From gdevenyi at gmail.com Thu Jul 2 09:57:13 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Thu, 2 Jul 2015 09:57:13 -0400 Subject: [MINC-users] Conversion from ITK transform to minc transform? Message-ID: Hi all, Does anyone know of a tool to convert ITK .mat/.nii transforms to minc-style .xfm/grid.mnc transforms? It looks like itk_convert can handle the .nii->.mnc step but I don't see anything for .mat->.xfm Thanks! -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com From vladimir.fonov at gmail.com Thu Jul 2 10:07:56 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 2 Jul 2015 10:07:56 -0400 Subject: [MINC-users] Conversion from ITK transform to minc transform? In-Reply-To: References: Message-ID: Hello, there is functionality in ITK4 to read/write MINC style .XFM files as composite ITK transform. So, If you read .nii /.mat transformation in , and then write it out - you can have itk transformation conversion tool. On Jul 2, 2015, at 9:57 AM, Gabriel A. Devenyi wrote: > Hi all, > > Does anyone know of a tool to convert ITK .mat/.nii transforms to > minc-style .xfm/grid.mnc transforms? > > It looks like itk_convert can handle the .nii->.mnc step but I don't see > anything for .mat->.xfm > > Thanks! > > -- > Gabriel A. Devenyi B.Eng. Ph.D. > Research Computing Associate > Computational Brain Anatomy Laboratory > Cerebral Imaging Center > Douglas Mental Health University Institute > McGill University > t: 514.761.6131x4781 > e: gdevenyi at gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users Best regards, Vladimir S. FONOV ~ v.s.fonov ilmarin.info From vladimir.fonov at gmail.com Thu Jul 2 12:51:53 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 02 Jul 2015 12:51:53 -0400 Subject: [MINC-users] Conversion from ITK transform to minc transform? In-Reply-To: References: Message-ID: <55956C29.7050809@gmail.com> Hello, I made an example: https://github.com/BIC-MNI/EZminc/blob/ITK4/tools/itk_convert_xfm.cpp works with ITK4, and will be included in the next version of minc-toolkit-v2 On 15-07-02 09:57 AM, Gabriel A. Devenyi wrote: > Hi all, > > Does anyone know of a tool to convert ITK .mat/.nii transforms to > minc-style .xfm/grid.mnc transforms? > > It looks like itk_convert can handle the .nii->.mnc step but I don't see > anything for .mat->.xfm > > Thanks! > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From vladimir.fonov at gmail.com Tue Jul 14 18:20:19 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Tue, 14 Jul 2015 18:20:19 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 Message-ID: Hello Everybody, I have finally made a new release of minc-toolkit-v2 (formerly minc-toolkit experimental branch 1.9.XX). The new release if available at http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#sServicesSoftware.ServicesSoftwareMincToolKit_3 and includes a lot of fixes and updates, the most significant are following: 1. latest version of libminc , which includes a lots of bug fixes - hopefully it will become release 2.3 some time soon 2. latest version of minc-tools , with updated dcm2mnc 3. ITK version 4.8 4. latest version of ANTS package, which includes support for MINC-style XFM files in the antsRegistration tool 5. latest version of Elastix with minc support. 6. mincified version of ABC tissue classification tool ( http://www.nitrc.org/projects/abc/ ) P.S. It would be great if somebody who have access would update https://www.mcgill.ca/bic/software/minc/minctoolkit to reflect this changes. -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com From gdevenyi at gmail.com Tue Jul 14 18:30:08 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Tue, 14 Jul 2015 18:30:08 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References: Message-ID: Thanks Vlad! That's awesome news! Thanks for all your hard work. On Jul 14, 2015 6:20 PM, "Vladimir S. FONOV" wrote: > Hello Everybody, > > > I have finally made a new release of minc-toolkit-v2 (formerly minc-toolkit > experimental branch 1.9.XX). > > The new release if available at > > http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#sServicesSoftware.ServicesSoftwareMincToolKit_3 > > and includes a lot of fixes and updates, the most significant are > following: > > 1. latest version of libminc , which includes a lots of bug fixes - > hopefully it will become release 2.3 some time soon > > 2. latest version of minc-tools , with updated dcm2mnc > > 3. ITK version 4.8 > > 4. latest version of ANTS package, which includes support for MINC-style > XFM files in the antsRegistration tool > > 5. latest version of Elastix with minc support. > > 6. mincified version of ABC tissue classification tool ( > http://www.nitrc.org/projects/abc/ ) > > P.S. It would be great if somebody who have access would update > https://www.mcgill.ca/bic/software/minc/minctoolkit to reflect this > changes. > > -- > Best regards, > > Vladimir S. Fonov ~ vladimir fonov gmail com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Wed Jul 15 07:53:39 2015 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 15 Jul 2015 21:53:39 +1000 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References:

