Hi guys-
I have just talked to Stefan, and his recent mail below contained a slip:
> In the interleaved mode, the information given by Peter Erhard is correct;
for the rest it's clear anyway.
...did in fact refer to Dan's original mailing (as far as I can see).
Bottom line: watch out for the Feet>>Head or Head>>Feet setting and consider
the difference to analyze images you may perform the slice timing on (!).
Otherwise, Dan's ordinal slice list looks ok to me.
Best regards-
Andreas
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Dr. Andreas J. Bartsch phone: +49 (0)931-201-0
Division of Neuroradiology,
ecr.: -34791
BJMU Wuerzburg pager:
#3253
Josef-Schneider-Str. 11 fax: +49 (0)
931-201-34685
97080 Wuerzburg email:
[log in to unmask]
Germany
[log in to unmask]
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----- Original Message -----
From: "Thesen Stefan" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Wednesday, November 05, 2003 1:28 PM
Subject: Re: Request for info about order of acquisition on a Siemens Trio
> Dear group,
>
> the following may be helpful when dealing with the mosaic issue:
>
> There are basically two software versions for the Siemens systems:
>
> a) Numaris 3/3.5 (used for Open, Impact, Vision and older Harmony,
Symphony systems; easy to recognize as the operating system is SUN OS). Here
the image-order in the mosaics is the acquisition order (so the layout
changes if you switch e.g. from ascending to interleaved).
>
> b) Syngo based systems (used for Concerto, Harmony, Symphony, Trio,
Allegra; easy to recognize as the operating system is Windows). Mosaics can
be detected due to the V4 image type (dicom information), which states
"MOSAIC". Here the image-order in the mosaics is dependent on the image
numbering. Usually this is set to Feet>>Head, but this can be changed in the
measurement protocol by the user.
> The timing can be found out most easily by looking into some shadow
information: In any image from the syngo systems the measurement-protocol is
present (in ascii). You may find it by looking for "### ASCCONV BEGIN ###"
and "### ASCCONV END ###". Here you may also find the slice positions of the
single images.
> Now find "sSliceArray.ucMode". This is
> 0x1 for ascending
> 0x2 for descending
> 0x4 for interleaved
> In the interleaved mode, the information given by Peter Erhard is correct;
for the rest it's clear anyway.
> To calculate the timing, you just have to look at TR, delay_time_in_tr and
the number of slices. For example for TR=4100, delay=500ms, Slices=36, the
single slices are acquired each 100ms followed by a 500ms pause. As these
numbers a highly precise, you may calculate the relative time of any slice
within your experiment from this. This information is much more accurate
than looking at the acquisition time information within the dicom header.
>
> Hope this helps.
>
> best wishes, Stefan
>
> --------------------------------------------------------------------------
-
> Dr. Stefan Thesen
> Siemens AG Medical Solutions MR Applications Development
> MREA Neuro - Brain Mapping and Intervention
> Karl Schall Str. 6, D-91052 Erlangen, Germany
> phone: ++49-9131-84-7242 fax: ++49-9131-84-2186 email:
[log in to unmask]
> --------------------------------------------------------------------------
-
>
>
>
> -----Original Message-----
> From: Dr Krish Singh [mailto:[log in to unmask]]
> Sent: Mittwoch, 5. November 2003 10:01
> To: [log in to unmask]
> Subject: Re: Request for info about order of acquisition on a Siemens
> Trio
>
>
> Dear Peter,
>
> Many thanks for your response.
>
> Your answer seems to contradict most people's answers so far (unless I've
> misunderstood).
>
> In the Mosaic files the images are stored from inferior to superior in an
> non-interleaved fashion i.e. In straight anatomical sequence.
>
> In contrast to this, most of the answers I've received seem to suggest
that
> slices are acquired in an interleaved fashion, which is not reflected in
the
> slice-ordering within the Mosaic file.
>
> All the best,
>
> Krish
>
>
> On 5/11/03 8:51 am, "Peter Erhard" <[log in to unmask]> wrote:
>
> > I've been told by some Siemens guy (Edgar I guess) that you can see the
> > order of acquisition by looking at the intact mosaic image. The
subimages
> > are in the order of acquisition.
> > You can easily cut of the Dicom head with a 'tail' command and create a
> > .hdr with MRIcro.
> > Best,
> > Peter
> >
> > On Wed, 5 Nov 2003, Daniel Kimberg wrote:
> >
> >> Krish Singh <[log in to unmask]> wrote:
> >>> Slices: 25 Axial slices. Proscribed from inferior to superior.
> >> ...
> >>> 1) Is it possible to determine the order of slice acquisition
(interleaved
> >>> etc.) from the Mosaic DICOM files?
> >>>
> >>> 2) failing that, what is the default order of acquisition for the
> >>> epifid2d1_64 pulse sequence?
> >>
> >> Krish, hi. We had some back and forth on this topic with the Siemens
guys,
> >> and the upshot is that slice timing information is discarded for
mosaiced
> >> images. So barring some low level hacking of the Siemens code (I can't
> >> remember when in the pipeline this information is lost, but it was
early
> >> enough that I punted on doing the hacking), you have to fall back on
option
> >> 2 (which makes me uncomfortable, but it's the best we can do). I
suspect
> >> if enough people ask, they'll patch this at some point. They seem
quite
> >> responsive and proactive about these kinds of things. Incidentally, we
> >> have a trio here, but I believe without tremendous justification this
> >> applies as well to other up-to-date Siemens systems.
> >>
> >> Anyway, we checked on the slice order by acquiring non-mosaiced images
via
> >> a spin echo sequence, which someone assured us would have the same
slice
> >> order, and which are properly time stamped in the appropriate dicom
> >> fields. Here is a list of when (ordinally) each slice is acquired,
going
> >> from inferior to superior (for axial acquisition).
> >>
> >> for odd number of slices (example = 9)
> >> 0 2 4 6 8 1 3 5 7
> >>
> >> for even number of slices (example = 8)
> >> 1 3 5 7 0 2 4 6
> >>
> >> These are the ordinal indices of the slices, starting with the most
> >> inferior. So for odd, the most inferior slice is acquired first. For
> >> even, the most inferior slice is acquired second.
> >>
> >> Hope this helps!
> >>
> >> dan
> >>
> >
>
> --
> Dr K.D. Singh
> Senior Lecturer and Convenor of the Neuroimaging Research Group
> Neurosciences Research Institute
> Aston University, Birmingham B4 7ET, U.K.
> Tel/Fax: +44 (0)121 [359 3611 ext 5176/5190]/[333 4220]
> [log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
>
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