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SPM  May 2010

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Subject:

Re: Slice Time Correction

From:

Thilo Kellermann <[log in to unmask]>

Reply-To:

Thilo Kellermann <[log in to unmask]>

Date:

Wed, 19 May 2010 12:29:48 +0200

Content-Type:

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Hi Ed,

to make things a little more complicated: Usually you are right, that odd 
slices are measured first followed by the even ones. On a Siemens Trio 
machine, however, this is not always true (unless you use a self-programmed 
sequence). On a Trio the order depends on the number of slices - if you have 
an even number, the even slices are measured first and then the odd slices. 
Only if you have an odd number of slices the "normal" sequence (odd first, 
then even) is used.

In this case the slice order specification from top to bottom should be:
nslices = 28;
[nlsices-1:-2:1 nslices:-2:1]

The slices are numbered from bottom to top and the sequence gives the 
acquisition order. So if you are measuring from top to bottom and your number 
of slices is 28 on a Siemens Trio, the first slice you measure is no. 27, 
according to this numbering.

In this case slices 1 and 28 are measured in the middle within a TR and the 
choice of either one should be ok. If you are more interested in dorsal parts 
of the brain 28 might be more appropriate. Unfortunately when acquiring 
slices interleaved you never know, when the most interesting slice is being 
measured. If the region you are interested in is spreaded over more than one 
slice, this region will be measured at quite different times within a TR 
anyway (namely with a delay of about TR/2).

Good luck,
Thilo


On Monday 17 May 2010 19:53, Modestino, Edward J *HS wrote:
> Hello,
> I am in the process of attempting slice timing correction after completing
> realignment.  I have two questions: (1) I noticed that in the SPM8 manual
> there is mention that slice timing correction will be removed in the
> future.  Why?
>
> (2) My EPI data is collect on a Siemens 3T MAGNETOM Trio in an interleaved
> (odd slices first: odd 1:27 followed by even 2:28) sequence staring from
> the top to bottom with 28 slices and a TR of 2 seconds.  Slice timing is
> not working.  So, here are my specs.  Please let me know if I have
> something wrong:
>
> number of slices: 28
> TR: 2
> TA: 2-2/28
> Slice Order:  I am choosing the option for interleaved top->bottom, so I
> follow the input examples given there: TOP TO BOTTOM accoring to John
> Christopher
> interleaved top->down [nslices:-2:1, nslices-1:-2:1]
> 28:-2:1, 28-1:-2:1
> displays [28 26 24 22 20 18 16 14 12 10 8 6 4 2 27 25 23 21 19 17 15 13 11
> 9 7 5 3 1]
>
> Shouldn't this order be the following instead [1 3 5 7 9 11 13 15 17 19 21
> 23 25 27 2 4 6 8 10 12 14 16 18 20 22 24 26 28]
>
> What does it mean that bottom slice = 1, as we are going top to bottom and
> the top slice is 1?  How can the bottom slice be 1?
>
> Reference slice: 2 (or I could use slice 27)
>
> Thanks,
> Ed Modestino
>
> Edward Justin Modestino, Ph.D.
> Postdoctoral Research Associate
> Ray Westphal Neuroimaging Laboratory
> Division of Perceptual Studies
> Department of Psychiatry and Neurobehavioral Sciences
> University of Virginia

-- 
Thilo Kellermann
RWTH Aachen University
Department of Psychiatry and Psychotherapy
JARA Translational Brain Medicine
Pauwelsstr. 30
52074 Aachen
Germany
Tel.: +49 (0)241 / 8089977
Fax.: +49 (0)241 / 8082401
E-Mail: [log in to unmask]

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