Message-ID: Indeed good news. Thanks for continuing to put the effort in Vladimir! a On 15 July 2015 at 08:30, Gabriel A. Devenyi wrote: > Thanks Vlad! > > That's awesome news! Thanks for all your hard work. > On Jul 14, 2015 6:20 PM, "Vladimir S. FONOV" > wrote: > >> Hello Everybody, >> >> >> I have finally made a new release of minc-toolkit-v2 (formerly minc-toolkit >> experimental branch 1.9.XX). >> >> The new release if available at >> >> http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#sServicesSoftware.ServicesSoftwareMincToolKit_3 >> >> and includes a lot of fixes and updates, the most significant are >> following: >> >> 1. latest version of libminc , which includes a lots of bug fixes - >> hopefully it will become release 2.3 some time soon >> >> 2. latest version of minc-tools , with updated dcm2mnc >> >> 3. ITK version 4.8 >> >> 4. latest version of ANTS package, which includes support for MINC-style >> XFM files in the antsRegistration tool >> >> 5. latest version of Elastix with minc support. >> >> 6. mincified version of ABC tissue classification tool ( >> http://www.nitrc.org/projects/abc/ ) >> >> P.S. It would be great if somebody who have access would update >> https://www.mcgill.ca/bic/software/minc/minctoolkit to reflect this >> changes. >> >> -- >> Best regards, >> >> Vladimir S. Fonov ~ vladimir fonov gmail com >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From gdevenyi at gmail.com Wed Jul 15 13:26:15 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Wed, 15 Jul 2015 13:26:15 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References:

Message-ID: Hey Vlad, Is there an up-to-date list of dependencies for installing the toolkit in ubuntu? In the current list the following packages don?t exist: E: Package 'libgl1' has no installation candidate E: Package 'libtiff4' has no installation candidate ? -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Tue, Jul 14, 2015 at 6:30 PM, Gabriel A. Devenyi wrote: > Thanks Vlad! > > That's awesome news! Thanks for all your hard work. > On Jul 14, 2015 6:20 PM, "Vladimir S. FONOV" > wrote: > >> Hello Everybody, >> >> >> I have finally made a new release of minc-toolkit-v2 (formerly >> minc-toolkit >> experimental branch 1.9.XX). >> >> The new release if available at >> >> http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#sServicesSoftware.ServicesSoftwareMincToolKit_3 >> >> and includes a lot of fixes and updates, the most significant are >> following: >> >> 1. latest version of libminc , which includes a lots of bug fixes - >> hopefully it will become release 2.3 some time soon >> >> 2. latest version of minc-tools , with updated dcm2mnc >> >> 3. ITK version 4.8 >> >> 4. latest version of ANTS package, which includes support for MINC-style >> XFM files in the antsRegistration tool >> >> 5. latest version of Elastix with minc support. >> >> 6. mincified version of ABC tissue classification tool ( >> http://www.nitrc.org/projects/abc/ ) >> >> P.S. It would be great if somebody who have access would update >> https://www.mcgill.ca/bic/software/minc/minctoolkit to reflect this >> changes. >> >> -- >> Best regards, >> >> Vladimir S. Fonov ~ vladimir fonov gmail com >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > From vladimir.fonov at gmail.com Wed Jul 15 13:31:03 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 15 Jul 2015 13:31:03 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References:

