From yoshi.kumakura at gmail.com Thu Nov 5 00:50:12 2015 From: yoshi.kumakura at gmail.com (Yoshitaka KUMAKURA) Date: Thu, 5 Nov 2015 14:50:12 +0900 Subject: [MINC-users] dcm2mnc for Siemens Biograph mCT 64 PET/CT scanner Message-ID: Dear MINC experts, We would like to use MINC tools to analyze dynamic PET files of a Siemens Biograph mCT 64 PET/CT scanner in an affiliated hospital in Copenhagen. We are not new to MINC, because we are former BIC researchers (currently in Albert Gjedde's lab). But, we are a small PET research group with no computer scientist. We have a favor to ask. We've tried dcm2mnc to convert a set of dynamic 4D PET Dicom files to a minc files, and found that it just makes a 3D minc file, missing the 4th time dimension. Has anybody encountered the same issue? Is a dcm2mnc utility for the scanner available? We are in great need of the minc converter customized for the PET/CT scanner. We would appreciate it very much, if you could find us a solution. Best regards, Yoshi Yoshitaka Kumakura MD, PhD, Manou Vafaee, PhD, and Albert Gjedde MD, DSc Department of Neuroscience and Pharmacology University of Copenhagen From a.janke at gmail.com Thu Nov 5 00:53:50 2015 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 5 Nov 2015 15:53:50 +1000 Subject: [MINC-users] dcm2mnc for Siemens Biograph mCT 64 PET/CT scanner In-Reply-To: References: Message-ID: Hi Yoshi, Which version of dcm2mnc are you using (dcm2mnc -version will tell you), Bert has put a lot of work into the converter as of late to get it up to speed. My guess is that the converter cannot separate the frames and thus only keeps the first frame, you can get around this but let's see which version you are running first. a On 5 November 2015 at 15:50, Yoshitaka KUMAKURA wrote: > Dear MINC experts, > > We would like to use MINC tools to analyze dynamic PET files of a Siemens > Biograph mCT 64 PET/CT scanner in an affiliated hospital in Copenhagen. We > are not new to MINC, because we are former BIC researchers (currently in > Albert Gjedde's lab). But, we are a small PET research group with no > computer scientist. > > We have a favor to ask. We've tried dcm2mnc to convert a set of dynamic 4D > PET Dicom files to a minc files, and found that it just makes a 3D minc > file, missing the 4th time dimension. Has anybody encountered the same > issue? Is a dcm2mnc utility for the scanner available? We are in great need > of the minc converter customized for the PET/CT scanner. We would > appreciate it very much, if you could find us a solution. > > Best regards, > Yoshi > > Yoshitaka Kumakura MD, PhD, Manou Vafaee, PhD, and Albert Gjedde MD, DSc > Department of Neuroscience and Pharmacology > University of Copenhagen > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From yoshi.kumakura at gmail.com Thu Nov 5 01:12:53 2015 From: yoshi.kumakura at gmail.com (Yoshitaka KUMAKURA) Date: Thu, 5 Nov 2015 15:12:53 +0900 Subject: [MINC-users] dcm2mnc for Siemens Biograph mCT 64 PET/CT scanner In-Reply-To: References: Message-ID: Hi Andrew, The dcm2mnc version I am using is "program: 2.0.07 built Sep 26 2012". Thank you for your quick response. Yoshi On Thu, Nov 5, 2015 at 2:53 PM, Andrew Janke wrote: > Hi Yoshi, > > Which version of dcm2mnc are you using (dcm2mnc -version will tell > you), Bert has put a lot of work into the converter as of late to get > it up to speed. > > My guess is that the converter cannot separate the frames and thus > only keeps the first frame, you can get around this but let's see > which version you are running first. > > > a > > > On 5 November 2015 at 15:50, Yoshitaka KUMAKURA > wrote: > > Dear MINC experts, > > > > We would like to use MINC tools to analyze dynamic PET files of a Siemens > > Biograph mCT 64 PET/CT scanner in an affiliated hospital in Copenhagen. > We > > are not new to MINC, because we are former BIC researchers (currently in > > Albert Gjedde's lab). But, we are a small PET research group with no > > computer scientist. > > > > We have a favor to ask. We've tried dcm2mnc to convert a set of dynamic > 4D > > PET Dicom files to a minc files, and found that it just makes a 3D minc > > file, missing the 4th time dimension. Has anybody encountered the same > > issue? Is a dcm2mnc utility for the scanner available? We are in great > need > > of the minc converter customized for the PET/CT scanner. We would > > appreciate it very much, if you could find us a solution. > > > > Best regards, > > Yoshi > > > > Yoshitaka Kumakura MD, PhD, Manou Vafaee, PhD, and Albert Gjedde MD, DSc > > Department of Neuroscience and Pharmacology > > University of Copenhagen > > _______________________________________________ > > 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 a.janke at gmail.com Thu Nov 5 01:17:01 2015 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 5 Nov 2015 16:17:01 +1000 Subject: [MINC-users] dcm2mnc for Siemens Biograph mCT 64 PET/CT scanner In-Reply-To: References: Message-ID: Ah, first things first, please upgrade to the latest release which has a number of changes to dcm2mnc (v1.9.1 of minc-toolkit): http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#1.9.10 a On 5 November 2015 at 16:12, Yoshitaka KUMAKURA wrote: > Hi Andrew, > > The dcm2mnc version I am using is "program: 2.0.07 built Sep 26 2012". > > Thank you for your quick response. > Yoshi > > On Thu, Nov 5, 2015 at 2:53 PM, Andrew Janke wrote: > >> Hi Yoshi, >> >> Which version of dcm2mnc are you using (dcm2mnc -version will tell >> you), Bert has put a lot of work into the converter as of late to get >> it up to speed. >> >> My guess is that the converter cannot separate the frames and thus >> only keeps the first frame, you can get around this but let's see >> which version you are running first. >> >> >> a >> >> >> On 5 November 2015 at 15:50, Yoshitaka KUMAKURA >> wrote: >> > Dear MINC experts, >> > >> > We would like to use MINC tools to analyze dynamic PET files of a Siemens >> > Biograph mCT 64 PET/CT scanner in an affiliated hospital in Copenhagen. >> We >> > are not new to MINC, because we are former BIC researchers (currently in >> > Albert Gjedde's lab). But, we are a small PET research group with no >> > computer scientist. >> > >> > We have a favor to ask. We've tried dcm2mnc to convert a set of dynamic >> 4D >> > PET Dicom files to a minc files, and found that it just makes a 3D minc >> > file, missing the 4th time dimension. Has anybody encountered the same >> > issue? Is a dcm2mnc utility for the scanner available? We are in great >> need >> > of the minc converter customized for the PET/CT scanner. We would >> > appreciate it very much, if you could find us a solution. >> > >> > Best regards, >> > Yoshi >> > >> > Yoshitaka Kumakura MD, PhD, Manou Vafaee, PhD, and Albert Gjedde MD, DSc >> > Department of Neuroscience and Pharmacology >> > University of Copenhagen >> > _______________________________________________ >> > 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 >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From vladimir.fonov at gmail.com Thu Nov 5 11:07:46 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 5 Nov 2015 11:07:46 -0500 Subject: [MINC-users] dcm2mnc for Siemens Biograph mCT 64 PET/CT scanner In-Reply-To: References: Message-ID: <563B7ED2.4060405@gmail.com> Hello Yoshi, I had a similar situation some time ago, I found that I had to rely on dcmdump from dcmtk first to split all the DICOM files into individual 3D volumes, then run dcm2mnc on each set independently, and finally concatenating them with mincconcat along time dimension. On 15-11-05 12:50 AM, Yoshitaka KUMAKURA wrote: > Dear MINC experts, > > We would like to use MINC tools to analyze dynamic PET files of a Siemens > Biograph mCT 64 PET/CT scanner in an affiliated hospital in Copenhagen. We > are not new to MINC, because we are former BIC researchers (currently in > Albert Gjedde's lab). But, we are a small PET research group with no > computer scientist. > > We have a favor to ask. We've tried dcm2mnc to convert a set of dynamic 4D > PET Dicom files to a minc files, and found that it just makes a 3D minc > file, missing the 4th time dimension. Has anybody encountered the same > issue? Is a dcm2mnc utility for the scanner available? We are in great need > of the minc converter customized for the PET/CT scanner. We would > appreciate it very much, if you could find us a solution. -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From louis.dieumegarde at crulrg.ulaval.ca Fri Nov 6 10:38:36 2015 From: louis.dieumegarde at crulrg.ulaval.ca (Louis Dieumegarde) Date: Fri, 6 Nov 2015 15:38:36 +0000 Subject: [MINC-users] post to list Message-ID: <9E6BA6B8-DBB3-40F0-9FB6-5E161F1377AA@ulaval.ca> Hi, I need to post a question about MIDAS dataset. Is it the right place? My email is at the bottom. Thank you. Louis Dieumegarde B.Sc. Biologie Geologie Professionnel de recherche Laboratoire Medics, local F-3568 Centre de Recherche de l'Institut Universitaire en Sante Mentale de Quebec 2601 Chemin de la Canardiere, Quebec G1J 2G3 (418) 663-5000, poste 6716 [1]louis.dieumegarde at crulrg.ulaval.ca References 1. mailto:louis.dieumegarde at crulrg.ulaval.ca From wadhah.ayadi at yahoo.fr Fri Nov 6 11:28:03 2015 From: wadhah.ayadi at yahoo.fr (ayadi wadhah) Date: Fri, 6 Nov 2015 16:28:03 +0000 (UTC) Subject: [MINC-users] post to list In-Reply-To: <9E6BA6B8-DBB3-40F0-9FB6-5E161F1377AA@ulaval.ca> References: <9E6BA6B8-DBB3-40F0-9FB6-5E161F1377AA@ulaval.ca> Message-ID: <1192662301.1467432.1446827283480.JavaMail.yahoo@mail.yahoo.com> hi sir, ?I have many problem with minc file. how i can change it to another extension file? or how can read it with Matlab? ?Thank you in advance.Best regards.?Ayadi? Ayadi WadhahLaboratoire ?Electronique et micro-?lectroniqueFacult? des Sciences de MonastirTel: (+216) 41 327 380Email:?wadhah.ayadi at yahoo.fr Le Vendredi 6 novembre 2015 16h42, Louis Dieumegarde a ?crit : ? Hi, ? I need to post a question about MIDAS dataset. Is it the right place? ? My email is at the bottom. Thank you. ? Louis Dieumegarde ? B.Sc. Biologie Geologie ? Professionnel de recherche ? Laboratoire Medics, local F-3568 ? Centre de Recherche de l'Institut Universitaire en Sante Mentale de ? Quebec ? 