Hi,
Last month, our TRIO system has been upgraded. We found out that, if the
acquisition parameter is set to "ascending", the acquisition happens from Start
to end (see "help" on console) . What is Start? That depends on the patient
registration: if you register a subject's position as "head first - supine",
then "start" is top of the head. So scanning "ascending" means: H-->F, although
you've set the slice numbering from F-->H!!
It seems that "acquisition order" and "slice numbering" are two independent
things for the system! This means that if you scan "ascending", and your image
numbering is F-->H, the chronological order of your slices is [nslices:-1:1]
(indeed: opposite)! So what you call "first slice" was acquired as last slice.
Same for interleaved scanning, only one thing: it looks like the scanner always
starts with the first slice surrounded by two other slices (which already start
relaxation during this short period (max. TR/2)). We think the interleaved
acquisition order (with image numbering F-->H) is then: [nslices-1:-2:1
nslices:-2:1].
It's nearly impossible to check this with an EPI sequence, because the system
creates a mosaic image in which all exact slice timing information is lost. We
checked this with a diffusion sequence (I think it was ep2d_diff - must check
this). This sequence generates different images.
We are still in contact with the Siemens engineer to become a confirmation about
all this.
All the best with this issue!
Benedicte
Citeren Darren G <[log in to unmask]>:
> thanks
>
> I know about the sSliceArray.ucMode flag. However, it seems that siemens is
> tricky with the order
> of the slices. assuming the slices are numbered from 1 (foot) to n (head),
> for an interleaved
> acquisition it appears that the slice order is
>
> For an odd number of slices (N = odd)
> 1:2:N, 2:2:N-1
>
> For an even number of slices (N = even)
> 2:2:N, 1:2:N-1
>
> is this what others have? or is there a way to verify it?
>
> thanks
> darren
>
> ==============Original message text===============
> On Mon, 30 Oct 2006 12:49:31 pm CDT Roland Marcus Rutschmann wrote:
>
> On Monday 30 October 2006 15:52, Darren G wrote:
> > Hi
>
> Hi,
>
> > For Siemens Trio files, does anyone know what field in the DICOM header
> > contains the slice acquisition order information for functional MRI files.
>
> try medcon: http://xmedcon.sourceforge.net/You need the command line tool not
> the GUI.
> say medcon -f file
>
> in the output look for sSliceArray.ucMode the numbers meen
> 1 ascc
> 2 desc
> 4 interl
>
> This works at least here for our Allegra.
>
> > Thanks,
> > Darren
>
> You're welcome,
>
> Roland
>
> --
> Dr. Roland Marcus Rutschmann
> <[log in to unmask]>
> Institute for Experimental Psychology, University of Regensburg
> Universitätsstraße 31, 93053 Regensburg, Germany
> Tel: +49 941 943 2533, Fax: +49 941 943 3233
> http://www.psychologie.uni-regensburg.de/Rutschmann===========End of original
> message text===========
>
>
>
> --------------------------------
> Darren R. Gitelman, M.D.
> Cognitive Neurology and the Alzheimer's Disease Center
> Northwestern Univ., 320 E. Superior St., Searle 11-470, Chicago, IL 60611
> Voice: (312) 908-9023 Fax: (312) 908-8789
> --------------------------------
>
>
>
--
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