 180
> > T2 weighted images for each subject.
> >
> > Can I enter them in second level analysis or not, because of
> > this difference in the TR?
> >
> > Thanks for any help.
> >
> > Best wishes,
> >
> > Danai
> >
>
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