[Mrtrix-discussion] mrconvert DICOM file order

[Félix C. Morency]

Donald,

Thank you for the fast answer. Here are partial informations of
000[1-4].dcm using read_dicom:

0001.dcm
[DCM] 20 10 SH 2 2588 StudyID : [ 1 ]
[DCM] 20 11 IS 2 2598 SeriesNumber : [ 4 ]
[DCM] 20 12 IS 2 2608 AcquisitionNumber : [ 1 ]
[DCM] 20 13 IS 2 2618 InstanceNumber : [ 1 ]

0002.dcm
[DCM] 20 10 SH 2 2694 StudyID : [ 1 ]
[DCM] 20 11 IS 2 2704 SeriesNumber : [ 4 ]
[DCM] 20 12 IS 4 2714 AcquisitionNumber : [ 256 ]
[DCM] 20 13 IS 2 2726 InstanceNumber : [ 2 ]

0003.dcm
[DCM] 20 10 SH 2 2694 StudyID : [ 1 ]
[DCM] 20 11 IS 2 2704 SeriesNumber : [ 4 ]
[DCM] 20 12 IS 4 2714 AcquisitionNumber : [ 258 ]
[DCM] 20 13 IS 2 2726 InstanceNumber : [ 3 ]

0004.dcm
[DCM] 20 10 SH 2 2690 StudyID : [ 1 ]
[DCM] 20 11 IS 2 2700 SeriesNumber : [ 4 ]
[DCM] 20 12 IS 2 2710 AcquisitionNumber : [ 3 ]
[DCM] 20 13 IS 2 2720 InstanceNumber : [ 4 ]

The data is public domain (Pittsburgh brain competition 2009 [1]). I
can upload the data somewhere if you like.

[1]: http://pbc.lrdc.pitt.edu/?q=2009b-download

-F

On Mon, Jul 23, 2012 at 7:32 PM, Donald Tournier
<d.tournier at brain.org.au> wrote:
> Hi Félix,
>
> I agree that doesn't sound too good. I don't understand how this could
> happen, unless the series numbers stored in the DICOM header for each file
> are also in the wrong order - this is what MRtrix uses to order the volumes.
> My first guess would be that this is the problem. You can easily check by
> running read_dicom on each file to see what series number it reports, and
> whether they match the order you expected. If not, I'd need to take a look
> at the data - any chance you could send me these files?
>
> Cheers,
>
> Donald.
>
>
> On 24 July 2012 03:57, Félix C. Morency <felix.morency at gmail.com> wrote:
>>
>> Hi,
>>
>> I am trying to create a 4D Nifti volume from multiple Siemens DICOM
>> mosaic. The XYZ axis seem to be fine. However, slices along the time
>> axis are presented in random (?) order.
>>
>> I reproduced the issue with four original DICOM mosaic: 000[1-4].dcm.
>> I convert them to 4D Nifti using mrconvert. The resulting time axis is
>> ordered as following: 0001, 0004, 0002, 0003, which is not the
>> expected behaviour.
>>
>> Do you have any idea what's going on?
>>
>> 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
>
>
>
>
> --
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9035 7033



-- 
--
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