[Mrtrix-discussion] patch for DICOM mosaics

["Samuel Gröschel"]

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