2601 Chemin de la Canardiere, Quebec ? G1J 2G3 ? (418) 663-5000, poste 6716 ? [1]louis.dieumegarde at crulrg.ulaval.ca References ? 1. mailto:louis.dieumegarde at crulrg.ulaval.ca _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From robert.d.vincent at mcgill.ca Fri Nov 6 12:01:43 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Fri, 6 Nov 2015 12:01:43 -0500 Subject: [MINC-users] post to list In-Reply-To: <1192662301.1467432.1446827283480.JavaMail.yahoo@mail.yahoo.com> References: <9E6BA6B8-DBB3-40F0-9FB6-5E161F1377AA@ulaval.ca> <1192662301.1467432.1446827283480.JavaMail.yahoo@mail.yahoo.com> Message-ID: Hi Ayadi, There are a number of conversion tools that can convert MINC files to other formats. We provide a tool for converting to the "NIfTI-1" format called "mnc2nii". It is part of the MINC toolkit, available here: http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit -bert On Fri, Nov 6, 2015 at 11:28 AM, ayadi wadhah wrote: > hi sir, > I have many problem with minc file. how i can change it to another > extension file? or how can read it with Matlab? > Thank you in advance.Best regards. Ayadi > > Ayadi WadhahLaboratoire Electronique et micro-?lectroniqueFacult? des > Sciences de MonastirTel: (+216) 41 327 380Email: wadhah.ayadi at yahoo.fr > > > Le Vendredi 6 novembre 2015 16h42, Louis Dieumegarde < > louis.dieumegarde at crulrg.ulaval.ca> a ?crit : > > > Hi, > I need to post a question about MIDAS dataset. Is it the right place? > My email is at the bottom. Thank you. > Louis Dieumegarde > B.Sc. Biologie Geologie > Professionnel de recherche > Laboratoire Medics, local F-3568 > Centre de Recherche de l'Institut Universitaire en Sante Mentale de > Quebec > 2601 Chemin de la Canardiere, Quebec > G1J 2G3 > (418) 663-5000, poste 6716 > [1]louis.dieumegarde at crulrg.ulaval.ca > > References > > 1. mailto:louis.dieumegarde at crulrg.ulaval.ca > _______________________________________________ > 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 pierre.bellec at criugm.qc.ca Fri Nov 6 13:00:40 2015 From: pierre.bellec at criugm.qc.ca (Pierre Bellec) Date: Fri, 6 Nov 2015 13:00:40 -0500 Subject: [MINC-users] post to list In-Reply-To: <1192662301.1467432.1446827283480.JavaMail.yahoo@mail.yahoo.com> References: <9E6BA6B8-DBB3-40F0-9FB6-5E161F1377AA@ulaval.ca> <1192662301.1467432.1446827283480.JavaMail.yahoo@mail.yahoo.com> Message-ID: Dear Wadhah, I am not sure what type of data you are trying to manipulate, but for 3D structural MRIs or 4D functional MRI datasets there is the following toolbox called MOMINC. Links for downloading MOMINC version 0.2 are here https://github.com/SIMEXP/mominc/releases/tag/v0.2 To install, just uncompress and add the .m files to your path. Reading a minc file in matlab will look like: [hdr,vol] = minc_read('file.mc'); More details on the outputs are here: https://github.com/SIMEXP/mominc/blob/master/README.md There is currently no writer, but the reader should work well. ? I hope this helps. Best, Pierre From sorench at gmail.com Fri Nov 6 17:02:39 2015 From: sorench at gmail.com (Soren Christensen) Date: Fri, 6 Nov 2015 14:02:39 -0800 Subject: [MINC-users] Issue with register Message-ID: Hi, I am using register built from from minc-tool release-1.0.07 and when placing manual land marks it invariably crashes on landmark number 4 with the following error: XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":0" after 2294 requests (2294 known processed) with 0 events remaining. This is on Ubuntu 14.04 and with the dependencies shown below. Has anyone else seen this issue? Thanks Soren ldd /usr/local/MNI/bin/register linux-vdso.so.1 => (0x00007ffd255db000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f765a58c000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f765a286000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f765a082000) libglut.so.3 => /usr/lib/x86_64-linux-gnu/libglut.so.3 (0x00007f7659e38000) libGL.so.1 => /usr/lib/nvidia-346-updates/libGL.so.1 (0x00007f7659ae0000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f765971b000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f76594fd000) /lib64/ld-linux-x86-64.so.2 (0x00007f765a794000) libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f76591c8000) libXi.so.6 => /usr/lib/x86_64-linux-gnu/libXi.so.6 (0x00007f7658fb8000) libXxf86vm.so.1 => /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1 (0x00007f7658db2000) libnvidia-tls.so.346.96 => /usr/lib/nvidia-346-updates/tls/libnvidia-tls.so.346.96 (0x00007f7658baf000) libnvidia-glcore.so.346.96 => /usr/lib/nvidia-346-updates/libnvidia-glcore.so.346.96 (0x00007f7655ed1000) libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f7655cbf000) libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f7655aa0000) libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f765589c000) libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f7655696000) From robert.d.vincent at mcgill.ca Fri Nov 6 17:06:15 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Fri, 6 Nov 2015 17:06:15 -0500 Subject: [MINC-users] Issue with register In-Reply-To: References: Message-ID: Hi Soren, Yes, this is triggered by certain versions of FreeGLUT (see https://github.com/BIC-MNI/Register/issues/1). I have fixed the problem, but it is not yet in the release. -bert On Fri, Nov 6, 2015 at 5:02 PM, Soren Christensen wrote: > Hi, > I am using register built from from minc-tool release-1.0.07 and when > placing manual land marks it invariably crashes on landmark number 4 with > the following error: > XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":0" > after 2294 requests (2294 known processed) with 0 events remaining. > > This is on Ubuntu 14.04 and with the dependencies shown below. > > Has anyone else seen this issue? > > > Thanks > Soren > > > ldd /usr/local/MNI/bin/register > linux-vdso.so.1 => (0x00007ffd255db000) > librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f765a58c000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f765a286000) > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f765a082000) > libglut.so.3 => /usr/lib/x86_64-linux-gnu/libglut.so.3 (0x00007f7659e38000) > libGL.so.1 => /usr/lib/nvidia-346-updates/libGL.so.1 (0x00007f7659ae0000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f765971b000) > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x00007f76594fd000) > /lib64/ld-linux-x86-64.so.2 (0x00007f765a794000) > libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f76591c8000) > libXi.so.6 => /usr/lib/x86_64-linux-gnu/libXi.so.6 (0x00007f7658fb8000) > libXxf86vm.so.1 => /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1 > (0x00007f7658db2000) > libnvidia-tls.so.346.96 => > /usr/lib/nvidia-346-updates/tls/libnvidia-tls.so.346.96 > (0x00007f7658baf000) > libnvidia-glcore.so.346.96 => > /usr/lib/nvidia-346-updates/libnvidia-glcore.so.346.96 (0x00007f7655ed1000) > libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f7655cbf000) > libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f7655aa0000) > libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f765589c000) > libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 > (0x00007f7655696000) > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Fri Nov 6 17:15:28 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 6 Nov 2015 17:15:28 -0500 Subject: [MINC-users] Issue with register In-Reply-To: References: Message-ID: <563D2680.5030802@gmail.com> It's also possible to fix this issue by building minc-toolkit with USE_SYSTEM_GLUT:BOOL=OFF - it will build internal version of Freeglut that works. On 15-11-06 05:06 PM, Robert D. Vincent wrote: > Hi Soren, > > Yes, this is triggered by certain versions of FreeGLUT (see > https://github.com/BIC-MNI/Register/issues/1). > > I have fixed the problem, but it is not yet in the release. > > -bert > > > On Fri, Nov 6, 2015 at 5:02 PM, Soren Christensen wrote: > >> Hi, >> I am using register built from from minc-tool release-1.0.07 and when >> placing manual land marks it invariably crashes on landmark number 4 with >> the following error: >> XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":0" >> after 2294 requests (2294 known processed) with 0 events remaining. >> >> This is on Ubuntu 14.04 and with the dependencies shown below. >> >> Has anyone else seen this issue? >> >> >> Thanks >> Soren >> >> >> ldd /usr/local/MNI/bin/register >> linux-vdso.so.1 => (0x00007ffd255db000) >> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f765a58c000) >> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f765a286000) >> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f765a082000) >> libglut.so.3 => /usr/lib/x86_64-linux-gnu/libglut.so.3 (0x00007f7659e38000) >> libGL.so.1 => /usr/lib/nvidia-346-updates/libGL.so.1 (0x00007f7659ae0000) >> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f765971b000) >> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 >> (0x00007f76594fd000) >> /lib64/ld-linux-x86-64.so.2 (0x00007f765a794000) >> libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f76591c8000) >> libXi.so.6 => /usr/lib/x86_64-linux-gnu/libXi.so.6 (0x00007f7658fb8000) >> libXxf86vm.so.1 => /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1 >> (0x00007f7658db2000) >> libnvidia-tls.so.346.96 => >> /usr/lib/nvidia-346-updates/tls/libnvidia-tls.so.346.96 >> (0x00007f7658baf000) >> libnvidia-glcore.so.346.96 => >> /usr/lib/nvidia-346-updates/libnvidia-glcore.so.346.96 (0x00007f7655ed1000) >> libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f7655cbf000) >> libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f7655aa0000) >> libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f765589c000) >> libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 >> (0x00007f7655696000) >> _______________________________________________ >> 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 > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From sorench at gmail.com Fri Nov 6 18:04:34 2015 From: sorench at gmail.com (Soren Christensen) Date: Fri, 6 Nov 2015 15:04:34 -0800 Subject: [MINC-users] Issue with register In-Reply-To: <563D2680.5030802@gmail.com> References: <563D2680.5030802@gmail.com> Message-ID: Thanks!!! Soren On Fri, Nov 6, 2015 at 2:15 PM, Vladimir S. FONOV wrote: > It's also possible to fix this issue by building minc-toolkit with > USE_SYSTEM_GLUT:BOOL=OFF - it will build internal version of Freeglut that > works. > > > On 15-11-06 05:06 PM, Robert D. Vincent wrote: > >> Hi Soren, >> >> Yes, this is triggered by certain versions of FreeGLUT (see >> https://github.com/BIC-MNI/Register/issues/1). >> >> I have fixed the problem, but it is not yet in the release. >> >> -bert >> >> >> On Fri, Nov 6, 2015 at 5:02 PM, Soren Christensen >> wrote: >> >> Hi, >>> I am using register built from from minc-tool release-1.0.07 and when >>> placing manual land marks it invariably crashes on landmark number 4 with >>> the following error: >>> XIO: fatal IO error 11 (Resource temporarily unavailable) on X server >>> ":0" >>> after 2294 requests (2294 known processed) with 0 events >>> remaining. >>> >>> This is on Ubuntu 14.04 and with the dependencies shown below. >>> >>> Has anyone else seen this issue? >>> >>> >>> Thanks >>> Soren >>> >>> >>> ldd /usr/local/MNI/bin/register >>> linux-vdso.so.1 => (0x00007ffd255db000) >>> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f765a58c000) >>> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f765a286000) >>> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f765a082000) >>> libglut.so.3 => /usr/lib/x86_64-linux-gnu/libglut.so.3 >>> (0x00007f7659e38000) >>> libGL.so.1 => /usr/lib/nvidia-346-updates/libGL.so.1 (0x00007f7659ae0000) >>> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f765971b000) >>> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 >>> (0x00007f76594fd000) >>> /lib64/ld-linux-x86-64.so.2 (0x00007f765a794000) >>> libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f76591c8000) >>> libXi.so.6 => /usr/lib/x86_64-linux-gnu/libXi.so.6 (0x00007f7658fb8000) >>> libXxf86vm.so.1 => /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1 >>> (0x00007f7658db2000) >>> libnvidia-tls.so.346.96 => >>> /usr/lib/nvidia-346-updates/tls/libnvidia-tls.so.346.96 >>> (0x00007f7658baf000) >>> libnvidia-glcore.so.346.96 => >>> /usr/lib/nvidia-346-updates/libnvidia-glcore.so.346.96 >>> (0x00007f7655ed1000) >>> libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 >>> (0x00007f7655cbf000) >>> libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f7655aa0000) >>> libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f765589c000) >>> libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 >>> (0x00007f7655696000) >>> _______________________________________________ >>> 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 >> >> > > -- > 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 yoshi.kumakura at gmail.com Mon Nov 9 09:31:10 2015 From: yoshi.kumakura at gmail.com (Yoshitaka KUMAKURA) Date: Mon, 9 Nov 2015 23:31:10 +0900 Subject: [MINC-users] dcm2mnc for Siemens Biograph mCT 64 PET/CT scanner In-Reply-To: <563B7ED2.4060405@gmail.com> References: <563B7ED2.4060405@gmail.com> Message-ID: Thank you very much, Andrew and Vladimir. Here is my progress. 1) I've installed dcm2mnc version 2.01.01 (built 2015), and found it working much better. Now, MINC files converted from DICOM of Biograph PET/CT can be viewed on MNI-register, and they look good, though I haven't checked voxel values in detail yet. In terms of recording the time dimension, I see dcm2mnc behave differently from ecattominc. Frame MID times are extracted by dcm2mnc. But, this is a bit confusing for old Siemens PET users, because frame START times were extracted by (the good old days) ecattominc. We already have a lot of tools customized for that. time = 15, 45, 75, 105, 135, 165, 210, 270, 330, 390, 450... time-width = 30, 30, 30, 30, 30, 30, 60, 60, 60, 60, 60, 180, 180, 180, 180... So, I would be even more grateful if it could be like: time = 0, 30, 60, 90.... Is there any good idea to solve or avoid the issue of ambiguity in recording "time" between dcm2mnc and ecattominc? I am also wondering where this has come from. 2) Our PET experiment is consisted of two PET/CT scans on the same day. They are separated by a 30-min scanning break, and need to be concatenated. The first scan's frame width is incremental, like typical dynamic PET scans. The second scan's frame width is constant, 360sec (x 10 frames). Some header lines that seem to be related to this issue are shown below. SCAN1(incremental frame time-width) double time(time) ; time:start = 15. ; time:spacing = "irregular" ; time:alignment = "start_" ; time = 15, 45, 75, 105, 135, 165, 210, 270, 330, 390, 450, 570, 750, 930, 1110, 1350, 1650, 1950, 2250, 2550,.....(truncated) time-width = 30, 30, 30, 30, 30, 30, 60, 60, 60, 60, 60, 180, 180, 180, 180, 300, 300, 300, 300, 300, 300, 300, 300 ; SCAN2 (360 sec x 10 fr) double time(time) ; time:start = 179. ; time:spacing = "regular__" ; time:alignment = "start_" ; time = 179, 539, 899, 1259, 1619, 1979, 2339, 2699,.....(truncated) Here, time-with is unavailable in the 2nd scan's header. It would be very nice if MINC experts could implement an option that forces dcm2mnc to work in the "irregular" mode, so that the constant time-width would be explicitly recovered in the 2nd scan's MINC header. In this way, MINC uses like myself can feel more comfortable, when concatenating two dissimilar files (after time adjustment, decay correction, head motion correction etc, of course). 3) Sometimes, stuck in "Argument list too long". Please help me learn how to use find and xargs commands properly... Best regards, Yoshi On Fri, Nov 6, 2015 at 1:07 AM, Vladimir S. FONOV wrote: > Hello Yoshi, > > I had a similar situation some time ago, I found that I had to rely on > dcmdump from dcmtk first to split all the DICOM files into individual 3D > volumes, then run dcm2mnc on each set independently, and finally > concatenating them with mincconcat along time dimension. > > > On 15-11-05 12:50 AM, Yoshitaka KUMAKURA wrote: > >> Dear MINC experts, >> >> We would like to use MINC tools to analyze dynamic PET files of a Siemens >> Biograph mCT 64 PET/CT scanner in an affiliated hospital in Copenhagen. We >> are not new to MINC, because we are former BIC researchers (currently in >> Albert Gjedde's lab). But, we are a small PET research group with no >> computer scientist. >> >> We have a favor to ask. We've tried dcm2mnc to convert a set of dynamic 4D >> PET Dicom files to a minc files, and found that it just makes a 3D minc >> file, missing the 4th time dimension. Has anybody encountered the same >> issue? Is a dcm2mnc utility for the scanner available? We are in great >> need >> of the minc converter customized for the PET/CT scanner. We would >> appreciate it very much, if you could find us a solution. >> > > > -- > 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 emmanuelle.renauld.1 at ulaval.ca Mon Nov 9 09:33:47 2015 From: emmanuelle.renauld.1 at ulaval.ca (Emmanuelle Renauld) Date: Mon, 9 Nov 2015 14:33:47 +0000 Subject: [MINC-users] Problems with mri_nu_correct.mni In-Reply-To: <1446834694775.56073@ulaval.ca> References: <1446834694775.56073@ulaval.ca> Message-ID: <1447079662794.57996@ulaval.ca> ​ Hi, I have just installed FreeSurfer, and I have problems running recon-all. I think the problem is linked to mni. The error log says nothing, only "exited with ERRORS" after running the following line: mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz If I go in freesurfer/mri/ and run this line, the output says many warnings such as defined(@array) is deprecated at /usr/local/FreeSurfer//mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) And then stops while running the following line: nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4145/0/ ./tmp.mri_nu_correct.mni.4145/nu0.mnc ./tmp.mri_nu_correct.mni.4145/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct I found many threads about similar problems, but none were solved, and they were all old. One recommanded adding more memory to the VirtualBox, and since it is my case, I did so, but the bug stays. Any ideas? Thank you very much, Emmanuelle From robert.d.vincent at mcgill.ca Mon Nov 9 09:59:23 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Mon, 9 Nov 2015 09:59:23 -0500 Subject: [MINC-users] dcm2mnc for Siemens Biograph mCT 64 PET/CT scanner In-Reply-To: References: <563B7ED2.4060405@gmail.com> Message-ID: Hi Yoshi, 1. We read the frame times from specific DICOM fields, so it is likely that the DICOM itself is recording the mid point. Again, if you can provide a scan, we can change the behavior of the program to record the initial frame time. 2. This could be easily done, but it should not make any actual difference. Does mincconcat work properly with the regular/irregular dimensions? 