> I would like to replace the faulty images by the mean of the surrounding
> images. For this I would use ImCalc in SPM12 with the following expression:
Yes, although you could also use 'mean(X)' and activate "load images
into matrix". Or you could use a combination of spm_select, spm_vol,
spm_read_vols and spm_write_vol, but either way should work.
> My question is: Is this newly created volume 3 “accepted” by SPM as the
> third volume, e.g. when I specify first-level statistics? Or is
> information in the header used for this?
SPM will take the images as you supply them, assuming you know what you
are doing. So if you select the images in a given order, they will be
assumed to be in this order, temporally.
> The header information is probably wrong in the newly created file, and
> therefore it may mess up the assignment of files to timesteps SPM
> internally (e.g. having file1 – timestep1; file 2 – timestep2; file3
> (newly created, wrong header) – ignored; file4 –timestep 3 = from now on
> all onsets are wrong by one TR)
If you supply one "new" image for each image missing, the information in
the remaining "original" images should be correct.
> If my solution doesn’t work, is there another easy and straightforward
> way without the need to just leave out the image and adjust the onset
> vectors? For instance, adjusting the header.
I have not used it much but I think what you want can pretty easily be
achieved by the ArtRepair toolbox.
> (having an extra regressor for the bad volumes doesn’t work here because
> they result in SPM error messages and abortion of the processing)
This should not happen - if, in the ensuing analyses, you enter a null
regressor for each volume you replaced, this should not lead to an error
(unless you thus overspecify the model, with 60 regressors for 50 scans
or so)?? Such a regressor would not, or should not, be different from
any other regressor you enter, and should not lead to an error per se.
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
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