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]>
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
>> >> >
>> >>
>> >>
>> >
>