3. You are getting "Argument list too long" when running dcm2mnc? This should be easily avoidable. You can generally just specify a directory name for a set of DICOM files: dcm2mnc Alternatively, you can read a list of files from standard input: find -name "*.dcm" | dcm2mnc -stdin -bert On Mon, Nov 9, 2015 at 9:31 AM, Yoshitaka KUMAKURA wrote: > Thank you very much, Andrew and Vladimir. > > Here is my progress. > > 1) I've installed dcm2mnc version 2.01.01 (built 2015), and found it > working much better. Now, MINC files converted from DICOM of Biograph > PET/CT can be viewed on MNI-register, and they look good, though I haven't > checked voxel values in detail yet. > > In terms of recording the time dimension, I see dcm2mnc behave differently > from ecattominc. Frame MID times are extracted by dcm2mnc. But, this is a > bit confusing for old Siemens PET users, because frame START times were > extracted by (the good old days) ecattominc. We already have a lot of tools > customized for that. > > > time = 15, 45, 75, 105, 135, 165, 210, 270, 330, 390, 450... > time-width = 30, 30, 30, 30, 30, 30, 60, 60, 60, 60, 60, 180, 180, 180, > 180... > > So, I would be even more grateful if it could be like: > time = 0, 30, 60, 90.... > > Is there any good idea to solve or avoid the issue of ambiguity in > recording "time" between dcm2mnc and ecattominc? I am also wondering where > this has come from. > > 2) Our PET experiment is consisted of two PET/CT scans on the same day. > They are separated by a 30-min scanning break, and need to be concatenated. > The first scan's frame width is incremental, like typical dynamic PET > scans. The second scan's frame width is constant, 360sec (x 10 frames). > Some header lines that seem to be related to this issue are shown below. > > SCAN1(incremental frame time-width) > double time(time) ; > time:start = 15. ; > time:spacing = "irregular" ; > time:alignment = "start_" ; > > time = 15, 45, 75, 105, 135, 165, 210, 270, 330, 390, 450, 570, > 750, 930, 1110, 1350, 1650, 1950, 2250, 2550,.....(truncated) > > time-width = 30, 30, 30, 30, 30, 30, 60, 60, 60, 60, 60, 180, 180, 180, > 180, > 300, 300, 300, 300, 300, 300, 300, 300 ; > > > SCAN2 (360 sec x 10 fr) > double time(time) ; > time:start = 179. ; > time:spacing = "regular__" ; > time:alignment = "start_" ; > > > time = 179, 539, 899, 1259, 1619, 1979, 2339, 2699,.....(truncated) > > Here, time-with is unavailable in the 2nd scan's header. It would be very > nice if MINC experts could implement an option that forces dcm2mnc to work > in the "irregular" mode, so that the constant time-width would be > explicitly recovered in the 2nd scan's MINC header. In this way, MINC uses > like myself can feel more comfortable, when concatenating two dissimilar > files (after time adjustment, decay correction, head motion correction etc, > of course). > > 3) Sometimes, stuck in "Argument list too long". Please help me learn > how to use find and xargs commands properly... > > Best regards, > Yoshi > > On Fri, Nov 6, 2015 at 1:07 AM, Vladimir S. FONOV < > vladimir.fonov at gmail.com> > wrote: > > > Hello Yoshi, > > > > I had a similar situation some time ago, I found that I had to rely on > > dcmdump from dcmtk first to split all the DICOM files into individual 3D > > volumes, then run dcm2mnc on each set independently, and finally > > concatenating them with mincconcat along time dimension. > > > > > > On 15-11-05 12:50 AM, Yoshitaka KUMAKURA wrote: > > > >> Dear MINC experts, > >> > >> We would like to use MINC tools to analyze dynamic PET files of a > Siemens > >> Biograph mCT 64 PET/CT scanner in an affiliated hospital in Copenhagen. > We > >> are not new to MINC, because we are former BIC researchers (currently in > >> Albert Gjedde's lab). But, we are a small PET research group with no > >> computer scientist. > >> > >> We have a favor to ask. We've tried dcm2mnc to convert a set of dynamic > 4D > >> PET Dicom files to a minc files, and found that it just makes a 3D minc > >> file, missing the 4th time dimension. Has anybody encountered the same > >> issue? Is a dcm2mnc utility for the scanner available? We are in great > >> need > >> of the minc converter customized for the PET/CT scanner. We would > >> appreciate it very much, if you could find us a solution. > >> > > > > > > -- > > 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 ptcougopinto at gmail.com Wed Nov 11 14:48:18 2015 From: ptcougopinto at gmail.com (Pedro Telles Cougo Pinto) Date: Wed, 11 Nov 2015 17:48:18 -0200 Subject: [MINC-users] mritotal models (OS X) Message-ID: <05866741-ED19-4657-B03E-5AA273DE9636@gmail.com> Hi, I installed minc-toolkit for OS X (minc-toolkit-1.9.10-20150710-Darwin-10.9-x86_64.dmg ) and I?m having some issues with models for mritotal. I would appreciate any help. First, the installation puts mritotal.cfg (and other mritotal .cfg files) at /opt/minc-itk4/etc, however mritotal still tries to find the .cfg files at /opt/minc-itk4/etc/mni_autoreg/ . I simply moved the .cfg files to a newly created /opt/minc-itk4/etc/mni_autoreg directory, but I?m not sure about the best definitive fix for this (changing the package file architecture?). I used the most recent model files from http://packages.bic.mni.mcgill.ca: bic-mni-models-0.1.1-20120421.dmg to get ICBM152 files and mni305_lin_minc2.zip (README gives compiling instructions, but the zip comes only with the .mnc files) for the 305 model, all located to /opt/minc/share (mritotal.cfg was edited to reflect this). Running mritotal gives the following message: Loading configuration file /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.cfg Loading protocol default (protocol file = /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.default.cfg) /opt/minc/share/average305_t1_tal_lin_16_blur.mnc does not exist /opt/minc/share/average305_t1_tal_lin_8_blur.mnc does not exist /opt/minc/share/average305_t1_tal_lin_8_dxyz.mnc does not exist /opt/minc/share/average305_t1_tal_lin_16_mask.mnc does not exist /opt/minc/share/average305_t1_tal_lin_8_mask.mnc does not exist Died at /opt/minc-itk4/bin/mritotal line 728. Were these 305 files supposed to be built as part of compiling? Both bic-mni-models-0.1.1-20120421.dmg and mni305_lin_minc2.zip were from 2012; am I trying to get the models from wrong sources? Thanks, Pedro From vladimir.fonov at gmail.com Wed Nov 11 15:10:38 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 11 Nov 2015 15:10:38 -0500 Subject: [MINC-users] mritotal models (OS X) In-Reply-To: <05866741-ED19-4657-B03E-5AA273DE9636@gmail.com> References: <05866741-ED19-4657-B03E-5AA273DE9636@gmail.com> Message-ID: <5643A0BE.7080901@gmail.com> Hello Pedro, these files are meant to work with newer version of the script - called bestlinreg_s , you can replace the call to mritotal to bestlinreg_s -lsq7 -nmi /opt/minc/share/average305_t1_tal_lin.mnc On 15-11-11 02:48 PM, Pedro Telles Cougo Pinto wrote: > Hi, > > I installed minc-toolkit for OS X (minc-toolkit-1.9.10-20150710-Darwin-10.9-x86_64.dmg ) and I?m having some issues with models for mritotal. I would appreciate any help. > > First, the installation puts mritotal.cfg (and other mritotal .cfg files) at /opt/minc-itk4/etc, however mritotal still tries to find the .cfg files at /opt/minc-itk4/etc/mni_autoreg/ . I simply moved the .cfg files to a newly created /opt/minc-itk4/etc/mni_autoreg directory, but I?m not sure about the best definitive fix for this (changing the package file architecture?). > > I used the most recent model files from http://packages.bic.mni.mcgill.ca: bic-mni-models-0.1.1-20120421.dmg to get ICBM152 files and mni305_lin_minc2.zip (README gives compiling instructions, but the zip comes only with the .mnc files) for the 305 model, all located to /opt/minc/share (mritotal.cfg was edited to reflect this). Running mritotal gives the following message: > > Loading configuration file /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.cfg > Loading protocol default (protocol file = /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.default.cfg) > /opt/minc/share/average305_t1_tal_lin_16_blur.mnc does not exist > /opt/minc/share/average305_t1_tal_lin_8_blur.mnc