Message-ID: <55A698D7.1050607@gmail.com> Which version of Ubuntu are you using? On 15-07-15 01:26 PM, Gabriel A. Devenyi wrote: > Hey Vlad, > > Is there an up-to-date list of dependencies for installing the toolkit in > ubuntu? In the current list the following packages don?t exist: > > E: Package 'libgl1' has no installation candidate > E: Package 'libtiff4' has no installation candidate -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From gdevenyi at gmail.com Wed Jul 15 13:39:12 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Wed, 15 Jul 2015 13:39:12 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: <55A698D7.1050607@gmail.com> References:

<55A698D7.1050607@gmail.com> Message-ID: 14.04 (in a docker container) -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Wed, Jul 15, 2015 at 1:31 PM, Vladimir S. FONOV wrote: > Which version of Ubuntu are you using? > > On 15-07-15 01:26 PM, Gabriel A. Devenyi wrote: > >> Hey Vlad, >> >> Is there an up-to-date list of dependencies for installing the toolkit in >> ubuntu? In the current list the following packages don?t exist: >> >> E: Package 'libgl1' has no installation candidate >> E: Package 'libtiff4' has no installation candidate >> > > > -- > Best regards, > > Vladimir S. FONOV ~ vladimir.fonov gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Wed Jul 15 13:48:25 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 15 Jul 2015 13:48:25 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References:

<55A698D7.1050607@gmail.com> Message-ID: <55A69CE9.6050504@gmail.com> That's strange. Running on Ubuntu 14.04 : # lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 14.04.2 LTS Release: 14.04 Codename: trusty # dpkg -i minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb Selecting previously unselected package minc-toolkit-itk4. (Reading database ... 26113 files and directories currently installed.) Preparing to unpack minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb ... Unpacking minc-toolkit-itk4 (1.9.10) ... dpkg: dependency problems prevent configuration of minc-toolkit-itk4: minc-toolkit-itk4 depends on imagemagick; however: Package imagemagick is not installed. then running apt-get install -f successfully installs imagemagick with dependencies. On 15-07-15 01:39 PM, Gabriel A. Devenyi wrote: > 14.04 (in a docker container) > Vladimir S. FONOV > >wrote: >> >Which version of Ubuntu are you using? >> > >> >On 15-07-15 01:26 PM, Gabriel A. Devenyi wrote: >> > >>> >>Hey Vlad, >>> >> >>> >>Is there an up-to-date list of dependencies for installing the toolkit in >>> >>ubuntu? In the current list the following packages don?t exist: >>> >> >>> >>E: Package 'libgl1' has no installation candidate >>> >>E: Package 'libtiff4' has no installation candidate >>> >> >> > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From vladimir.fonov at gmail.com Wed Jul 15 13:50:51 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 15 Jul 2015 13:50:51 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References:

<55A698D7.1050607@gmail.com> Message-ID: <55A69D7B.5080600@gmail.com> Also, dpkg-deb -I minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb new debian package, version 2.0. size 165590438 bytes: control archive=183076 bytes. 265 bytes, 10 lines control 537996 bytes, 6127 lines md5sums Package: minc-toolkit-itk4 Version: 1.9.10 Section: science Priority: optional Architecture: amd64 Depends: perl, imagemagick, libstdc++6, libc6 Installed-Size: 852998 Maintainer: Vladimir Fonov Description: minc image processing toolkit On 15-07-15 01:39 PM, Gabriel A. Devenyi wrote: > 14.04 (in a docker container) > >> >wrote: >> >Which version of Ubuntu are you using? >> > >> >On 15-07-15 01:26 PM, Gabriel A. Devenyi wrote: >> > >>> >>Hey Vlad, >>> >> >>> >>Is there an up-to-date list of dependencies for installing the toolkit in >>> >>ubuntu? In the current list the following packages don?t exist: >>> >> >>> >>E: Package 'libgl1' has no installation candidate >>> >>E: Package 'libtiff4' has no installation candidate >>> >> >> > >> > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From gdevenyi at gmail.com Wed Jul 15 13:49:36 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Wed, 15 Jul 2015 13:49:36 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: <55A69CE9.6050504@gmail.com> References:

