[Mrtrix-discussion] patch for DICOM mosaics

[Donald Tournier]

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
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>



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