[Neuroimaging] slice timing check

[Christophe Pallier]

Oops ofr the bug. Thx.

Here were the parameters for SPM:

matlabbatch{1}.spm.temporal.st.nslices = 40;
matlabbatch{1}.spm.temporal.st.tr = 1;
matlabbatch{1}.spm.temporal.st.ta = 0.975;
matlabbatch{1}.spm.temporal.st.so = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40];
matlabbatch{1}.spm.temporal.st.refslice = 1;

I though maybe I did the slice delay shifts in the wrong direction, so I
modified the script to output two images, one with positive and one with
negative shifts (as if one was acquired in ascending order and the other in
descending order, but I applied the slice timing with 'ascending' to both)

The new script, the output files and the files with slice timing corrected
are at:

https://github.com/chrplr/slice-timing-check.git


On Thu, Feb 15, 2018 at 8:56 AM, Bertrand Thirion <bertrand.thirion at inria.fr
> wrote:

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


-- 
--
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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