<55A698D7.1050607@gmail.com> <55A69CE9.6050504@gmail.com> Message-ID: Ah, I was referring to the following line on the webpage http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#sServicesSoftware.ServicesSoftwareMincToolKit_3 ``` Installing On Debian/Ubuntu install dependencies: sudo apt-get install libc6 libstdc++6 imagemagick perl freeglut3 libgl1 libxcb1 libxdmcp6 libx11-6 libxext6 libxau6 libuuid1 libjpeg62 libexpat1 libtiff4 ``` I'll try it your way instead :) -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Wed, Jul 15, 2015 at 1:48 PM, Vladimir S. FONOV wrote: > That's strange. > > Running on Ubuntu 14.04 : > > # lsb_release -a > No LSB modules are available. > Distributor ID: Ubuntu > Description: Ubuntu 14.04.2 LTS > Release: 14.04 > Codename: trusty > > > # dpkg -i minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb > Selecting previously unselected package minc-toolkit-itk4. > (Reading database ... 26113 files and directories currently installed.) > Preparing to unpack minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb > ... > Unpacking minc-toolkit-itk4 (1.9.10) ... > dpkg: dependency problems prevent configuration of minc-toolkit-itk4: > minc-toolkit-itk4 depends on imagemagick; however: > Package imagemagick is not installed. > > > then running apt-get install -f > successfully installs imagemagick with dependencies. > > > > > On 15-07-15 01:39 PM, Gabriel A. Devenyi wrote: > >> 14.04 (in a docker container) >> > > > > Vladimir S. FONOV > >>> >wrote: >>> >Which version of Ubuntu are you using? >>> > >>> >On 15-07-15 01:26 PM, Gabriel A. Devenyi wrote: >>> > >>> >>>> >>Hey Vlad, >>>> >> >>>> >>Is there an up-to-date list of dependencies for installing the >>>> toolkit in >>>> >>ubuntu? In the current list the following packages don?t exist: >>>> >> >>>> >>E: Package 'libgl1' has no installation candidate >>>> >>E: Package 'libtiff4' has no installation candidate >>>> >> >>>> >>> > >>> >> > > -- > Best regards, > > Vladimir S. FONOV ~ vladimir.fonov gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Wed Jul 15 13:53:02 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 15 Jul 2015 13:53:02 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References:

<55A698D7.1050607@gmail.com> <55A69CE9.6050504@gmail.com> Message-ID: <55A69DFE.9010408@gmail.com> Ok, I should remove those... On 15-07-15 01:49 PM, Gabriel A. Devenyi wrote: > Ah, I was referring to the following line on the webpage > http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#sServicesSoftware.ServicesSoftwareMincToolKit_3 > ``` > Installing > On Debian/Ubuntu > install dependencies: sudo apt-get install libc6 libstdc++6 imagemagick > perl freeglut3 libgl1 libxcb1 libxdmcp6 libx11-6 libxext6 libxau6 libuuid1 > libjpeg62 libexpat1 libtiff4 > ``` > > I'll try it your way instead :) > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From gdevenyi at gmail.com Wed Jul 15 14:52:55 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Wed, 15 Jul 2015 14:52:55 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: <55A69DFE.9010408@gmail.com> References:

