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<DIV>Hi :)<BR></DIV>
<DIV>Greetings to MRtrixers, </DIV>
<DIV> </DIV>
<DIV>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. </DIV>
<DIV> </DIV>
<DIV>regards, </DIV>
<DIV> </DIV>
<DIV>vin</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>----- Original Message ----<BR>From: Samuel Gröschel <S.Groeschel@gmx.org><BR>To: Donald Tournier <d.tournier@brain.org.au><BR>Cc: mrtrix-discussion@www.nitrc.org<BR>Sent: Tuesday, September 23, 2008 7:45:53 PM<BR>Subject: Re: [Mrtrix-discussion] patch for DICOM mosaics<BR><BR>Thanks, Donald, it works beautifully!! Samuel<BR><BR>-------- Original-Nachricht --------<BR>> Datum: Tue, 23 Sep 2008 10:20:07 +1000<BR>> Von: "Donald Tournier" <<A href="mailto:d.tournier@brain.org.au" ymailto="mailto:d.tournier@brain.org.au">d.tournier@brain.org.au</A>><BR>> An: "Samuel Gröschel" <<A href="mailto:S.Groeschel@gmx.org" ymailto="mailto:S.Groeschel@gmx.org">S.Groeschel@gmx.org</A>><BR>> CC: <A href="mailto:mrtrix-discussion@www.nitrc.org" ymailto="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</A><BR>> Betreff: Re: [Mrtrix-discussion] patch for DICOM mosaics<BR><BR>> Hi Samuel,<BR>>
<BR>> I think we've finally cracked your upside-down DICOM issue. The<BR>> remaining problem was due to the use of the comma as the decimal<BR>> separator in German (i.e. 3,14 rather than 3.14). When the system is<BR>> set to German (or French or lots of other languages), there was a very<BR>> specific portion of the MRtrix code that got a bit confused when<BR>> trying to read in a number written using a decimal point (i.e. the US<BR>> convention). I've got that fixed up in this latest patch. As far as I<BR>> can tell, the rest of the code is not prone to this problem. Obviously<BR>> do let me know if any other strange things happen!<BR>> <BR>> Install this patch as per the previous instructions. As before, don't<BR>> worry about whether you've installed the previous patches or not, this<BR>> new version should overwrite the previous changes anyway.<BR>> <BR>> Let me know if this works...<BR>>
Cheers!<BR>> <BR>> Donald.<BR>> <BR>> <BR>> On Mon, Sep 8, 2008 at 9:37 PM, "Samuel Gröschel" <<A href="mailto:S.Groeschel@gmx.org" ymailto="mailto:S.Groeschel@gmx.org">S.Groeschel@gmx.org</A>><BR>> wrote:<BR>> > Hi Donald,<BR>> ><BR>> > Sorry to bring this up again but with the new patch it doesn't work<BR>> either. This time, no error message occurs but the image is turned upside down<BR>> as it used to be. Initially I stored the DICOM files (T1, EPI, T2) from one<BR>> subject all in one folder. After "seperating" the EPI-files in another<BR>> folder, the DICOM-reading process indicates "mrview: DICOM image contains<BR>> mosaic files - reformating... 100%" which sounds perfect. Still, when the<BR>> mrview-window pops up the image remains upside down.<BR>> ><BR>> > I find it strange that this does not happen when YOU try to read the<BR>> identical DICOM files. So there must be
a problem with my setting. Can you<BR>> think of anything that might be different?<BR>> ><BR>> > Thanks and regards,<BR>> ><BR>> > Samuel<BR>> ><BR>> > -------- Original-Nachricht --------<BR>> >> Datum: Mon, 8 Sep 2008 09:17:46 +1000<BR>> >> Von: "Donald Tournier" <<A href="mailto:d.tournier@brain.org.au" ymailto="mailto:d.tournier@brain.org.au">d.tournier@brain.org.au</A>><BR>> >> An: <A href="mailto:S.Groeschel@gmx.org" ymailto="mailto:S.Groeschel@gmx.org">S.Groeschel@gmx.org</A><BR>> >> CC: <A href="mailto:mrtrix-discussion@www.nitrc.org" ymailto="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</A><BR>> >> Betreff: Re: [Mrtrix-discussion] patch for DICOM mosaics<BR>> ><BR>> >> Hi Samuel,<BR>> >><BR>> >> No, you didn't do anything wrong. That message could easily have been<BR>> >> caused by the
patch. It sounds like there might be some odd cases that<BR>> >> I hadn't considered when reading these DICOM mosaics. Here's a new<BR>> >> patch that *should* work no matter what (fingers crossed). Don't worry<BR>> >> if you've already installed the previous patch, this one will<BR>> >> overwrite any changes made by the previous one. Obviously, you can<BR>> >> also apply this patch on an unmodified MRtrix 0.2.5 installation.<BR>> >><BR>> >> Let me know how it goes.<BR>> >><BR>> >> Donald.<BR>> >><BR>> >><BR>> >> On Fri, Sep 5, 2008 at 7:46 PM, <<A href="mailto:S.Groeschel@gmx.org" ymailto="mailto:S.Groeschel@gmx.org">S.Groeschel@gmx.org</A>> wrote:<BR>> >> > Hi Donald,<BR>> >> ><BR>> >> > Thanks very much for the patch which should sort out my<BR>> slice-ordering<BR>> >> > issue.
