[Mrtrix-discussion] SV10 format

[Félix C. Morency]

Donald,

Thank you for your answer. I tried the patched version of mrtrix but I
obtains the same error. The data seems to come from a Siemens scanner.
You will find in [1] a sample of the data I'm trying to convert. Maybe
I'm doing something wrong. I asked a colleague of mine to test it and
he has the same error. Can you tell me if it works on your side?

  [1]: http://dl.dropbox.com/u/2543037/sample.tar.gz

Regards,
-F

On Mon, Oct 22, 2012 at 8:34 PM, Donald Tournier
<d.tournier at brain.org.au> wrote:
> 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
>
>



-- 
--
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