does not exist > /opt/minc/share/average305_t1_tal_lin_8_dxyz.mnc does not exist > /opt/minc/share/average305_t1_tal_lin_16_mask.mnc does not exist > /opt/minc/share/average305_t1_tal_lin_8_mask.mnc does not exist > Died at /opt/minc-itk4/bin/mritotal line 728. > > Were these 305 files supposed to be built as part of compiling? Both bic-mni-models-0.1.1-20120421.dmg and mni305_lin_minc2.zip were from 2012; am I trying to get the models from wrong sources? > > Thanks, > Pedro > _______________________________________________ > 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 yoshi.kumakura at gmail.com Thu Nov 12 03:39:23 2015 From: yoshi.kumakura at gmail.com (Yoshitaka KUMAKURA) Date: Thu, 12 Nov 2015 17:39:23 +0900 Subject: [MINC-users] dcm2mnc for Siemens Biograph mCT 64 PET/CT scanner In-Reply-To: References: <563B7ED2.4060405@gmail.com> Message-ID: Hi Bert, 1. I've uploaded two DICOM tar.gz files to BIC. PM sent. 2. As far as I checked, time-width gets lost completely after running mincconcat for an "irregular-regular" pair. Some important tools we use regularly (e.g. TAC extraction) don't work, due to lack of time-width. Thank you again for your help. I appreciate it very much. Best regards, Yoshi On Mon, Nov 9, 2015 at 11:59 PM, Robert D. Vincent < robert.d.vincent at mcgill.ca> wrote: > Hi Yoshi, > > 1. We read the frame times from specific DICOM fields, so it is likely that > the DICOM itself is recording the mid point. Again, if you can provide a > scan, we can change the behavior of the program to record the initial frame > time. > > 2. This could be easily done, but it should not make any actual difference. > Does mincconcat work properly with the regular/irregular dimensions? > > 3. You are getting "Argument list too long" when running dcm2mnc? This > should be easily avoidable. You can generally just specify a directory name > for a set of DICOM files: > > dcm2mnc > > Alternatively, you can read a list of files from standard input: > > find -name "*.dcm" | dcm2mnc -stdin > > -bert > > > On Mon, Nov 9, 2015 at 9:31 AM, Yoshitaka KUMAKURA < > yoshi.kumakura at gmail.com > > wrote: > > > Thank you very much, Andrew and Vladimir. > > > > Here is my progress. > > > > 1) I've installed dcm2mnc version 2.01.01 (built 2015), and found it > > working much better. Now, MINC files converted from DICOM of Biograph > > PET/CT can be viewed on MNI-register, and they look good, though I > haven't > > checked voxel values in detail yet. > > > > In terms of recording the time dimension, I see dcm2mnc behave > differently > > from ecattominc. Frame MID times are extracted by dcm2mnc. But, this is a > > bit confusing for old Siemens PET users, because frame START times were > > extracted by (the good old days) ecattominc. We already have a lot of > tools > > customized for that. > > > > > > time = 15, 45, 75, 105, 135, 165, 210, 270, 330, 390, 450... > > time-width = 30, 30, 30, 30, 30, 30, 60, 60, 60, 60, 60, 180, 180, 180, > > 180... > > > > So, I would be even more grateful if it could be like: > > time = 0, 30, 60, 90.... > > > > Is there any good idea to solve or avoid the issue of ambiguity in > > recording "time" between dcm2mnc and ecattominc? I am also wondering > where > > this has come from. > > > > 2) Our PET experiment is consisted of two PET/CT scans on the same > day. > > They are separated by a 30-min scanning break, and need to be > concatenated. > > The first scan's frame width is incremental, like typical dynamic PET > > scans. The second scan's frame width is constant, 360sec (x 10 frames). > > Some header lines that seem to be related to this issue are shown below. > > > > SCAN1(incremental frame time-width) > > double time(time) ; > > time:start = 15. ; > > time:spacing = "irregular" ; > > time:alignment = "start_" ; > > > > time = 15, 45, 75, 105, 135, 165, 210, 270, 330, 390, 450, 570, > > 750, 930, 1110, 1350, 1650, 1950, 2250, 2550,.....(truncated) > > > > time-width = 30, 30, 30, 30, 30, 30, 60, 60, 60, 60, 60, 180, 180, 180, > > 180, > > 300, 300, 300, 300, 300, 300, 300, 300 ; > > > > > > SCAN2 (360 sec x 10 fr) > > double time(time) ; > > time:start = 179. ; > > time:spacing = "regular__" ; > > time:alignment = "start_" ; > > > > > > time = 179, 539, 899, 1259, 1619, 1979, 2339, 2699,.....(truncated) > > > > Here, time-with is unavailable in the 2nd scan's header. It would be very > > nice if MINC experts could implement an option that forces dcm2mnc to > work > > in the "irregular" mode, so that the constant time-width would be > > explicitly recovered in the 2nd scan's MINC header. In this way, MINC > uses > > like myself can feel more comfortable, when concatenating two dissimilar > > files (after time adjustment, decay correction, head motion correction > etc, > > of course). > > > > 3) Sometimes, stuck in "Argument list too long". Please help me learn > > how to use find and xargs commands properly... > > > > Best regards, > > Yoshi > > > > On Fri, Nov 6, 2015 at 1:07 AM, Vladimir S. FONOV < > > vladimir.fonov at gmail.com> > > wrote: > > > > > Hello Yoshi, > > > > > > I had a similar situation some time ago, I found that I had to rely on > > > dcmdump from dcmtk first to split all the DICOM files into individual > 3D > > > volumes, then run dcm2mnc on each set independently, and finally > > > concatenating them with mincconcat along time dimension. > > > > > > > > > On 15-11-05 12:50 AM, Yoshitaka KUMAKURA wrote: > > > > > >> Dear MINC experts, > > >> > > >> We would like to use MINC tools to analyze dynamic PET files of a > > Siemens > > >> Biograph mCT 64 PET/CT scanner in an affiliated hospital in > Copenhagen. > > We > > >> are not new to MINC, because we are former BIC researchers (currently > in > > >> Albert Gjedde's lab). But, we are a small PET research group with no > > >> computer scientist. > > >> > > >> We have a favor to ask. We've tried dcm2mnc to convert a set of > dynamic > > 4D > > >> PET Dicom files to a minc files, and found that it just makes a 3D > minc > > >> file, missing the 4th time dimension. Has anybody encountered the same > > >> issue? Is a dcm2mnc utility for the scanner available? We are in great > > >> need > > >> of the minc converter customized for the PET/CT scanner. We would > > >> appreciate it very much, if you could find us a solution. > > >> > > > > > > > > > -- > > > 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 > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From ptcougopinto at gmail.com Thu Nov 12 14:54:53 2015 From: ptcougopinto at gmail.com (Pedro Telles Cougo Pinto) Date: Thu, 12 Nov 2015 17:54:53 -0200 Subject: [MINC-users] mritotal models (OS X) In-Reply-To: <5643A0BE.7080901@gmail.com> References: <05866741-ED19-4657-B03E-5AA273DE9636@gmail.com> <5643A0BE.7080901@gmail.com> Message-ID: <729873A8-227F-480D-99EF-8A9177C22A57@gmail.com> Thanks for the quick response, Vladimir. I see elastix is also part of the minc-toolkit; should we prefer it for nonlinear registration? Is mritotal deprecated in general? Best regards, Pedro > On Nov 11, 2015, at 18:10, Vladimir S. FONOV wrote: > > Hello Pedro, > > these files are meant to work with newer version of the script - called bestlinreg_s , you can replace the call to mritotal to > > bestlinreg_s -lsq7 -nmi /opt/minc/share/average305_t1_tal_lin.mnc > > > > > On 15-11-11 02:48 PM, Pedro Telles Cougo Pinto wrote: >> Hi, >> >> I installed minc-toolkit for OS X (minc-toolkit-1.9.10-20150710-Darwin-10.9-x86_64.dmg ) and I?m having some issues with models for mritotal. I would appreciate any help. >> >> First, the installation puts mritotal.cfg (and other mritotal .cfg files) at /opt/minc-itk4/etc, however mritotal still tries to find the .cfg files at /opt/minc-itk4/etc/mni_autoreg/ . I simply moved the .cfg files to a newly created /opt/minc-itk4/etc/mni_autoreg directory, but I?m not sure about the best definitive fix for this (changing the package file architecture?). >> >> I used the most recent model files from http://packages.bic.mni.mcgill.ca: bic-mni-models-0.1.1-20120421.dmg to get ICBM152 files and mni305_lin_minc2.zip (README gives compiling instructions, but the zip comes only with the .mnc files) for the 305 model, all located to /opt/minc/share (mritotal.cfg was edited to reflect this). Running mritotal gives the following message: >> >> Loading configuration file /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.cfg >> Loading protocol default (protocol file = /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.default.cfg) >> /opt/minc/share/average305_t1_tal_lin_16_blur.mnc does not exist >> /opt/minc/share/average305_t1_tal_lin_8_blur.mnc does not exist >> /opt/minc/share/average305_t1_tal_lin_8_dxyz.mnc does not exist >> /opt/minc/share/average305_t1_tal_lin_16_mask.mnc does not exist >> /opt/minc/share/average305_t1_tal_lin_8_mask.mnc does not exist >> Died at /opt/minc-itk4/bin/mritotal line 728. >> >> Were these 305 files supposed to be built as part of compiling? Both bic-mni-models-0.1.1-20120421.dmg and mni305_lin_minc2.zip were from 2012; am I trying to get the models from wrong sources? >> >> Thanks, >> Pedro >> _______________________________________________ >> 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 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From vladimir.fonov at gmail.com Thu