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]
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
Many thanks for your response.
Your answer seems to contradict most people's answers so far (unless I've
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,
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.
> 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!
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/