[Mrtrix-discussion] connectivity map on seed region
Donald Tournier
d.tournier at brain.org.au
Wed Oct 1 00:53:38 PDT 2008
Hi Vin,
There is no easy way to do that at the moment, but I was about to
start working on a command to do just that. It shouldn't be
particularly difficult, but unfortunately it'll have to wait until I
have the time...
Cheers,
Donald.
On Wed, Oct 1, 2008 at 5:49 PM, vinod kumar <mail.vinod at yahoo.com> wrote:
> Hi :)
> Greetings to MRtrixers,
>
> Is there any way, that I can select one ROI and than 6 target region, and
> than can see the which part of the seed projected to which target. sorry
> bit confusing. well, just same like FSL, thalamus connectivity map.
>
> regards,
>
> vin
>
>
> ----- Original Message ----
> From: Samuel Gröschel <S.Groeschel at gmx.org>
> To: Donald Tournier <d.tournier at brain.org.au>
> Cc: mrtrix-discussion at www.nitrc.org
> Sent: Tuesday, September 23, 2008 7:45:53 PM
> Subject: Re: [Mrtrix-discussion] patch for DICOM mosaics
>
> 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
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--
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078
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