[Mrtrix-discussion] SV10 format
Félix C. Morency
felix.morency at gmail.com
Wed Oct 24 04:40:20 PDT 2012
Hi Donald,
Thank you for your quick reply. Everything works as expected with the
new patch. Thanks a lot!
Regards,
-F
On Wed, Oct 24, 2012 at 1:06 AM, Donald Tournier
<d.tournier at brain.org.au> wrote:
> Hi Felix,
>
> Thanks for sending through the sample data, I now know what the issue is:
> I'd left out one tiny little change from the patch. I've attached a new
> version of that same patch including the required change (basically changes
> lib/file/dicom/csa_entry.h:78 to report a warning about the SV10 issue
> rather than throw an exception). The issue with your data is that it looks
> like the Siemens private CSA fields have been completely blanked out - they
> are entirely zero-valued. Obviously MRtrix expects data to be contained in
> these fields. The fix is to simply report the problem but carry on
> regardless...
>
> This new version of the patch now works fine on your data:
>
> $ mrinfo sample
> mrinfo: scanning DICOM folder "sample" - ok
> mrinfo: reading DICOM series "AXIAL SE T1"... 100%
> mrinfo: WARNING: slice gap detected
> ************************************************
> Image: "Patient #4 [MR] AXIAL SE T1"
> ************************************************
> Format: DICOM
> Dimensions: 208 x 256 x 20
> Voxel size: 0.859375 x 0.859375 x 7.20001
> Dimension labels: 0. left->right (mm)
> 1. posterior->anterior (mm)
> 2. inferior->superior (mm)
> Data type: unsigned 16 bit integer (little endian)
> Data layout: [ -0 -1 +2 ]
> Data scaling: offset = 0, multiplier = 1
> Comments: Patient #4 [MR] AXIAL SE T1
> study: IRM tete
> DOB: 00/00/0000
> DOS: 00/00/0000 00:00:00
> Transform: 0.9999 2.225e-10 -0.01303 -86.54
> -0.001631 0.9921 -0.1252 -86.87
> 0.01293 0.1252 0.9921 -98.26
> 0 0 0 1
>
>
> The other thing is that the instructions I sent through may not necessarily
> force a rebuild, leaving the executables unchanged. Use these instructions
> instead:
>
> $ cd mrtrix
> $ tar xvfj mrtrix-0.2.10_DICOM_multiframe_patch.tar.bz2
> $ ./build clean
> $ ./build
> $ sudo ./build install
>
>
> Let me know how you go with that.
> Cheers,
>
> Donald.
>
>
>
> On 24 October 2012 01:17, Félix C. Morency <felix.morency at gmail.com> wrote:
>>
>> 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
>
>
>
>
> --
> 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
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