Hi Ged,
I thought that nobody answered this question because it was a foolish thing.
Thank you for your reply and your cue about imcalc.
I suspect that imcalc step is necessary otherwise spm does not consider mask
image. Maybe for this reason I got the same results both without mask and
with mask. Now I will try again using imcalc.
Every other suggestion is appreciated.
Best,
Federico.
-----Messaggio originale-----
Da: Ged Ridgway [mailto:[log in to unmask]]
Inviato: venerd́ 19 gennaio 2007 12.46
A: Federico Tubaldi
Cc: [log in to unmask]
Oggetto: Re: [SPM] Explicit mask of gray matter in SPM5
Hi Federico,
> In SPM 5 when I specify model at the 1st level I can select an
> explicit mask. I select smwc1_subxx.img as explicit mask. I obtain
> this image with segmentation (mwc1_subxx.img) and after I smooth it
> with the same FWHM (8
> mm) as EPI
...
> Following this procedure I expect to model only gray matter
> activations and also I expect to have more statistical power when I
> apply FWE or FDR
I was reluctant to comment on this, since I have no experience of functional
imaging, but it seems no-one else has, so...
I think it sounds broadly reasonable, certainly FWE correction will be less
harsh with a smaller search volume, FDR probably also, though I think it's
harder to predict. I think how much of a good idea it is might depend on how
good your segmentations look (are they from separate structural MRI? If so,
are they well-aligned with the normalised EPI?).
An important point to note is that the stats masking uses (mask>0) to decide
if a voxel should be included; the smoothed segmentation will actually have
very small but non-zero values out quite far from the edge of the original
segment (overall kernel size, rather than kernel
FWHM) so your mask will probably be a lot bigger than you expect it to be.
You probably want to first threshold and binarize the segmentation, at a
threshold like 0.05, 0.1, or maybe 0.2. E.g. with imcalc, something like
'i1>0.1'.
Personally, I'd recommend thresholding at several levels and then having a
look with check reg to compare the mask with the original segmentation, and
with the images you intend to use it on.
Best,
Ged.
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