Dear Helmut,
Thank you very much for your reply.
> 1) smoothing was applied accidentally another time / with a larger smoothing kernel (trivial)
I don't change the standard parameters for smoothing in any processing step, so it could have happened only by mistakenly changing a parameter without noticing. However, I did the analysis twice, once quite a while ago in SPM8 (and this was actually with students running the analysis individually on their lab computers), and now with SPM12. I think it is very unlikely that this mistake would have happened twice.
> 2) the raw data were acquired with a (very) large voxel size, interpolation to 2x2x2 mm^3 would result in many more voxels
No, physical scanning resolution was 3x3mm in-plane resolution, 3mm thick, no gap, interleaved slice acquisition. The site I scanned was a proper research setting with two well-maintained scanners and expert personnel. This, of course, doesn’t exclude mistakes, but it seems rather unlikely. Also, scanning was spread across two days and all data show the problem.
> 3) high spatial autocorrelation on single-subject level due to some global effects (massive drifts?)
a) How could I check for this?
b) Shouldn't the HP filter remove such massive drifts? (HP filter was 1/165s)
> 4) possibly overfitted models, resulting in very small residuals (?)
It was a blocked design with 35s block length. Indeed, all blocks are modelled (convolved HRF). However, blocks were separated by 4s (2 TRs) inter-block-interval to display the instructions, and these 4s were not modelled. However, I used this procedure many times and never had problems with it. The design matrix is attached.
We had 2 sessions, each with ~500 volumes (TR 2s), i.e. roughly 1000 volumes in total. There are 12 different experimental conditions, and each conditions has been repeated 6 times (3 times per session). Not all conditions had the same duration. Some conditions will be combined for analysis.
> Thus, do you observe the FWHM for all your subjects (how much variability is there?),
I checked based on the first-level contrasts for each subject. Yes, it is bad (even worse) on the single-subject level:
For most subjects, 1 resel consists of 10000-13000 voxels, up to 17000 voxels. This means, that many participants have only 10-50 resels in the whole brain.
FWHM is usually in the range of 18-25mm in each dimension.
On the single-subject level, smoothness is identical for all contrasts.
On the second level, smoothness varies but is always poor. I didn't check all possible contrasts, but I observed values between 1655 and 9400 voxels constituting one resel.
Just as a reminder, while all these things are strange, the pattern of activated brain areas is as expected. This seems to preclude any severe errors, e.g. a struggling DICOM import filter sorting the files in the wrong order, or alike...
I'm happy to do any further checks if that is of any help.
Best wishes,
Andre
_______________________________________________________
Dr André J. Szameitat
Reader in Psychology
Co-Director Centre for Cognition and Neuroimaging (CCNI)
T +44(0)18952 67387 | E [log in to unmask]
Gaskel Building, Room GASK263
Office hours: Wed 11.30-12.30, Thu 13.30-14.30
_______________________________________________________
> -----Original Message-----
> From: H. Nebl [mailto:[log in to unmask]]
> Sent: 22 June 2015 14:13
> To: [log in to unmask]; Andre Szameitat
> Subject: Re: Huge resels? (1 resel = 2400 voxel)
>
> Dear Andre,
>
> The voxel count within the volume sounds reasonable for a whole-brain analysis
> (minus possibly the most dorsal or ventral parts reflecting the field of view). The
> FWHM seems to be very large though. In general, it might be large due to
> (unusually) large applied or intrinsic smoothness, maybe
> 1) smoothing was applied accidentally another time / with a larger smoothing
> kernel (trivial)
> 2) the raw data were acquired with a (very) large voxel size, interpolation to
> 2x2x2 mm^3 would result in many more voxels, which are highly dependent
> though (might also be a scanner setting, some sequences offer to reconstruct
> the data with a higher spatial resolution than that with which it was acquired)
> 3) high spatial autocorrelation on single-subject level due to some global effects
> (massive drifts?)
> 4) possibly overfitted models, resulting in very small residuals (?)
>
> Thus, do you observe the FWHM for all your subjects (how much variability is
> there?), or only on the group level (which might be affected by a very extreme
> subject)? In the later case, is this just for a particular contrast / that particular
> one-sample t-test or for all the contrasts?
>
> Best
>
> Helmut
>
>
> --
> This message has been scanned for viruses and dangerous content by
> MailScanner, and is believed to be clean.
|