Nov 12 15:32:16 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 12 Nov 2015 15:32:16 -0500 Subject: [MINC-users] mritotal models (OS X) In-Reply-To: <729873A8-227F-480D-99EF-8A9177C22A57@gmail.com> References: <05866741-ED19-4657-B03E-5AA273DE9636@gmail.com> <5643A0BE.7080901@gmail.com> <729873A8-227F-480D-99EF-8A9177C22A57@gmail.com> Message-ID: <5644F750.6030709@gmail.com> mritotal is a perl script that uses minctracc, bestlinreg_s is also perl script that uses minctracc, minctracc is not depricated. If you want to do non-linear registration there are several options - nlfit_s (uses minctracc), elastix, ANTs - all included in minc-toolkit. I didn't maintain mritotal because I switched to bestlinreg_s in my scripts. On 15-11-12 02:54 PM, Pedro Telles Cougo Pinto wrote: > Thanks for the quick response, Vladimir. I see elastix is also part of the minc-toolkit; should we prefer it for nonlinear registration? Is mritotal deprecated in general? > > Best regards, > Pedro > >> On Nov 11, 2015, at 18:10, Vladimir S. FONOV wrote: >> >> Hello Pedro, >> >> these files are meant to work with newer version of the script - called bestlinreg_s , you can replace the call to mritotal to >> >> bestlinreg_s -lsq7 -nmi /opt/minc/share/average305_t1_tal_lin.mnc >> >> >> >> >> On 15-11-11 02:48 PM, Pedro Telles Cougo Pinto wrote: >>> Hi, >>> >>> I installed minc-toolkit for OS X (minc-toolkit-1.9.10-20150710-Darwin-10.9-x86_64.dmg ) and I?m having some issues with models for mritotal. I would appreciate any help. >>> >>> First, the installation puts mritotal.cfg (and other mritotal .cfg files) at /opt/minc-itk4/etc, however mritotal still tries to find the .cfg files at /opt/minc-itk4/etc/mni_autoreg/ . I simply moved the .cfg files to a newly created /opt/minc-itk4/etc/mni_autoreg directory, but I?m not sure about the best definitive fix for this (changing the package file architecture?). >>> >>> I used the most recent model files from http://packages.bic.mni.mcgill.ca: bic-mni-models-0.1.1-20120421.dmg to get ICBM152 files and mni305_lin_minc2.zip (README gives compiling instructions, but the zip comes only with the .mnc files) for the 305 model, all located to /opt/minc/share (mritotal.cfg was edited to reflect this). Running mritotal gives the following message: >>> >>> Loading configuration file /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.cfg >>> Loading protocol default (protocol file = /opt/minc-itk4/bin/../etc/mni_autoreg/mritotal.default.cfg) >>> /opt/minc/share/average305_t1_tal_lin_16_blur.mnc does not exist >>> /opt/minc/share/average305_t1_tal_lin_8_blur.mnc does not exist >>> /opt/minc/share/average305_t1_tal_lin_8_dxyz.mnc does not exist >>> /opt/minc/share/average305_t1_tal_lin_16_mask.mnc does not exist >>> /opt/minc/share/average305_t1_tal_lin_8_mask.mnc does not exist >>> Died at /opt/minc-itk4/bin/mritotal line 728. >>> >>> Were these 305 files supposed to be built as part of compiling? Both bic-mni-models-0.1.1-20120421.dmg and mni305_lin_minc2.zip were from 2012; am I trying to get the models from wrong sources? >>> -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From a.janke at gmail.com Fri Nov 13 01:15:19 2015 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 13 Nov 2015 16:15:19 +1000 Subject: [MINC-users] viewnup2 Message-ID: So, I finally updated viewnup2 to MINC2 https://github.com/BIC-MNI/viewnup2 It should "build from the box" with the Makefile in there once you install gtkglarea and libpopt Vlad might even make me a CMakeLists.txt if he's feeling nice. Now if only I could get rid of all the bugs... a From vladimir.fonov at gmail.com Fri Nov 13 11:40:01 2015 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Fri, 13 Nov 2015 11:40:01 -0500 Subject: [MINC-users] viewnup2 In-Reply-To: References: Message-ID: <56461261.6050800@gmail.com> See develop branch. On 15-11-13 01:15 AM, Andrew Janke wrote: > So, I finally updated viewnup2 to MINC2 > > https://github.com/BIC-MNI/viewnup2 > > It should "build from the box" with the Makefile in there once you > install gtkglarea and libpopt > > Vlad might even make me a CMakeLists.txt if he's feeling nice. > > Now if only I could get rid of all the bugs... > > > a > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From redoute at cermep.fr Mon Nov 16 05:44:47 2015 From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=) Date: Mon, 16 Nov 2015 11:44:47 +0100 Subject: [MINC-users] V1 or V2? Message-ID: <5649B39F.10206@cermep.fr> Hi, I see there are 2 releases of Minc-toolkit, V1 or V2 that might be incompatible. Which version should we install? V1 has something that V2 can't do? this version is still supported? in evolution? Thanks J. Redout? From vladimir.fonov at gmail.com Mon Nov 16 09:04:21 2015 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Mon, 16 Nov 2015 09:04:21 -0500 Subject: [MINC-users] V1 or V2? In-Reply-To: <5649B39F.10206@cermep.fr> References: <5649B39F.10206@cermep.fr> Message-ID: <5649E265.8020400@gmail.com> Hello, the main difference is in that V2 comes with ITK 4.8 versus 3.20.1 in V1. And so, additional tools (a small subset of them actually) that are relying on ITK are working slightly differently and there are more of them in V2. Also registration (mni_autoreg, animal, etc) in V2 will produce slightly different results then in V1. So, if you want to maintain compatibility with earlier versions of tools - use V1, if you are starting from the scratch - better use V2. On 15-11-16 05:44 AM, J?r?me Redout? wrote: > Hi, > I see there are 2 releases of Minc-toolkit, V1 or V2 that might be > incompatible. > > Which version should we install? > > V1 has something that V2 can't do? this version is still supported? in > evolution? > > Thanks > J. Redout? > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From hihemanth08 at gmail.com Sat Nov 21 23:35:43 2015 From: hihemanth08 at gmail.com (Hemanth I (Hemambaradarahara Rao)) Date: Sun, 22 Nov 2015 10:05:43 +0530 Subject: [MINC-users] Small Query Message-ID: *Dear minc users,* *Currently I'm trying to do image fusion of T1,T2 and PD weighted images of brain.* *But here I'm unable to use those MINC Tool kit libraries along with opencv libraries for image processing applications.* *Can you briefly explain me the procedure to use those libraries for mnic format image reading and accessing pixel values* *then i will try to access along with Opencv libraries.* *It will be very helpful for my project if are able to guide me in accessing mnic image pixels.* *?**Thank you **?* -- Best Regards Hemanth Indlamuri From robert.d.vincent at mcgill.ca Sun Nov 22 07:43:38 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Sun, 22 Nov 2015 07:43:38 -0500 Subject: [MINC-users] Small Query In-Reply-To: References: Message-ID: Hi, I'm not familiar with OpenCV, so I can only give some general advice. The MINC toolkit includes several tools that can extract raw data from a MINC file, or convert a MINC file to another format. If you are programming in C (or C++), one of the easiest ways to read a MINC file is with the "volume_io" library that is part of the MINC library. I've enclosed a simple example. -bert On Sat, Nov 21, 2015 at 11:35 PM, Hemanth I (Hemambaradarahara Rao) < hihemanth08 at gmail.com> wrote: > *Dear minc users,* > *Currently I'm trying to do image fusion of T1,T2 and PD weighted images of > brain.* > *But here I'm unable to use those MINC Tool kit libraries along with opencv > libraries for image processing applications.* > *Can you briefly explain me the procedure to use those libraries for mnic > format image reading and accessing pixel values* > *then i will try to access along with Opencv libraries.* > *It will be very helpful for my project if are able to guide me > in accessing mnic image pixels.* > > *?**Thank you **?* > > -- > Best Regards > Hemanth Indlamuri > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From hihemanth08 at gmail.com Sun Nov 22 22:37:29 2015 From: hihemanth08 at gmail.com (Hemanth I (Hemambaradarahara Rao)) Date: Mon, 23 Nov 2015 09:07:29 +0530 Subject: [MINC-users] MINC-users Digest, Vol 123, Issue 8 In-Reply-To: References: Message-ID: Thank you Robert D. Vincent, The MINC toolkit includes several tools that can extract raw data from a MINC file.But I don't know which libraries are for what purpose , can you help to in finding the info regarding these libraries usage and Please Let me know the procedure to include those libraries (giving path for library locations in IDE etc..) for reading and accessing pixels of minc images. [I am using Qt Creator(IDE) for c++ programming] Thank you minc users!!! On Sun, Nov 22, 2015 at 10:30 PM, wrote: > Send MINC-users mailing list submissions to > minc-users at bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > or, via email, send a message with subject or body 'help' to > minc-users-request at bic.mni.mcgill.ca > > You can reach the person managing the list at > minc-users-owner at bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MINC-users digest..." > > > Today's Topics: > > 1. Small Query (Hemanth I (Hemambaradarahara Rao)) > 2. Re: Small Query (Robert D. Vincent) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 22 Nov 2015 10:05:43 +0530 > From: "Hemanth I (Hemambaradarahara Rao)" > To: minc-users at bic.mni.mcgill.ca > Subject: [MINC-users] Small Query > Message-ID: > XQRYkSyG12W+M7bn2Vk0w42j4F+z0G7do_8n0nvOgNkA at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > *Dear minc users,* > *Currently I'm trying to do image fusion of T1,T2 and PD weighted images of > brain.