After applying it, however, the following error message occurs<BR>> >> > when trying to 'mrview' the ("incorrectly-ordered") dicom files.<BR>> >> ><BR>> >> > mrview: reading DICOM series "ep2d_diff_tra_22x20x20_69#"... 100%<BR>> >> > mrview: lib/file/dicom/image.cpp:141: bool<BR>> >> > MR::File::Dicom::Image::operator<(const MR::File::Dicom::Image&)<BR>> const:<BR>> >> > Assertion `!gsl_isnan(distance)' failed.<BR>> >> > Aborted<BR>> >> ><BR>> >> > Did I do anything wrong during installation? Can anyone help?<BR>> >> ><BR>> >> > Regards, Samuel<BR>> >> ><BR>> >> ><BR>> >> >> Hi everyone,<BR>> >> >><BR>> >> >> Here is a patch to fix occasional slice-ordering issues when loading<BR>> >> >> DICOM mosaic images. The images would
sometimes be loaded<BR>> upside-down,<BR>> >> >> due to my complete ignorance of Siemens' obscure 'SliceNormalVector'<BR>> >> >> CSA entry in the image headers (thanks to the SPM5 code for pointing<BR>> >> >> me in right direction...). Note that this problem really shouldn't<BR>> >> >> affect anything else: if you haven't had this problem yet, there is<BR>> >> >> nothing to worry about. You might want to wait until the next<BR>> release<BR>> >> >> of MRtrix which will contain this fix anyway.<BR>> >> >><BR>> >> >> To apply the patch, simply unpack the files into the MRtrix code<BR>> >> >> folder - this should overwrite the 3 modified files. You should then<BR>> >> >> issue the ./build command and install as normal. In other words,<BR>> >> >> assuming you have already downloaded the
patch file into the<BR>> >> >> mrtrix-0.2.5/ folder:<BR>> >> >><BR>> >> >> > cd mrtrix-0.2.5/<BR>> >> >> > tar xfjv mrtrix-0.2.5_dicom_mosaic_patch_2008-09-05.tar.bz2<BR>> >> >> > ./build<BR>> >> >><BR>> >> >> and copy over into your final installation folder as you would<BR>> >> normally.<BR>> >> >><BR>> >> >> Regards,<BR>> >> >><BR>> >> >> Donald.<BR>> >> >><BR>> >> >><BR>> >> >> --<BR>> >> >> Jacques-Donald Tournier (PhD)<BR>> >> >> Brain Research Institute, Melbourne, Australia<BR>> >> >> Tel: +61 (0)3 9496 4078<BR>> >> > _______________________________________________<BR>> >> > Mrtrix-discussion mailing list<BR>> >> > <A
href="mailto:Mrtrix-discussion@www.nitrc.org" ymailto="mailto:Mrtrix-discussion@www.nitrc.org">Mrtrix-discussion@www.nitrc.org</A><BR>> >> > <A href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target=_blank>http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</A><BR>> >> ><BR>> >><BR>> >><BR>> >><BR>> >> --<BR>> >> Jacques-Donald Tournier (PhD)<BR>> >> Brain Research Institute, Melbourne, Australia<BR>> >> Tel: +61 (0)3 9496 4078<BR>> ><BR>> <BR>> <BR>> <BR>> -- <BR>> Jacques-Donald Tournier (PhD)<BR>> Brain Research Institute, Melbourne, Australia<BR>> Tel: +61 (0)3 9496 4078<BR>_______________________________________________<BR>Mrtrix-discussion mailing list<BR><A href="mailto:Mrtrix-discussion@www.nitrc.org" ymailto="mailto:Mrtrix-discussion@www.nitrc.org">Mrtrix-discussion@www.nitrc.org</A><BR><A
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