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
------------------------------------------------------------------------
---
|