<55A698D7.1050607@gmail.com> <55A69CE9.6050504@gmail.com> <55A69DFE.9010408@gmail.com> Message-ID: Hi Vlad, I see mincANTS is gone but ANTS is there instead, does ANTS have the xfm support as well? -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Wed, Jul 15, 2015 at 1:53 PM, Vladimir S. FONOV wrote: > Ok, > > I should remove those... > > On 15-07-15 01:49 PM, Gabriel A. Devenyi wrote: > >> Ah, I was referring to the following line on the webpage >> >> http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#sServicesSoftware.ServicesSoftwareMincToolKit_3 >> ``` >> Installing >> On Debian/Ubuntu >> install dependencies: sudo apt-get install libc6 libstdc++6 imagemagick >> perl freeglut3 libgl1 libxcb1 libxdmcp6 libx11-6 libxext6 libxau6 libuuid1 >> libjpeg62 libexpat1 libtiff4 >> ``` >> >> I'll try it your way instead :) >> >> > > -- > Best regards, > > Vladimir S. FONOV ~ vladimir.fonov gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Wed Jul 15 14:58:37 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 15 Jul 2015 14:58:37 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References:

<55A698D7.1050607@gmail.com> <55A69CE9.6050504@gmail.com> <55A69DFE.9010408@gmail.com> Message-ID: <55A6AD5D.9080609@gmail.com> Hello, yes, it does. If you specify output file with .xfm extension it will create MINC-style transformation file. On 15-07-15 02:52 PM, Gabriel A. Devenyi wrote: > Hi Vlad, > > I see mincANTS is gone but ANTS is there instead, does ANTS have the xfm > support as well? > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From vladimir.fonov at gmail.com Wed Jul 15 19:14:18 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 15 Jul 2015 19:14:18 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References: Message-ID: Hello Everybody, it turns out that there is a problem with reading and writing minc-style transformation files (.xfm) in the 64 bit build for Debian 6 and for Ubuntu 10.04 , both are using gcc 4.4. Strangely enough, this does not happen on CentOS 6 which also uses gcc 4.4. I am still trying to figure out how to fix it... On Tue, Jul 14, 2015 at 6:20 PM, Vladimir S. FONOV wrote: > Hello Everybody, > > > I have finally made a new release of minc-toolkit-v2 (formerly > minc-toolkit experimental branch 1.9.XX). > > The new release if available at > http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#sServicesSoftware.ServicesSoftwareMincToolKit_3 > > and includes a lot of fixes and updates, the most significant are > following: > > 1. latest version of libminc , which includes a lots of bug fixes - > hopefully it will become release 2.3 some time soon > > 2. latest version of minc-tools , with updated dcm2mnc > > 3. ITK version 4.8 > > 4. latest version of ANTS package, which includes support for MINC-style > XFM files in the antsRegistration tool > > 5. latest version of Elastix with minc support. > > 6. mincified version of ABC tissue classification tool ( > http://www.nitrc.org/projects/abc/ ) > > P.S. It would be great if somebody who have access would update > https://www.mcgill.ca/bic/software/minc/minctoolkit to reflect this > changes. > > -- > Best regards, > > Vladimir S. Fonov ~ vladimir fonov gmail com > -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com From vladimir.fonov at gmail.com Wed Jul 15 19:20:46 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 15 Jul 2015 19:20:46 -0400 Subject: [MINC-users] minc-toolkit-v2 new release 1.9.10 In-Reply-To: References:

Message-ID: and the same happens on 32bit build for Ubuntu 10.04. On Wed, Jul 15, 2015 at 7:14 PM, Vladimir S. FONOV wrote: > Hello Everybody, > > it turns out that there is a problem with reading and writing minc-style > transformation files (.xfm) in the 64 bit build for Debian 6 and for Ubuntu > 10.04 , both are using gcc 4.4. Strangely enough, this does not happen on > CentOS 6 which also uses gcc 4.4. > I am still trying to figure out how to fix it... > > On Tue, Jul 14, 2015 at 6:20 PM, Vladimir S. FONOV < > vladimir.fonov at gmail.com> wrote: > >> Hello Everybody, >> >> >> I have finally made a new release of minc-toolkit-v2 (formerly >> minc-toolkit experimental branch 1.9.XX). >> >> The new release if available at >> http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#sServicesSoftware.ServicesSoftwareMincToolKit_3 >> >> and includes a lot of fixes and updates, the most significant are >> following: >> >> 1. latest version of libminc , which includes a lots of bug fixes - >> hopefully it will become release 2.3 some time soon >> >> 2. latest version of minc-tools , with updated dcm2mnc >> >> 3. ITK version 4.8 >> >> 4. latest version of ANTS package, which includes support for MINC-style >> XFM files in the antsRegistration tool >> >> 5. latest version of Elastix with minc support. >> >> 6. mincified version of ABC tissue classification tool ( >> http://www.nitrc.org/projects/abc/ ) >> >> P.S. It would be great if somebody who have access would update >> https://www.mcgill.ca/bic/software/minc/minctoolkit to reflect this >> changes. >> >> -- >> Best regards, >> >> Vladimir S. Fonov ~ vladimir fonov gmail com >> > > > > -- > Best regards, > > Vladimir S. Fonov ~ vladimir fonov gmail com > -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com From winterburn.julie at gmail.com Mon Jul 20 15:55:20 2015 From: winterburn.julie at gmail.com (Julie Winterburn) Date: Mon, 20 Jul 2015 15:55:20 -0400 Subject: [MINC-users] RMINC: mincIO.readVolume Error Message-ID: Hey all, I'm using mincIO.readVolume (part of RMINC) to read mnc images into R, and every now and then I get the following error on one of my images: 'File filename.mnc does not appear to be a valid minc volume' The files themselves seem to be fine: mincinfo produces a normal output, and I can open them in Display/register. mincIO.readVolume is the only place where I have a problem. Any ideas what the problem might be? Thanks, Julie From vladimir.fonov at gmail.com Mon Jul 20 16:00:43 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Mon, 20 Jul 2015 16:00:43 -0400 Subject: [MINC-users] RMINC: mincIO.readVolume Error In-Reply-To: References: Message-ID: Could be in MINC1 file format. You can check with file command, i.e file input.mnc it will say Hierarchical Data Format (version 5) data for MINC2 and NetCDF Data Format data for MINC1. On Mon, Jul 20, 2015 at 3:55 PM, Julie Winterburn < winterburn.julie at gmail.com> wrote: > Hey all, > > I'm using mincIO.readVolume (part of RMINC) to read mnc images into R, and > every now and then I get the following error on one of my images: > > 'File filename.mnc does not appear to be a valid minc volume' > > The files themselves seem to be fine: mincinfo produces a normal output, > and I can open them in Display/register. mincIO.readVolume is the only > place where I have a problem. Any ideas what the problem might be? > > Thanks, > Julie > _______________________________________________ > 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 mishkind at gmail.com Mon Jul 20 16:02:16 2015 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Mon, 20 Jul 2015 10:02:16 -1000 Subject: [MINC-users] RMINC: mincIO.readVolume Error In-Reply-To: References: Message-ID: Hi Julie, Sounds like it could be minc1 vs minc2. Could you post the output of: file badmincfile.mnc.gz mincinfo badmincfile.mnc.gz On Mon, Jul 20, 2015 at 9:55 AM, Julie Winterburn wrote: > Hey all, > > I'm using mincIO.readVolume (part of RMINC) to read mnc images into R, and > every now and then I get the following error on one of my images: > > 'File filename.mnc does not appear to be a valid minc volume' > > The files themselves seem to be fine: mincinfo produces a normal output, > and I can open them in Display/register. mincIO.readVolume is the only > place where I have a problem. Any ideas what the problem might be? > > Thanks, > Julie > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From winterburn.julie at gmail.com Mon Jul 20 16:09:55 2015 From: winterburn.julie at gmail.com (Julie Winterburn) Date: Mon, 20 Jul 2015 16:09:55 -0400 Subject: [MINC-users] RMINC: mincIO.readVolume Error In-Reply-To: References:

