Is this concern about using 3D nifti still applicable to SPM at this point (SPM8)? I remember this being a concern on the list with some version of SPM5, but I've been using 4D nifti files with SPM8 extensively and have not noticed any issues.
-Mike
--
Mike Angstadt
Research Computer Specialist / PANLab Lab Manager
Department of Psychiatry / University of Michigan
(734) 936-8229
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Neggers, S.F.W.
Sent: Monday, November 19, 2012 3:56 PM
To: [log in to unmask]
Subject: Re: [SPM] Preprocessing Compatability
to add a few notes:
... also make sure that:
- you have 3D rather than 4D nifti (note that FSL uses 4D!)
- have all your 3D nifti images resliced the same way (same voxel2world mapping in the header for each image)
- voxel2world mapping in header is correct (I think shears are bad)
I remember that some older packages do not always store header info correctly, that is, not according to nifti specs, or misrepresent space. As Jonathan already stressed, laterality issues are notorious here (search the list for 'left-right flipping'). The Nifti standard solved that issue in theory, but in practice not all programmers adhere to it well. One might want to stick a vitamin capsule to the right temple of at least some of the subjects, allowing a conclusive check.
But when everything is 3D, in the same space and fully according to nifti specs you should be fine.
Best,
Bas
--------------------------------------------------
Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
Room B.01.1.03
Mail : Huispost B01.206, P.O. Box 85500
3508 GA Utrecht, the Netherlands
Tel : +31 (0)88 7559609
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Web : http://www.neuromri.nl/people/bas-neggers
: http://www.brainsciencetools.com (CEO)
--------------------------------------------------
________________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Jonathan Peelle [[log in to unmask]]
Sent: Monday, November 19, 2012 9:27 PM
To: [log in to unmask]
Subject: Re: [SPM] Preprocessing Compatability
Dear Landrew,
> Do SPM statistical procedures for fMRI assume or require that the data
> have been preprocessed using the modules within SPM? Phrased
> differently, are there any contraindications for preprocessing
> imagines in another software packing and conducting later analyses in SPM?
In principle there is no problem using SPM to analyze data that has been preprocessed using other packages. You just need to be aware what has already been done, and what is a standard part of the SPM first level model. For example, some software packages may write out data that has been highpass filtered; If you have data like this, you may want to turn off the highpass filter when setting up your SPM first level model.
With recent data I wouldn't expect there to be any laterality issues (assuming everything is Nifti compliant), but for older or nonstandard data this is always worth checking.
Hope this helps!
Best regards,
Jonathan
--
Jonathan Peelle, PhD
Department of Otolaryngology
Washington University in St. Louis
Office: (314) 362-9044
http://peellelab.org || http://jonathanpeelle.net
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