[Neuroimaging] slice timing check

[Bertrand Thirion]

Samll error: slices_times = linspace(0, TR - (TR / nz), nz) # delays 
Otherwise I'm surprised too. What parameters do you give to SPM12 ? 

B 
----- Mail original -----

> De: "Christophe Pallier" <christophe at pallier.org>
> À: "Neuroimaging analysis in Python" <neuroimaging at python.org>
> Envoyé: Mercredi 14 Février 2018 19:57:05
> Objet: [Neuroimaging] slice timing check

> Hello,

> I am trying to check various implementations of slice timing correction,
> including the pure python version in pypreprocess.

> To this end, I have written a python script (attached) to generate a sinewave
> 'activation' pattern shifted along the z axis.

> The result (`sinewave.nii`, included in the attached zip file) looks fine.

> However, when I run the slicetiming correction with SPM (ot for that matter
> pypreprocess), with what I believe are the correct parameters, the delays of
> the various slices are not corrected as I would have expected (see
> asinewave.nii: I would have expected the z delays to be corrected and the
> image to be essentially uniform; the parameters for SPM are simply TR=1s,
> slice order=ascending; 40 slices)

> I apologize because this is not really a Python question, but if I solve the
> issue, I may be able to convince colleagues that the pure python slice
> timing correction in pypreprocess is doing the right thing. So, basically, I
> hope that someone points out my mistake.

> Best,

> --
> --
> Christophe Pallier < christophe at pallier.org >
> INSERM-CEA Cognitive Neuroimaging Lab, Neurospin, bat 145,
> 91191 Gif-sur-Yvette Cedex, France
> Tel: 00 33 1 69 08 79 34
> Personal web site: http://www.pallier.org
> Lab web site: http://www.unicog.org

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