The relationship between voxel index and anatomical location will be
dependent on the orientation in which the data is stored.
If the 3rd dimension is stored with a "Inferior-to-Superior"
orientation, then data(:,:,1) will indeed be inferior-most anatomically.
However, if its "Superior-to-Inferior" then that slice will be superior-
most anatomically.
cheers,
-Mike H.
On Fri, 2010-05-21 at 15:09 +0200, Thilo Kellermann wrote:
> 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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