* > *But here I'm unable to use those MINC Tool kit libraries along with opencv > libraries for image processing applications.* > *Can you briefly explain me the procedure to use those libraries for mnic > format image reading and accessing pixel values* > *then i will try to access along with Opencv libraries.* > *It will be very helpful for my project if are able to guide me > in accessing mnic image pixels.* > > *?**Thank you **?* > > -- > Best Regards > Hemanth Indlamuri > > > ------------------------------ > > Message: 2 > Date: Sun, 22 Nov 2015 07:43:38 -0500 > From: "Robert D. Vincent" > To: MINC users mailing list > Subject: Re: [MINC-users] Small Query > Message-ID: > < > CAAd5DeSYg9K2+R4t7eJvV4JZ47o7oNTDn+RY+Jxq1KTrU2wN_g at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > > I'm not familiar with OpenCV, so I can only give some general advice. > > The MINC toolkit includes several tools that can extract raw data from a > MINC file, or convert a MINC file to another format. > > If you are programming in C (or C++), one of the easiest ways to read a > MINC file is with the "volume_io" library that is part of the MINC library. > I've enclosed a simple example. > > -bert > > On Sat, Nov 21, 2015 at 11:35 PM, Hemanth I (Hemambaradarahara Rao) < > hihemanth08 at gmail.com> wrote: > > > *Dear minc users,* > > *Currently I'm trying to do image fusion of T1,T2 and PD weighted images > of > > brain.* > > *But here I'm unable to use those MINC Tool kit libraries along with > opencv > > libraries for image processing applications.* > > *Can you briefly explain me the procedure to use those libraries for mnic > > format image reading and accessing pixel values* > > *then i will try to access along with Opencv libraries.* > > *It will be very helpful for my project if are able to guide me > > in accessing mnic image pixels.* > > > > *?**Thank you **?* > > > > -- > > Best Regards > > Hemanth Indlamuri > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > ------------------------------ > > _______________________________________________ > MINC-users mailing list > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > End of MINC-users Digest, Vol 123, Issue 8 > ****************************************** > -- Best Regards Hemanth Indlamuri From eskild at gmail.com Mon Nov 23 07:38:16 2015 From: eskild at gmail.com (Simon Eskildsen) Date: Mon, 23 Nov 2015 13:38:16 +0100 Subject: [MINC-users] register and [0-1] float volumes In-Reply-To: References: Message-ID: Hi Bert, Would it be possible to merge the fix into the master branch? At least it would be good if minc-toolkit-v2 included a version of Register that has the fix. I'm using the master branch of minc-toolkit-v2. Thanks, Simon On Mon, Oct 12, 2015 at 5:43 PM, Robert D. Vincent < robert.d.vincent at mcgill.ca> wrote: > Hi Alex, > > There is a recent commit that should fix this issue. In a nutshell, I made > the code recognize volumes that cannot use an integral colour table, and > use a full colour mapping instead. > On Oct 12, 2015 11:37 AM, "Alex Zijdenbos" wrote: > > > Hi all, > > > > In the flurry of recent improvements to Display/register (thank you Bert > et > > al.!), I was wondering if the problem of register not being able to > display > > float volumes with a range [0,1] has been addressed? AFAIC that is the > > single most annoying issue with register (I am keeping a register 1.3.6. > > build from 2009 around that still works for such volumes; or I use a > > wrapper that converts to byte/short on the fly). > > > > Thanks, > > > > -- Alex > > _______________________________________________ > > 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 robert.d.vincent at mcgill.ca Mon Nov 23 14:18:59 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Mon, 23 Nov 2015 14:18:59 -0500 Subject: [MINC-users] register and [0-1] float volumes In-Reply-To: References: Message-ID: Hi Simon, I plan to merge many of my changes into the master branch for bicpl, bicgl, Display, and Register soon. However, the minc-toolkit and minc-toolkit-v2 packages pick specific commits from the submodules, so they don't automatically track what is in master for a given project. In fact, minc-toolkit-v2 uses commits from late June or thereabouts, so it's neither develop nor master. -bert On Mon, Nov 23, 2015 at 7:38 AM, Simon Eskildsen wrote: > Hi Bert, > > Would it be possible to merge the fix into the master branch? At least it > would be good if minc-toolkit-v2 included a version of Register that has > the fix. I'm using the master branch of minc-toolkit-v2. > > Thanks, > Simon > > On Mon, Oct 12, 2015 at 5:43 PM, Robert D. Vincent < > robert.d.vincent at mcgill.ca> wrote: > > > Hi Alex, > > > > There is a recent commit that should fix this issue. In a nutshell, I > made > > the code recognize volumes that cannot use an integral colour table, and > > use a full colour mapping instead. > > On Oct 12, 2015 11:37 AM, "Alex Zijdenbos" wrote: > > > > > Hi all, > > > > > > In the flurry of recent improvements to Display/register (thank you > Bert > > et > > > al.!), I was wondering if the problem of register not being able to > > display > > > float volumes with a range [0,1] has been addressed? AFAIC that is the > > > single most annoying issue with register (I am keeping a register > 1.3.6. > > > build from 2009 around that still works for such volumes; or I use a > > > wrapper that converts to byte/short on the fly). > > > > > > Thanks, > > > > > > -- Alex > > > _______________________________________________ > > > 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 > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From robert.d.vincent at mcgill.ca Mon Nov 23 14:36:58 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Mon, 23 Nov 2015 14:36:58 -0500 Subject: [MINC-users] MINC-users Digest, Vol 123, Issue 8 In-Reply-To: References: Message-ID: Hi, The tools that might be of interest are minctoraw and mincextract. Or you can convert MINC files to NIfTI files with mnc2nii, if you have access to a library that reads NIfTI-1 files. The library paths depend on your specific platform and configuration, but you are looking for libminc2 and/or libvolume_io2. -bert On Sun, Nov 22, 2015 at 10:37 PM, Hemanth I (Hemambaradarahara Rao) < hihemanth08 at gmail.com> wrote: > Thank you Robert D. Vincent, > The MINC toolkit includes several tools that can extract raw data from a > MINC file.But I don't know which libraries are for what purpose , > can you help to in finding the info regarding these libraries usage and > Please Let me know the procedure to include those libraries (giving path > for library locations in IDE etc..) for reading and accessing pixels of > minc images. > > [I am using Qt Creator(IDE) for c++ programming] > > > Thank you minc users!!! > > On Sun, Nov 22, 2015 at 10:30 PM, > wrote: > > > Send MINC-users mailing list submissions to > > minc-users at bic.mni.mcgill.ca > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > or, via email, send a message with subject or body 'help' to > > minc-users-request at bic.mni.mcgill.ca > > > > You can reach the person managing the list at > > minc-users-owner at bic.mni.mcgill.ca > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of MINC-users digest..." > > > > > > Today's Topics: > > > > 1. Small Query (Hemanth I (Hemambaradarahara Rao)) > > 2. Re: Small Query (Robert D. Vincent) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sun, 22 Nov 2015 10:05:43 +0530 > > From: "Hemanth I (Hemambaradarahara Rao)" > > To: minc-users at bic.mni.mcgill.ca > > Subject: [MINC-users] Small Query > > Message-ID: > > > XQRYkSyG12W+M7bn2Vk0w42j4F+z0G7do_8n0nvOgNkA at mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > *Dear minc users,* > > *Currently I'm trying to do image fusion of T1,T2 and PD weighted images > of > > brain.* > > *But here I'm unable to use those MINC Tool kit libraries along with > opencv > > libraries for image processing applications.* > > *Can you briefly explain me the procedure to use those libraries for mnic > > format image reading and accessing pixel values* > > *then i will try to access along with Opencv libraries.* > > *It will be very helpful for my project if are able to guide me > > in accessing mnic image pixels.* > > > > *?**Thank you **?* > > > > -- > > Best Regards > > Hemanth Indlamuri > > > > > > ------------------------------ > > > > Message: 2 > > Date: Sun, 22 Nov 2015 07:43:38 -0500 > > From: "Robert D. Vincent" > > To: MINC users mailing list > > Subject: Re: [MINC-users] Small Query > > Message-ID: > > < > > CAAd5DeSYg9K2+R4t7eJvV4JZ47o7oNTDn+RY+Jxq1KTrU2wN_g at mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Hi, > > > > I'm not familiar with OpenCV, so I can only give some general advice. > > > > The MINC toolkit includes several tools that can extract raw data from a > > MINC file, or convert a MINC file to another format. > > > > If you are programming in C (or C++), one of the easiest ways to read a > > MINC file is with the "volume_io" library that is part of the MINC > library. > > I've enclosed a simple example. > > > > -bert > > > > On Sat, Nov 21, 2015 at 11:35 PM, Hemanth I (Hemambaradarahara Rao) < > > hihemanth08 at gmail.com> wrote: > > > > > *Dear minc users,* > > > *Currently I'm trying to do image fusion of T1,T2 and PD weighted > images > > of > > > brain.