Marko,
Thank you very much for your reply.
> 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.
That is good to know. Although I always took good care to select them in the right order during first level specification, I always thought that I make more fuss about this as necessary. I would have thought that SPM at least re-orders by filename.
Kind Regards,
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: Marko Wilke [mailto:[log in to unmask]]
> Sent: 09 June 2015 13:02
> To: Andre Szameitat; [log in to unmask]
> Subject: Re: [SPM] How to create a mean of two images - and tell SPM about it?
>
> 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/
> ____________________________________________________
>
>
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