[Mrtrix-discussion] patch for DICOM mosaics

Mon Oct 27 21:32:23 PDT 2008

Hi Samuel,

Guess that last patch still had a few issues...

This (hopefully) final patch should fix your remaining problem with
the origin of the images being incorrectly set for "inverted" Siemens
DICOM mosaics. Install as before, will override any previous patch.

Let me know how you go.
Cheers,

Donald.

On Wed, Sep 24, 2008 at 4:45 AM, "Samuel Gröschel" <S.Groeschel at gmx.org> wrote:
> Thanks, Donald, it works beautifully!! Samuel
>
> -------- Original-Nachricht --------
>> Datum: Tue, 23 Sep 2008 10:20:07 +1000
>> Von: "Donald Tournier" <d.tournier at brain.org.au>
>> An: "Samuel Gröschel" <S.Groeschel at gmx.org>
>> CC: mrtrix-discussion at www.nitrc.org
>> Betreff: Re: [Mrtrix-discussion] patch for DICOM mosaics
>
>> Hi Samuel,
>>
>> I think we've finally cracked your upside-down DICOM issue. The
>> remaining problem was due to the use of the comma as the decimal
>> separator in German (i.e. 3,14 rather than 3.14). When the system is
>> set to German (or French or lots of other languages), there was a very
>> specific portion of the MRtrix code that got a bit confused when
>> trying to read in a number written using a decimal point (i.e. the US
>> convention). I've got that fixed up in this latest patch. As far as I
>> can tell, the rest of the code is not prone to this problem. Obviously
>> do let me know if any other strange things happen!
>>
>> Install this patch as per the previous instructions. As before, don't
>> worry about whether you've installed the previous patches or not, this
>> new version should overwrite the previous changes anyway.
>>
>> Let me know if this works...
>> Cheers!
>>
>> Donald.
>>
>>
>> On Mon, Sep 8, 2008 at 9:37 PM, "Samuel Gröschel" <S.Groeschel at gmx.org>
>> wrote:
>> > Hi Donald,
>> >
>> > Sorry to bring this up again but with the new patch it doesn't work
>> either. This time, no error message occurs but the image is turned upside down
>> as it used to be. Initially I stored the DICOM files (T1, EPI, T2) from one
>> subject all in one folder. After "seperating" the EPI-files in another
>> folder, the DICOM-reading process indicates "mrview: DICOM image contains
>> mosaic files - reformating... 100%" which sounds perfect. Still, when the
>> mrview-window pops up the image remains upside down.
>> >
>> > I find it strange that this does not happen when YOU try to read the
>> identical DICOM files. So there must be a problem with my setting. Can you
>> think of anything that might be different?
>> >
>> > Thanks and regards,
>> >
>> > Samuel
>> >
>> > -------- Original-Nachricht --------
>> >> Datum: Mon, 8 Sep 2008 09:17:46 +1000
>> >> Von: "Donald Tournier" <d.tournier at brain.org.au>
>> >> An: S.Groeschel at gmx.org
>> >> CC: mrtrix-discussion at www.nitrc.org
>> >> Betreff: Re: [Mrtrix-discussion] patch for DICOM mosaics
>> >
>> >> Hi Samuel,
>> >>
>> >> No, you didn't do anything wrong. That message could easily have been
>> >> caused by the patch. It sounds like there might be some odd cases that
>> >> I hadn't considered when reading these DICOM mosaics. Here's a new
>> >> patch that *should* work no matter what (fingers crossed). Don't worry
>> >> if you've already installed the previous patch, this one will
>> >> overwrite any changes made by the previous one. Obviously, you can
>> >> also apply this patch on an unmodified MRtrix 0.2.5 installation.
>> >>
>> >> Let me know how it goes.
>> >>
>> >> Donald.
>> >>
>> >>
>> >> On Fri, Sep 5, 2008 at 7:46 PM,  <S.Groeschel at gmx.org> wrote:
>> >> > Hi Donald,
>> >> >
>> >> > Thanks very much for the patch which should sort out my
>> slice-ordering
>> >> > issue. After applying it, however, the following error message occurs
>> >> > when trying to 'mrview' the ("incorrectly-ordered") dicom files.
>> >> >
>> >> > mrview: reading DICOM series "ep2d_diff_tra_22x20x20_69#"... 100%
>> >> > mrview: lib/file/dicom/image.cpp:141: bool
>> >> > MR::File::Dicom::Image::operator<(const MR::File::Dicom::Image&)
>> const:
>> >> > Assertion `!gsl_isnan(distance)' failed.
>> >> > Aborted
>> >> >
>> >> > Did I do anything wrong during installation? Can anyone help?
>> >> >
>> >> > Regards, Samuel
>> >> >
>> >> >
>> >> >> Hi everyone,
>> >> >>
>> >> >> Here is a patch to fix occasional slice-ordering issues when loading
>> >> >> DICOM mosaic images. The images would sometimes be loaded
>> upside-down,
>> >> >> due to my complete ignorance of Siemens' obscure 'SliceNormalVector'
>> >> >> CSA entry in the image headers (thanks to the SPM5 code for pointing
>> >> >> me in right direction...). Note that this problem really shouldn't
>> >> >> affect anything else: if you haven't had this problem yet, there is
>> >> >> nothing to worry about. You might want to wait until the next
>> release
>> >> >> of MRtrix which will contain this fix anyway.
>> >> >>
>> >> >> To apply the patch, simply unpack the files into the MRtrix code
>> >> >> folder - this should overwrite the 3 modified files. You should then
>> >> >> issue the ./build command and install as normal. In other words,
>> >> >> assuming you have already downloaded the patch file into the
>> >> >> mrtrix-0.2.5/ folder:
>> >> >>
>> >> >> > cd mrtrix-0.2.5/
>> >> >> > tar xfjv mrtrix-0.2.5_dicom_mosaic_patch_2008-09-05.tar.bz2
>> >> >> > ./build
>> >> >>
>> >> >> and copy over into your final installation folder as you would
>> >> normally.
>> >> >>
>> >> >> Regards,
>> >> >>
>> >> >> Donald.
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Jacques-Donald Tournier (PhD)
>> >> >> Brain Research Institute, Melbourne, Australia
>> >> >> Tel: +61 (0)3 9496 4078
>> >> > _______________________________________________
>> >> > 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 9496 4078
>> >
>>
>>
>>
>> --
>> Jacques-Donald Tournier (PhD)
>> Brain Research Institute, Melbourne, Australia
>> Tel: +61 (0)3 9496 4078
>

-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078
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