Hello,
I would like to add two remarks to John's mail:
>> 3) Within Normalise (Write) Writing Options, you must state the Voxel Sizes. Our acquisition voxel sizes are: 1.7 x 1.7 x 3. Would we then state 3 3 3 for the Voxel Size?
> Smaller voxel sizes are theoretically better (because the random field
> assumptions are best satisfied), but if the voxels are too small, then
> you quickly run out of disk space. Generally, I would suggest using
> the default settings of 2mm isotropic, which is what most people would
> do.
I think this is an interesting point as I usually normalize my
functional images (acquired at 3x3x3mm) to 3x3x3mm in order to avoid
interpolating too much (keep spm from "inventing voxels", so to say :) I
realize that even that is not quite correct as the scaling to MNI is
already on the order of 1.4, but thought it is better than to upscale to
a higher-than-original resolution. The multiple comparison issue also
comes into this equation at some point as fewer voxels = fewer tests.
The random field argument is not that much of an issue if you use
voxelwise FDR, which is independent of smoothness estimates. I must
admit, though, that I have not systematically investigated this. If
anyone has a more informed opinion than me on this issue, I would much
appreciate hearing it.
>> 4) Under Smooth, you must select the kernel size: "Highlight FWHM." We recall that many people double the voxel size. Therefore, if it is 3 as stated above, would we then choose 6 6 6 here?
> The optimal smoothing will depend on the size of the blobs you expect
> to find, the accuracy with which data can be aligned across subject,
> and various other factors. Random field theory is most accurate when
> the FWHM is a few times greater than the voxel sizes. More smoothing
> also means you have fewer independent tests, so statistics based on
> peak height will have fewer multiple comparisons to make (so smaller
> corrected p values). On the negative side, you can not be so specific
> about where the differences actually are. I could be wrong, but think
> most people currently use in the region of 8-12 mm FWHM of smoothing.
As it so happens, there was an interesting paper reviewing and
investigating this issue in today's issue of HBM: Ball et al.:
Variability of fMRI-response patterns at different spatial observation
scales, Hum Brain Mapp 33, 5: 1155–1171, see
http://onlinelibrary.wiley.com/doi/10.1002/hbm.21274/abstract
Cheers,
Marko
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PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
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http://www.medizin.uni-tuebingen.de/kinder/epn
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