Dear Freesurfers,

I spent some time and answered my own question, which (after thinking about the problem) is a really stupid one.
I only analyzed 15 subjects with the 160 slices MPRAGE.
If I'll have some more time I'll analyze the 176 versions also, but after these results It will have extremely low priority.

Theoretically the SNR gain from the extra 16 slices in my case is 4%. Which is further reduced a bit due to some other effects like inhomogenity, etc, but let's say it is the maximal 4%.

The inter-subject variance of SNR (in %) (i.e. CV) (SNR calculated in 3 ways: signal avg/sd of noise; (signal avg-noise avg)/sd of noise; signal avg/noise avg, whichever you prefer) is 9.20%, 9.28% and 8.13% respectively. The biggest differences between the highest and lowest SNR among the 15 patients in % are 30.6%, 30.9% and 33.6% respectively.

The SNR is so different between two measurements (which is not surprising, as it is affected by dozens of factors (even head size, but if you think about the contrast, as the MPRAGE is a T1 image, it's easy to understand that the T1 time of the tissue severely affects your measured signal, and T1 time differs in people around 10% in healthy young ones), but if you repeat the MPRAGE in the same subject within the same session and let the scanner adjust everything again, you will still get quite different SNRs, within the same patient)

I think it is very unlikely that the 4% of extra SNR would cause any bias in the comparison. 

Being honest, If it caused any bias, more serious problems would emerge: as you could not compare anybody, ever.
As the age, level of hydration (how much he/she drunk in the last few days), sex, periods in women, many more can all affect the SNR more than the 4% mentioned above.  

But as this problem can be discussed from many points of view, it would result in an endless ati/nvidia type thread, which would not beneficial and would be only the waste of time, so for me, the thread is closed.

Thank you for your replies and generous help.

Best Regards,

Gergely






2011/1/20 Michael Harms <mharms@conte.wustl.edu>

Hi Gergely,
Was this collected on a Siemens scanner? If so, the Siemen's MPRAGE
sequence is such that the "slices" form the "inner loop" of the
acquisition -- that is "Number of slices" lines in k-space are acquired
for each TR period.  So, having a differing number of slices theoretically
has an impact on the spatial filtering properties of the acquisition.  My
intuition suggests to me that this would be a minor effect that would be
washed out by other noise and inter-subject differences.  But perhaps
others have quantitative results in this regard...?  (e.g., collecting
both sequences on a set of subjects and then looking for differences using
an intra-subject design).

cheers,
-MH

> Hi Freesurfers,
>
> I have a quick question:
>
> I have two groups, both measured on the same scanner, with the same
> sequence
> (3D MPRAGE), and with almost
> the same parameters.
>
> TR/TE/TI/BW/MATRIX/FOV/FOV-phase/Flip angle/Slice thickness/in-plane
> resolution... everything is the same, but the number of slices.
> Total measurement time was also the same.
>
> One group was measured with 160 slices, the other with 176.
>
> Can I compare the two groups in freesurfer?
>
> Thanx,
>
> --
> Gergely Orsi
> biologist - research associate
> Diagnostic Center of Pécs
> H-7623 Pécs, Rét str. 2.
> Tel.: 0036-70-3174676
> E-mail: gergo.orsi@gmail.com
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--
Gergely Orsi
biologist - research associate
Diagnostic Center of Pécs
H-7623 Pécs, Rét str. 2.
Tel.: 0036-70-3174676
E-mail: gergo.orsi@gmail.com