I have only one question - but it needs a longer introduction:
After reading the many postings about slice timing settings for interleaved
data, I understand that the choice of reference slice is not as critical for
interleaved as it is for ascending or descending sequences. For ascending
and descending, I understand that the rationale behind the choice of
reference slice is to choose a slice that has been recorded in the middle of
a TR, in order to minimize the offsets to both ends of the TR. Furthermore,
I understand that SPM usually suggests the middle slice in space as the
reference slice and that the default sampled time bin is set to 1.
Nevertheless, the sampled time bin has to correspond to the reference slice,
no matter which slice one chooses.
Although I understand the premises, I am not sure about what the number 1
I enter when asked to specify a reference slice really refers to is it the
first slice in space or the first sampled slice (first slice in time)?
In order to point out the question more clearly, I would like to use our
settings as an example:
TR: 2.5 sec
38 slices
interleaved ascending sequence, starting with even slices, then odd slices:
(2
4
6
38
1
3
5
37)
total # of time bins: 16
reference slice: 1
time bin: 9
Our assumption leading to these settings was the following: reference slice
1 points to the first slice in space, i.e. the bottom slice which is in
our case the 20th sampled slice in time, recorded in the middle of the TR,
in time bin 9.
Now, I am not convinced that this assumption is correct because of the
following: when manually entering the data, SPM suggests slice 19 as
reference slice. It is unclear whether this points to the 19th slice in
space (which is in our case the middle slice in space indeed) OR to the 19th
sampled slice in time (which in our case would be slice 38 in space). This
of course influences the choice regarding the time bin setting, which is
important also for interleaved sequences.
If one enters the digit 1 when SPM asks for a reference slice, does this
digit really point out the spatial bottom slice 1 (recorded in the middle
of the TR in time bin 9), OR does SPM assume it is supposed to take slice
no. 1 in TIME (which in our case would be slice 2 in space, recorded in
time bin 1) as reference for slice timing?
So here is the question:
Does the number you enter in SPM for defining the desired reference slice
correspond to the number of slice in SPACE or in TIME?
In terms of the example: if I want to set the bottom slice 1 in space as
reference slice, do I have to type 1 or do I type 20 (bottom slice =
20th sampled slice in time)?
I am looking forward to your comments on this matter,
many thanks in advance,
Dina Schardt.
--
Dipl.-Psych. Dina Maria Schardt
Labor fόr Neuroimaging und klinische Neurophysiologie
Klinik fόr Psychiatrie und Psychotherapie
Johann Wolfgang Goethe-Universitδt Frankfurt
Heinrich-Hoffmann-Str. 10
D-60528 Frankfurt am Main
Germany
Tel: +49(0)69 6301 5389
Fax: +49(0)69 6301 3833
Email: [log in to unmask]
Web: http://www.bic.uni-frankfurt.de
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