I have confirmed that running the 'interleaved' option '0 2 4... 1 3 5
..' gives identical results to using a slice order text file written
'1 3 5 ... 2 4 6 ...'. (I also note that doing it the 'wrong' way, or
with no correction, doesn't make much difference, at least for my
analysis).
Dan
On 6/28/07, Steve Smith <[log in to unmask]> wrote:
> Hi Peter, Dan,
>
> Yes - apologies for the confusion - I'm afraid that for historical
> reasons the numbering in slice timing is pretty messy and
> inconsistent with most things in FSL.....we should really fix that
> though of course that will screw anyone already having working
> solutions....
>
> According to the doc in http://www.fmrib.ox.ac.uk/fsl/feat5/
> detail.html#prestats
> in a slice ordering file the lowest slice should be called 1 and not 0.
> As far as I know this is correct.
>
> Cheers.
>
>
>
>
> On 28 Jun 2007, at 15:51, Peter Fried wrote:
>
> > Hi Dan,
> >
> > To my knowledge, any slice or volume info put into FSL has to be
> > (n-1). I
> > assume that this is also the case for creating the slice-order
> > file. Can
> > anyone at FMRIB confirm this? Thanks.
> >
> > -Pete
> >
> >> Hi Peter and Andreas,
> >> Thank you. I now clearly understand that for an even number of
> >> slices, Siemens takes the second, fourth, sixth etc slice, then the
> > first, third, fifth, etc slice.
> >> But I am still not sure how to write that in the slice order file...
> > there are two ways to write it:
> >>
> >> 1) '2 4 6... 1 3 5 ...'
> >> or
> >> 2) '1 3 5... 0 2 4 ...'
> >>
> >> Peter's example shows method #2, but the Feat instructions for a
> >> slice
> > order file say "The first slice is number 1, not 0" which seems to
> > describe method #1.
> >>
> >> Sorry to belabor the issue, I am hoping for full clarity for
> >> myself and
> > those who come upon the same question later.
> >>
> >> Dan
> >>
> >>
> >> On 6/27/07, Andreas Bartsch <[log in to unmask]
> >> wuerzburg.de>
> > wrote:
> >>> Hi,
> >>> I think per default Siemens tries to avoid recording the most outer
> > slice last. Thus, for even slice numbers (N=6, for example) the
> > excitation reads:
> >>> 2 4 6 1 3 5
> >>> For odd (N = 5), you get:
> >>> 1 3 5 2 4
> >>> Furthermore, transversal slices are usually recorded feet->head,
> > sagittal slices right->left.
> >>> However, the image numbering may be set to non-default values. You
> > would
> >>> see that in the protocol entry
> >>> sSliceArray.ucImageNumb... = 0x1
> >>> And you must then check how this all translates into your converted
> > data;)!
> >>> Cheers-
> >>> Andreas
> >>> -----Ursprüngliche Nachricht-----
> >>> Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im
> > Auftrag von Peter Fried
> >>> Gesendet: Dienstag, 26. Juni 2007 22:00
> >>> An: [log in to unmask]
> >>> Betreff: Re: [FSL] Slice Order
> >>> To the best of my knowledge, yes.
> >>>> Hi Peter,
> >>>> Thank you! Does that mean that I was wrong about the Siemens
> >>>> scanner
> > collecting odd slices first, when the total number of slices is even?
> > Dan
> >>>>
> >>>> On 6/26/07, Peter Fried <[log in to unmask]> wrote:
> >>>>> Hi Dan,
> >>>>>
> >>>>> I ran into the same problem when I started. You'll want to
> >>>>> create a
> > text file that reads {1, 3, 5, ..., 0, 2, 4, ...} (each number on a
> > new line).
> >>>>>
> >>>>> This is fsl-speak for {2, 4, 6, ..., 1, 3, 5, ...}, which is the
> > interleaved order for an even number of Siemens' slices.
> >>>>>
> >>>>> I'll attach the version I use for a 34-slice acquisition on a
> >>> Siemens.
> >>>>> Note that it is a slice-order file, not a slice-timing file as the
> > name suggests.
> >>>>>
> >>>>> -Pete
> >>>>>
> >>>>>> Hello,
> >>>>>> I am not sure which slice order option to use. We use a
> >>>>>> Siemens 3T,
> >>>>> and
> >>>>>> collect an even number of
> >>>>>> slices; my understanding is that in this situation the odd slices
> > are collected first.
> >>>>>> The interleaved option "0 2 4... 1 3 5" looks like it is even
> > numbers first, but in the instructions for making a slice order
> > file, it says the first slice should be 1, not zero...so perhaps
> > the interleaved option is really doing odd slices first (ie, '0 2
> > 4' refers to the
> >>>>> first,
> >>>>>> third and fifth slice)? Is using a slice order text file that
> > says
> >>>>>> "1 3 5 ... 2 4 6..." the same as using
> >>>>> the
> >>>>>> interleaved option?
> >>>>>> Thanks,
> >>>>>> Dan
> >>>>>>
> >>>>>
> >>>>>
> >>>>
> >>
>
>
> ------------------------------------------------------------------------
> ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ------------------------------------------------------------------------
> ---
>
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