[Mrtrix-discussion] SV10 format

[Donald Tournier]

Hi Felix,

Not entirely sure why this would happen, but I'm guessing these are Siemens
data? SV10 refers to the format they use to store their CSA data within the
DICOM stream. The only time I've had that particular error is when trying
to read images stored using the newer DICOM multi-frame format. My
suggestion would be to install the patch that I released a few weeks ago
implementing support for multi-frame, which might also sort out a few other
issues. You can get the patch here:
http://www.nitrc.org/pipermail/mrtrix-discussion/2012-September/000528.html
.

For some reason, the NITRC mailing list backend seems to have removed all
the text from that message and left only the attachment. Here's the
original text with the installation instructions:

*Dear MRtrix users,*
*
*
*I've had a few requests recently about DICOM multi-frame support, so I've
finally done something about it. Attached is a patch implementing this,
which should apply cleanly against the current 0.2.10 source download. I'm
releasing it now as a patch since it required a fairly extensive rewrite of
the DICOM backend in MRtrix, and the chances are there will be a few bugs
that remain to be sorted out. That said, I've tried it out on a few
datasets from a range of manufacturers, and so far it seems to work
OK for both multi-frame and "traditional" DICOM data. It might also solve a
few issues others have reported recently when trying to extract the
diffusion information. *
*
*
*So I'd be grateful if people could give this a go, both for standard and
multi-frame DICOM data, and send me feedback about what works and what
doesn't (hopefully not much). Once I'm happy everything works OK, I'll put
out a new proper release. *
*
*
*To install the patch, dump it in your MRtrix source folder, and issue the
following commands (as per usual, amend as necessary):*
*
*
*$ cd mrtrix*
*$ tar xvfj mrtrix-0.2.10_DICOM_multiframe_patch.tar.bz2 *
*$ ./build*
*$ sudo ./build install*
*
*
*Cheers,*
*
*
*Donald.*



Let me whether or not this fixes the problem.
Cheers,

Donald.



On 23 October 2012 08:10, Félix C. Morency <felix.morency at gmail.com> wrote:

> Hi,
>
> I am trying to convert some DICOM files using mrconvert but have the
> following error:
>
>   mrconvert [DEBUG]: file "./IM000008" mapped at 0x7f3177e0f000, size
> 155050 (read-only)
>   mrconvert: CSA data is not in SV10 format
>   mrconvert [DEBUG]: unmapping file "./IM000008"
>   mrconvert: error reading series 3 of DICOM image "Patient #4  [MR]
> AXIAL SE T1"
>   mrconvert: error opening image "."
>   mrconvert [INFO]: closing image "."...
>
> I'm using MRtrix 0.2.10, glib 2.32.3, GSL 1.15
>
> Does anyone knows why this happens?
>
> Regards,
> --
> Félix C. Morency, M.Sc.
> Plateforme d’analyse et de visualisation d’images
> Centre Hospitalier Universitaire de Sherbrooke
> Centre de recherche clinique Étienne-Le Bel
> Local Z5-3031 | 819.346.1110 ext 16634
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>



-- 
*Dr Jacques-Donald Tournier
*
Research Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg  Vic  3084
Ph:  +61 3 9035 7033
Fax:  +61 3 9035 7307
www.florey.edu.au
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