Hi Carolyn,
in general: why should activation (or any voxel) location be at exact multiples of your voxel size? With the voxel-to-world mapping in the nifti header, world space coordinates can literally be anything, and still be perfectly according to specs.
See http://nifti.nimh.nih.gov/nifti-1/ for the full specs.
Or are you referring to a specific template space? If so, which one?
When you are (let's assume you work in human MNI152 space), check your bounding box in the normalization>write section. When that's not a multiple of your resample voxel size (during normalization), weird things can happen as SPM needs te squeeze a multiple of voxels in there somehow.
Just a hunch.
Cheers,
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
Fax : +31 (0)88 7555443
E-mail : [log in to unmask]<mailto:[log in to unmask]>
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 McGettigan, Carolyn [[log in to unmask]]
Sent: Thursday, November 15, 2012 4:28 PM
To: [log in to unmask]
Subject: [SPM] Shifted centring for 3x3x3mm resampled voxels
Dear SPM Users
I have been using the latest version of SPM8 and noticed that the coordinates for local peaks are showing values in the y and z axes that are not multiples of the resampled voxel size – for 3x3x3mm, which I use as standard, I have always previously found peaks centred at 0, 3, 6, 9, etc.. When I open the estimated SPM.mat in the current data set, I see that the origin voxel is centred at [0 –1 1] and when I simply correct the peaks for this offset, the values fit back into the familiar framework of multiples of 3 in all directions.
I am happy that a difference of ±1mm in my peak labels bears no impact on interpretation of the data and this is simply a reflection of how the grid of voxels is centred for this resampled size. But I don't understand why it doesn't happen consistently across data sets with 3x3x3 resampled voxels. I am also concerned that reviewers don't respond well to these unusual voxel labels - a colleague was pulled up on this very issue, but in his case values re-centred on [0 0 0] when he downloaded an updated version of SPM8 and re-analysed everything….
So, I have a couple of questions:
1. Can anyone offer me a little more detail on why this altered centring of a 3x3x3mm voxel grid isn't consistent across data sets?
2. If it is something we can't control for, would you find it acceptable to correct for the offset of the origin by simple addition and subtraction (i.e. +1 in the y, -1 in the z)? It seems to me that reviewers expect to see peaks that reflect the standard centring at [0 0 0].
Thanks and best wishes,
Carolyn McGettigan
------------------------------------------------------------------------------
De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
------------------------------------------------------------------------------
This message may contain confidential information and is intended exclusively
for the addressee. If you receive this message unintentionally, please do not
use the contents but notify the sender immediately by return e-mail. University
Medical Center Utrecht is a legal person by public law and is registered at
the Chamber of Commerce for Midden-Nederland under no. 30244197.
Please consider the environment before printing this e-mail.
|