Andre,
> 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:
>
> ‘(i1+i2)/2’
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.
Cheers
Marko
--
____________________________________________________
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
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
____________________________________________________
|