[Mrtrix-discussion] mrconvert: recognising multiple series

[Donald Tournier]

Hi Amanda,

OK, I think I have an idea what's going on. First of all, can I confirm
that all other relevant entries match, particularly the series number? You
can check what MRtrix thinks all these are on a per-file basis using the
MRtrix read_dicom tool - without any other options, this will print a terse
dump of the entries that MRtrix uses to sort and group the images (use the
-a option for a full dump of all entries).

Next, the (0018,1030) entry that you've modified (Protocol Name according
to the DICOM specs) is completely ignored by MRtrix. The one you're
interested in is (0008,1030) (Study Description) - you need to make sure
this also matches.

The reason for the non-reproducible behaviour is probably down to MRtrix
scanning the files in a different order for the two folders - it doesn't go
through them alphabetically, just as they're listed in the directory entry,
and that's in no way guaranteed to be the same for the two folders. I'm a
little surprised that it would lead to such differences, but that's the
only reasonable explanation for this that I can think of - other than a
nasty bug causing memory corruption... Might still turn out to be the
latter, in which case the simplest thing would be for you to send me the
data so I can hunt it down.

Hope this helps.
Cheers,

Donald.



On 14 June 2013 15:41, Amanda Ng <amanda.ng at monash.edu> wrote:

> Hi,
>
> I'm trying to convert DICOMs coming off our Agilent scanner using
> mrconvert. It's recognising two series, when I know it should only be one.
> I'm very sure this is a problem with the script creating the DICOMs.
>
> So here's my mrtrix problem/question: I'm trying to modify the DICOM
> headers (using dcmtk) so mrconvert recognises it as a single series. I've
> tried it on the same data twice:
>
> cp -r orig_data tmp1
> dcmodify -i "(0008,103e)=30dirs_b3000_0.38" -i "(0018,1030)=DTI-epip"
> tmp1/*.dcm
> cp -r orig_data tmp2
> dcmodify -i "(0008,103e)=30dirs_b3000_0.38" -i "(0018,1030)=DTI-epip"
> tmp2/*.dcm
>
> The first time it worked (ie recognises only one series), the second time
> it didn't. I used dcmdump to read the dicom headers and used diff to see
> where the differences were, and there are none. Ie:
>
> dcmdump tmp1/*.dcm > tmp1.txt
> dcmdump tmp2/*.dcm > tmp2.txt
> diff tmp1.txt tmp2.txt
>
> and no differences. :(
>
> Any idea what's going on, ie why it worked the first time and every
> subsequent time it doesn't? I'm assuming that mrtrix uses DICOM headers to
> work out if there's multiple series.
>
> Thanks in advance for any insight you can give me!
> Amanda
>
> --
> Amanda Ng
> Computational Biomedical Imaging Scientist
>
>      Monash Biomedical Imaging
>      Monash e-Research Centre
>      Life Sciences Computation Centre, VLSCI
>
>      Email: amanda.ng at monash.edu   Tel: +61 (0)3 9902 9804
>      Bldg 220, 770 Blackburn Rd, Monash University, Melbourne VIC 3800
>
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>
>


-- 
*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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