[Mrtrix-discussion] patch for DICOM mosaics

Wed Oct 29 18:49:52 PDT 2008

Sorry Donald,

I discovered the problem, it was really something wrong with my installation. Now it works. Perfect!!

Samuel

> Hi Samuel,
> 
> That's very odd. I just double checked everything, and it works for
> me. I went back to version 0.2.5 as released on the website, applied
> the previous DICOM patch, and had the same problem as you. I applied
> the new patch, and the problem was resolved. Are you sure everything
> was installed properly? You might want to type "./build clean", and
> then "./build" to make sure everything is up to date. Then also make
> sure you delete the previous installation, and copy your new
> executables & library over to your installation folder - there's a
> chance you might have been using a previous version. As a check, when
> you give the "-version" option to any mrtrix command, it will print
> out the date it was compiled. If it prints an older date than today,
> you are most likely using a previous version.
> 
> Hope this helps. If it doesn't, there's something very odd going on...
> Cheers,
> 
> Donald.
> 
> 
> On Thu, Oct 30, 2008 at 6:49 AM, "Samuel Gröschel" <S.Groeschel at gmx.org>
> wrote:
> > Hi Donald,
> >
> > Unfortunately, this patch did not resolve the problem for me. It does
> not change the setting for the diffusion data after 'mrconvert'ing them from
> DICOM files, in fact it does not seem to change anything (I checked that
> the old files are correctly replaced by the new ones). Some problem with my
> system or installation? How can I check this?
> >
> > Thanks, Samuel
> >
> >
> >> 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
> >
> 
> 
> 
> -- 
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9496 4078