From ayman.oweida at mail.mcgill.ca Wed May 7 11:39:55 2014 From: ayman.oweida at mail.mcgill.ca (Ayman Oweida) Date: Wed, 7 May 2014 15:39:55 +0000 Subject: [MINC-users] mnc2dcm? In-Reply-To: References: <53F3FD0032C9CC4BA836E8F0FC289065317BF46E@EXMBX2010-3.campus.MCGILL.CA> <53165372.1080909@gmail.com> Message-ID: <595C18E9-B2FD-4DB9-A986-F9F54FB21388@mail.mcgill.ca> Dear minc users, Is there anyway to revert from mnc to diccom? Thank you, Ayman Oweida PhD Candidate Department of Radiation Oncology, McGill University From sorench at gmail.com Wed May 7 12:16:14 2014 From: sorench at gmail.com (Soren Christensen) Date: Wed, 7 May 2014 09:16:14 -0700 Subject: [MINC-users] mnc2dcm? In-Reply-To: <595C18E9-B2FD-4DB9-A986-F9F54FB21388@mail.mcgill.ca> References: <53F3FD0032C9CC4BA836E8F0FC289065317BF46E@EXMBX2010-3.campus.MCGILL.CA> <53165372.1080909@gmail.com> <595C18E9-B2FD-4DB9-A986-F9F54FB21388@mail.mcgill.ca> Message-ID: Hi Ayman, I'm not aware of a turn key solution, but there was a discussion of this years back here - it's 6 years ago so things may have changed http://www.bic.mni.mcgill.ca/pipermail/minc-users/2008-October/002214.html If your data has an originating DICOM data set, you can re-use that header with a number of modifications, but there's a number of tags that need changing to provide a valid, derived, data set (including UIDs). Soren On Wed, May 7, 2014 at 8:39 AM, Ayman Oweida wrote: > > Dear minc users, > > Is there anyway to revert from mnc to diccom? > > Thank you, > > > Ayman Oweida > > PhD Candidate > Department of Radiation Oncology, McGill University > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From mathieu.desrosiers at criugm.qc.ca Fri May 9 15:18:29 2014 From: mathieu.desrosiers at criugm.qc.ca (Mathieu Desrosiers) Date: Fri, 9 May 2014 15:18:29 -0400 Subject: [MINC-users] No rule to make Message-ID: Hi Minc-users, FYI i try to install minc-toolkit on aopenSUSE 13.1 (x86_64) distro and it failed with those errors messages: *** No rule to make target `external/usr/local/mni/lib/libpcrecpp.a', needed by `oobicpl/create_lines'. Stop. make[2]: *** No rule to make target `external/usr/local/mni/lib/libpcre.a', needed by `oobicpl/create_lines'. Stop. make[2]: *** No rule to make target `external/usr/local/mni/lib/libgsl.a', needed by `EZminc/mincnlm/minc_anlm'. Stop. No rule to make target `external/usr/local/mni/lib/libgslcblas.a', needed by `EZminc/mincnlm/minc_anlm'. make[2]: *** No rule to make target `external/usr/local/mni/lib/libfftw3f.a', needed by `EZminc/mincnlm/minc_anlm'. Stop. Actually those libraries where found in external/usr/local/mni/lib64. Have a nice day. -- Mathieu From vladimir.fonov at gmail.com Fri May 9 16:18:55 2014 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 9 May 2014 16:18:55 -0400 Subject: [MINC-users] No rule to make In-Reply-To: References: Message-ID: I assume you are using minc-toolkit from https://github.com/BIC-MNI/minc-toolkit ? On Fri, May 9, 2014 at 3:18 PM, Mathieu Desrosiers wrote: > Hi Minc-users, > > FYI i try to install minc-toolkit on aopenSUSE 13.1 (x86_64) distro and it failed with those errors messages: > > *** No rule to make target `external/usr/local/mni/lib/libpcrecpp.a', needed by `oobicpl/create_lines'. Stop. > make[2]: *** No rule to make target `external/usr/local/mni/lib/libpcre.a', needed by `oobicpl/create_lines'. Stop. > make[2]: *** No rule to make target `external/usr/local/mni/lib/libgsl.a', needed by `EZminc/mincnlm/minc_anlm'. Stop. > No rule to make target `external/usr/local/mni/lib/libgslcblas.a', needed by `EZminc/mincnlm/minc_anlm'. > make[2]: *** No rule to make target `external/usr/local/mni/lib/libfftw3f.a', needed by `EZminc/mincnlm/minc_anlm'. Stop. > > Actually those libraries where found in external/usr/local/mni/lib64. > > > Have a nice day. > > -- > Mathieu > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com From mathieu.desrosiers at criugm.qc.ca Fri May 9 16:37:36 2014 From: mathieu.desrosiers at criugm.qc.ca (Mathieu Desrosiers) Date: Fri, 9 May 2014 16:37:36 -0400 Subject: [MINC-users] No rule to make In-Reply-To: References: Message-ID: <3B208675-A9B1-4C1E-BF9F-EEB5ED67E712@criugm.qc.ca> Absolutely _______________________________________ Mathieu Desrosiers Coordonnateur technique RNQ / RBIQ-QBIN Centre de recherche, Institut universitaire de g?riatrie de Montr?al Adresse postale: 4565, chemin Queen-Mary, Montr?al (Qu?bec) H3W 1W5 Adresse civique: 4545, chemin Queen-Mary, 6e ?tage, pi?ce M6827, Montr?al (Qu?bec) H3W 1W5 T?l.:(514) 340-3540 # 4897 T?l?c.:(514) 340-3530 Courriel: mathieu.desrosiers at criugm.qc.ca Web RBIQ: www.rbiq-qbin.qc.ca On 2014-05-09, at 4:18 PM, Vladimir S. FONOV wrote: > I assume you are using minc-toolkit from > https://github.com/BIC-MNI/minc-toolkit ? From vladimir.fonov at gmail.com Fri May 9 16:56:59 2014 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 9 May 2014 16:56:59 -0400 Subject: [MINC-users] No rule to make In-Reply-To: <3B208675-A9B1-4C1E-BF9F-EEB5ED67E712@criugm.qc.ca> References: <3B208675-A9B1-4C1E-BF9F-EEB5ED67E712@criugm.qc.ca> Message-ID: looks like a confusion between lib and lib64 2014-05-09 16:37 GMT-04:00 Mathieu Desrosiers : > Absolutely > > > > _______________________________________ > Mathieu Desrosiers > Coordonnateur technique RNQ / RBIQ-QBIN > Centre de recherche, Institut universitaire de g?riatrie de Montr?al > Adresse postale: 4565, chemin Queen-Mary, Montr?al (Qu?bec) H3W 1W5 > Adresse civique: 4545, chemin Queen-Mary, 6e ?tage, pi?ce M6827, Montr?al (Qu?bec) H3W 1W5 > T?l.:(514) 340-3540 # 4897 > T?l?c.:(514) 340-3530 > Courriel: mathieu.desrosiers at criugm.qc.ca > Web RBIQ: www.rbiq-qbin.qc.ca > > On 2014-05-09, at 4:18 PM, Vladimir S. FONOV wrote: > >> I assume you are using minc-toolkit from >> https://github.com/BIC-MNI/minc-toolkit ? > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com From elizabethw at msmri.medicine.ubc.ca Thu May 29 12:14:18 2014 From: elizabethw at msmri.medicine.ubc.ca (Elizabeth Wicks) Date: Thu, 29 May 2014 09:14:18 -0700 Subject: [MINC-users] minctracc - Order of Transformation using -lsq12 Message-ID: <53875CDA.3020005@msmri.medicine.ubc.ca> Hi all, I am wondering the exact order of the components in the /minctracc -lsq12/ transformation. That is, in what order are the rotation, translation, scaling and shear components done during the registration? For example, is the output matrix = rotation_matrix*skew_matrix*scale_matrix? And what are the forms of these individual matrices, e.g. is rotation_matrix = Rx*Ry*Rz or Rz*Ry*Rx? In particular, it would be helpful to know how /minctracc/ creates its output xfm matrix, given the individual transformation parameters, (essentially the breakdown of what /param2xfm/ does). Thanks in advance! Elizabeth From a.janke at gmail.com Thu May 29 20:11:46 2014 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 30 May 2014 10:11:46 +1000 Subject: [MINC-users] minctracc - Order of Transformation using -lsq12 In-Reply-To: <53875CDA.3020005@msmri.medicine.ubc.ca> References: <53875CDA.3020005@msmri.medicine.ubc.ca> Message-ID: Hi Elizabeth, I too had this same question a while back as I was trying to reverse engineer these parameters in perl for rotations larger than 90deg. 90deg is the max that minctracc will handle before it will give up. I just put this code on github here: https://github.com/BIC-MNI/minc-widgets/blob/master/xfmdecomp/xfmdecomp.pl In answer to your question, the bet would be to look at the code: https://github.com/BIC-MNI/mni_autoreg/blob/master/minctracc/Numerical/make_rots.c#L236 You will note a comment in the header which gives you the answer you want: mat = (T)(C)(S)(SH)(R)(-C) a On 30 May 2014 02:14, Elizabeth Wicks wrote: > Hi all, > > I am wondering the exact order of the components in the /minctracc -lsq12/ > transformation. That is, in what order are the rotation, translation, > scaling and shear components done during the registration? For example, is > the output matrix = rotation_matrix*skew_matrix*scale_matrix? And what are > the forms of these individual matrices, e.g. is rotation_matrix = Rx*Ry*Rz > or Rz*Ry*Rx? > > In particular, it would be helpful to know how /minctracc/ creates its > output xfm matrix, given the individual transformation parameters, > (essentially the breakdown of what /param2xfm/ does). > > Thanks in advance! > > Elizabeth > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users