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Subject:

Re: How to create a mean of two images - and tell SPM about it?

From:

Andre Szameitat <[log in to unmask]>

Reply-To:

Andre Szameitat <[log in to unmask]>

Date:

Tue, 9 Jun 2015 12:38:29 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1 lines)

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/

> ____________________________________________________

> 

> 

> --

> This message has been scanned for viruses and dangerous content by

> MailScanner, and is believed to be clean.





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