Hi Thilo,
In DICOM header file, there is a vector contains the acquisition time of each slice. In my experiment, this 32*1 vector is [992.5 0 1055 62.5 1117.5 125 1180 185 1242.5 247.5 1305 310 1365 372.5 1427.5 435 1490 497.5 1552.5 557.5 1615 620 1677.5 682.5 1737.5 745 1800 807.5 1862.5 870 1925 932.5]. So I think the Trio acquired even first. But from this DICOM header file I can't find anything about top-down acquisition or bottom-up acquisition. Do anyone know something about this?
-----Original Message-----
From: Thilo Kellermann [mailto:[log in to unmask]]
Sent: 2010年5月21日 21:09
To: Feng Lu
Cc: [log in to unmask]
Subject: RE: [SPM] Slice Time Correction
Hi Feng,
yes it was a mistake - sorry about that. Thanks also to Michael Erb who
brought my attention to that point. However, I am still confused,
because Michael wrote that the slice numbering in the header changes
when the acquisition is changed from bottom-up (bottom is 1, top is
nslices) to top-down (top is 1 and bottom is nslices).
If this numbering is preserved in the Nifti-header and in SPM, then
there are only two different specifications for the slice order:
[1:2:nslices 2:2:nslices] for odd number of slices
[2:2:nslices 1:2:nslices] for even number of slices
irrespective of bottom-up or top-down acquisition mode.
If, however (and this was my assumption), in SPM slice 1 is always the
lowermost slice and nslices is the topmost slice, the above mentioned
specifications for top-down acquisition will change to:
[nslices:-2:1 nslices-1:-2:1]
irrespective of odd or even number of slices, since nslices changes
accordingly...
In any way, one has to find out, in which chronology the slices are
acquired (and possibly numbered...) AND how SPM refers to the slices. Is
it correct, that in SPM the (spatial) slice reference is always
1:nslices, with 1 being the lowermost and nslices being the topmost
slice?
Sorry for messing things up......
Thilo
On Fri, 2010-05-21 at 09:42 +0800, Feng Lu wrote:
> Hi Thilo,
>
> Thank you for this mail because I met the same problem just now. But I feel confused. You said ' if you have an even number, the even slices are measured first and then the odd slices '. According to this, I think if the slice order specification from top to bottom and nslice = 28, the sequence should be [nslice:-2:2 nslice-1:-2:1]. Is it a small mistake?
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Thilo Kellermann
> Sent: 2010年5月19日 18:30
> To: [log in to unmask]
> Subject: Re: [SPM] Slice Time Correction
>
> 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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