The slice that SPM considers as the first is the one that has a voxel
coordinate of *,*,1 when you use the Display button. The ordering of
the slices in the volume is likely to depend on the way that the
original DICOM files were converted to NIFTI/ANALYZE. In the SPM DICOM
conversion, the planes are ordered so that the storage of the voxels has
the same handedness (see
http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14 ) every time
(providing that nobody messes with the flip settings). Therefore, for
axial images, the order of the slices would be reversed if one of the
within-plane directions is reversed. The within-plane directions often
depend on how the field of view of the scan is defined, and can be
changed by something as trivial whether the radiographer makes a
left-right drag of the mouse, or a right-left.

Best regards,
-John

-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On Behalf Of Pieter Vandemaele
Sent: Wednesday, November 29, 2006 10:36 AM
To: [log in to unmask]
Subject: Re: [SPM] Slice time correction: SPM5

Hi all

I looked into the code of SPM and my best guess is that SPM looks at the

slice position for each slice and makes the bottom slice (closest to the

neck as Darren stated) the first slice, regardless of the slice
acquisition order (maybe someone at the FIL could give some more
information?).
In spm_dicom_convert.m, lines 483-498 explain:

    % Orientation information
    %-------------------------------------------------------------------
    % Axial Analyze voxel co-ordinate system:
    % x increases right to left
    % y increases posterior to anterior
    % z increases inferior to superior
   
    % DICOM patient co-ordinate system:
    % x increases right to left
    % y increases anterior to posterior
    % z increases inferior to superior
   
    % T&T co-ordinate system:
    % x increases left to right
    % y increases posterior to anterior
    % z increases inferior to superior

Then you just have to know how your scanner aqcuired the slices. We have

investigated this (with a Siemens engineer) on a Siemens Trio Tim and
provided some feedback to the mailing list:
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0610&L=SPM&P=R66949&I=-3
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0610&L=SPM&P=R172136&I=-3
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0611&L=SPM&P=R19543&I=-3

I hope someone wants to retest so we can be sure about this topic.
Regards

Pieter

--
Pieter Vandemaele
MSc - Ing

Ghent University Hospital
NMR Department -1K12
GIfMI Research Group
De Pintelaan 185
9000 Ghent
BELGIUM
t: ++32 (0)9 240 48 20
f: ++32 (0)9 240 49 69
e: [log in to unmask]


Darren Gitelman schreef:
> Hi Mike
>
> Slice timing can be very confusing, and in fact we just went through a
> discussion here at the lab to get the order correct.
>
> First, one of the best pieces of advice ever, was from Dan Kimberg
about a
> month ago about confirming the order of the slices. Dan wrote:
>
>
>> Someone here at Penn verified this about three years ago, by running
an
>>
> EPI sequence that
>
>> saved each slice separately (in which case you actually get time
stamps
>>
> for each slice).
>
> After Dan suggested it we did it here and fortunately confirmed the
slice
> ordering we thought we were using, but you never know until you look.
>
> So first off, make sure you know your slice order. Siemens for example
uses
> a different slice ordering depending on whether one acquires an odd or
even
> number of slices. GE may have its own quirks. Superior and inferior
may also
> vary depending on the orientation of the images and the subject (or
what the
> scanner thinks the orientation is).
>
> In SPM parlance, slice 1 is always the most inferior slice, i.e.,
closest to
> the neck. This assumes the slices are acquired transversely. If the
slices
> were not acquired transversely, I'm not sure the software will deal
with it
> correctly (it may, I'm just not sure). According to your description
the
> bottom slice in the volume is acquired first followed by all the odd
slices
> until #25, then slice 2 followed by the even slices.
>
> In this case you should specify the slice order as [1:2:25, 2:2:24];
if you
> wanted the middle slice in time as the reference slice, you would
specify
> slice #25. To make this match up to the onsets for your tasks, in the
fMRI
> specification you would then specify the microtime resolution as 25,
and the
> microtime onset as 13 (this is the middle bin in time corresponding to
> anatomical slice#25 in your slice timing).
>
> Hope this helps, and feel free to let me know if it does not.
>
> Darren
>
> -----Original Message-----
> From: Glabus, Michael [mailto:[log in to unmask]]
> Sent: Tuesday, November 28, 2006 2:54 PM
> To: Darren Gitelman
> Subject: FW: [SPM] Slice time correction: SPM5
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On
> Behalf Of Mike Glabus
> Sent: Tuesday, November 21, 2006 11:08 AM
> To: [log in to unmask]
> Subject: [SPM] Slice time correction: SPM5
>
> We run a GE EPI BOLD sequence that collects slices in an interleaved
manner,
> superior -> inferior, i.e. top -> bottom in SPM5 parlance (which I
think is
> referring to the top and bottom of the head, although I might be
wrong..).
> So, as far as I know, the slice sequence is 1, 3, 5, 7, ...25;
>
> 2, 4, 6, ...24.
>
> When I use what I think is the appropriate the formula for this
sequence
>
> in the SPM5 manual - interleaved (top -> down): [nslices:-2:1,
> nslices-1:-
> 2:1] I get
>
> 25, 23, 21, 19, 17, 15, 13, 11, 9, 5, 3, 1, 24, 22, 20, 18, 16, 14,
12, 10,
> 8, 6, 4, 2
>
> which seems wrong as the order the vector is read is left to right,
where
> the last slice (24) should be first in the list. Some of the confusion
stems
> from the statement that "Bottom slice = 1" in the manual - (???)
>
> Could someone clarify this please.
>
> Many thanks - Mike
>