Message-ID: Hmm, I think you may be right: file input.mnc > input.mnc: x86 boot sector mincinfo input.mnc > image: unsigned short 0 to 65535 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 98 2 -90 yspace 116 2 -132 xspace 94 2 -96 On 20 July 2015 at 16:02, Mishkin Derakhshan wrote: > Hi Julie, > Sounds like it could be minc1 vs minc2. > Could you post the output of: > > file badmincfile.mnc.gz > mincinfo badmincfile.mnc.gz > > > On Mon, Jul 20, 2015 at 9:55 AM, Julie Winterburn > wrote: > > Hey all, > > > > I'm using mincIO.readVolume (part of RMINC) to read mnc images into R, > and > > every now and then I get the following error on one of my images: > > > > 'File filename.mnc does not appear to be a valid minc volume' > > > > The files themselves seem to be fine: mincinfo produces a normal output, > > and I can open them in Display/register. mincIO.readVolume is the only > > place where I have a problem. Any ideas what the problem might be? > > > > Thanks, > > Julie > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From ptcougopinto at gmail.com Fri Jul 24 17:18:33 2015 From: ptcougopinto at gmail.com (Pedro Telles Cougo-Pinto) Date: Fri, 24 Jul 2015 18:18:33 -0300 Subject: [MINC-users] Histogram stats Message-ID: Dear all, Is it possible to obtain skewness and kurtosis summary measures from MINC volumes? As far as I could see, mincstats does not offer this option. Thanks, Pedro From gdevenyi at gmail.com Fri Jul 24 17:21:49 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Fri, 24 Jul 2015 17:21:49 -0400 Subject: [MINC-users] Histogram stats In-Reply-To: References: Message-ID: Use pyminc interface and write your own with numpy perhaps? -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Fri, Jul 24, 2015 at 5:18 PM, Pedro Telles Cougo-Pinto < ptcougopinto at gmail.com> wrote: > Dear all, > > Is it possible to obtain skewness and kurtosis summary measures from MINC > volumes? As far as I could see, mincstats does not offer this option. > > Thanks, > Pedro > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Sat Jul 25 10:34:51 2015 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 26 Jul 2015 00:34:51 +1000 Subject: [MINC-users] Histogram stats In-Reply-To: References: Message-ID: Hi Pedro, You are correct, there is no calculation of kurtosis or skewness in mincstats. That said if you are after simple sample kurtosis it would be easy to add the calculation of the 3rd moment in mincstats here: https://github.com/BIC-MNI/minc-tools/blob/master/progs/mincstats/mincstats.c#L1360 a On 25 July 2015 at 07:18, Pedro Telles Cougo-Pinto wrote: > Dear all, > > Is it possible to obtain skewness and kurtosis summary measures from MINC > volumes? As far as I could see, mincstats does not offer this option. > > Thanks, > Pedro > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From ptcougopinto at gmail.com Sun Jul 26 14:13:43 2015 From: ptcougopinto at gmail.com (Pedro Pinto) Date: Sun, 26 Jul 2015 15:13:43 -0300 Subject: [MINC-users] Histogram stats In-Reply-To: References:

Message-ID: Thanks, I?ll look into both options. Thanks for pointing the code location, Andrew. Pedro On 25, Jul2015, at 11:34, Andrew Janke wrote: > Hi Pedro, > > You are correct, there is no calculation of kurtosis or skewness in > mincstats. That said if you are after simple sample kurtosis it would > be easy to add the calculation of the 3rd moment in mincstats here: > > https://github.com/BIC-MNI/minc-tools/blob/master/progs/mincstats/mincstats.c#L1360 > > > a > > > On 25 July 2015 at 07:18, Pedro Telles Cougo-Pinto > wrote: >> Dear all, >> >> Is it possible to obtain skewness and kurtosis summary measures from MINC >> volumes? As far as I could see, mincstats does not offer this option. >> >> Thanks, >> Pedro >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users