* > > > *But here I'm unable to use those MINC Tool kit libraries along with > > opencv > > > libraries for image processing applications.* > > > *Can you briefly explain me the procedure to use those libraries for > mnic > > > format image reading and accessing pixel values* > > > *then i will try to access along with Opencv libraries.* > > > *It will be very helpful for my project if are able to guide me > > > in accessing mnic image pixels.* > > > > > > *?**Thank you **?* > > > > > > -- > > > Best Regards > > > Hemanth Indlamuri > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > ------------------------------ > > > > _______________________________________________ > > MINC-users mailing list > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > End of MINC-users Digest, Vol 123, Issue 8 > > ****************************************** > > > > > > -- > Best Regards > Hemanth Indlamuri > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Mon Nov 23 15:17:51 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Mon, 23 Nov 2015 15:17:51 -0500 Subject: [MINC-users] register and [0-1] float volumes In-Reply-To: References: Message-ID: <5653746F.4080204@gmail.com> Hello, it looks like new patches are not quote ready for general use. I updated all the subprojects in minc-toolkit-v2 to the latest develop heads and rebuilt register. And I am getting following results: 1. running register on a float volume with range 0-8.57 - i have old behavior (i.e all the values between 0 and 1.0 are mapped to black) 2. running minccalc -express 'A[0]/10' test1.mnc test2.mnc (test2.mnc now have range 0 - 0.857) , followed by register test2.mnc - works properly . 3. running register test2.mnc test2.mnc results in segfault, register test1.mnc test1.mnc still works. 4. running minccalc -express 'A[0]*10' test2.mnc test3.mnc, register test3.mnc - works, but with old behavior register test3.mnc test3.mnc segfaults. You can download files to try it on your system: https://www.dropbox.com/sh/7vtg2tszawnlqyi/AAD8mN60UttvAdLxLYKtDcMha?dl=0 On 15-11-23 02:18 PM, Robert D. Vincent wrote: > Hi Simon, > > I plan to merge many of my changes into the master branch for bicpl, bicgl, > Display, and Register soon. However, the minc-toolkit and minc-toolkit-v2 > packages pick specific commits from the submodules, so they don't > automatically track what is in master for a given project. In fact, > minc-toolkit-v2 uses commits from late June or thereabouts, so it's neither > develop nor master. > > -bert > > On Mon, Nov 23, 2015 at 7:38 AM, Simon Eskildsen wrote: > >> Hi Bert, >> >> Would it be possible to merge the fix into the master branch? At least it >> would be good if minc-toolkit-v2 included a version of Register that has >> the fix. I'm using the master branch of minc-toolkit-v2. >> >> Thanks, >> Simon >> >> On Mon, Oct 12, 2015 at 5:43 PM, Robert D. Vincent < >> robert.d.vincent at mcgill.ca> wrote: >> >>> Hi Alex, >>> >>> There is a recent commit that should fix this issue. In a nutshell, I >> made >>> the code recognize volumes that cannot use an integral colour table, and >>> use a full colour mapping instead. >>> On Oct 12, 2015 11:37 AM, "Alex Zijdenbos" wrote: >>> >>>> Hi all, >>>> >>>> In the flurry of recent improvements to Display/register (thank you >> Bert >>> et >>>> al.!), I was wondering if the problem of register not being able to >>> display >>>> float volumes with a range [0,1] has been addressed? AFAIC that is the >>>> single most annoying issue with register (I am keeping a register >> 1.3.6. >>>> build from 2009 around that still works for such volumes; or I use a >>>> wrapper that converts to byte/short on the fly). >>>> >>>> Thanks, >>>> >>>> -- Alex >>>> _______________________________________________ >>>> 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 >>> >> _______________________________________________ >> 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 > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From a.janke at gmail.com Mon Nov 23 15:22:09 2015 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 24 Nov 2015 06:22:09 +1000 Subject: [MINC-users] register and [0-1] float volumes In-Reply-To: <5653746F.4080204@gmail.com> References: <5653746F.4080204@gmail.com> Message-ID: I haven't checked but while we are on the subject of register, has there been a bug-fix committed for the problem where you can't load some 4D (x,y,z,t) volumes on OSX? ta a On 24 November 2015 at 06:17, Vladimir S. FONOV wrote: > Hello, > > > it looks like new patches are not quote ready for general use. I updated all > the subprojects in minc-toolkit-v2 to the latest develop heads and rebuilt > register. And I am getting following results: > > > 1. running register on a float volume with range 0-8.57 - i have old > behavior (i.e all the values between 0 and 1.0 are mapped to black) > > 2. running minccalc -express 'A[0]/10' test1.mnc test2.mnc (test2.mnc now > have range 0 - 0.857) , followed by register test2.mnc - works properly . > > 3. running register test2.mnc test2.mnc results in segfault, register > test1.mnc test1.mnc still works. > > 4. running minccalc -express 'A[0]*10' test2.mnc test3.mnc, > register test3.mnc - works, but with old behavior > register test3.mnc test3.mnc segfaults. > > You can download files to try it on your system: > https://www.dropbox.com/sh/7vtg2tszawnlqyi/AAD8mN60UttvAdLxLYKtDcMha?dl=0 > > > > > > > > On 15-11-23 02:18 PM, Robert D. Vincent wrote: >> >> Hi Simon, >> >> I plan to merge many of my changes into the master branch for bicpl, >> bicgl, >> Display, and Register soon. However, the minc-toolkit and minc-toolkit-v2 >> packages pick specific commits from the submodules, so they don't >> automatically track what is in master for a given project. In fact, >> minc-toolkit-v2 uses commits from late June or thereabouts, so it's >> neither >> develop nor master. >> >> -bert >> >> On Mon, Nov 23, 2015 at 7:38 AM, Simon Eskildsen wrote: >> >>> Hi Bert, >>> >>> Would it be possible to merge the fix into the master branch? At least it >>> would be good if minc-toolkit-v2 included a version of Register that has >>> the fix. I'm using the master branch of minc-toolkit-v2. >>> >>> Thanks, >>> Simon >>> >>> On Mon, Oct 12, 2015 at 5:43 PM, Robert D. Vincent < >>> robert.d.vincent at mcgill.ca> wrote: >>> >>>> Hi Alex, >>>> >>>> There is a recent commit that should fix this issue. In a nutshell, I >>> >>> made >>>> >>>> the code recognize volumes that cannot use an integral colour table, and >>>> use a full colour mapping instead. >>>> On Oct 12, 2015 11:37 AM, "Alex Zijdenbos" wrote: >>>> >>>>> Hi all, >>>>> >>>>> In the flurry of recent improvements to Display/register (thank you >>> >>> Bert >>>> >>>> et >>>>> >>>>> al.!), I was wondering if the problem of register not being able to >>>> >>>> display >>>>> >>>>> float volumes with a range [0,1] has been addressed? AFAIC that is the >>>>> single most annoying issue with register (I am keeping a register >>> >>> 1.3.6. >>>>> >>>>> build from 2009 around that still works for such volumes; or I use a >>>>> wrapper that converts to byte/short on the fly). >>>>> >>>>> Thanks, >>>>> >>>>> -- Alex >>>>> _______________________________________________ >>>>> 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 >>>> >>> _______________________________________________ >>> 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 >> > > > -- > 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 robert.d.vincent at mcgill.ca Mon Nov 23 16:15:01 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Mon, 23 Nov 2015 16:15:01 -0500 Subject: [MINC-users] register and [0-1] float volumes In-Reply-To: References: <5653746F.4080204@gmail.com> Message-ID: Hi Andrew, No, there's no specific fix for that - I can't test on OS X easily yet. -bert On Mon, Nov 23, 2015 at 3:22 PM, Andrew Janke wrote: > I haven't checked but while we are on the subject of register, has > there been a bug-fix committed for the problem where you can't load > some 4D (x,y,z,t) volumes on OSX? > > ta > > a > > > > On 24 November 2015 at 06:17, Vladimir S. FONOV > wrote: > > Hello, > > > > > > it looks like new patches are not quote ready for general use. I updated > all > > the subprojects in minc-toolkit-v2 to the latest develop heads and > rebuilt > > register. And I am getting following results: > > > > > > 1. running register on a float volume with range 0-8.57 - i have old > > behavior (i.e all the values between 0 and 1.0 are mapped to black) > > > > 2. running minccalc -express 'A[0]/10' test1.mnc test2.mnc (test2.mnc now > > have range 0 - 0.857) , followed by register test2.mnc - works properly . > > > > 3. running register test2.mnc test2.mnc results in segfault, register > > test1.mnc test1.mnc still works. > > > > 4. running minccalc -express 'A[0]*10' test2.mnc test3.mnc, > > register test3.mnc - works, but with old behavior > > register test3.mnc test3.mnc segfaults. > > > > You can download files to try it on your system: > > > https://www.dropbox.com/sh/7vtg2tszawnlqyi/AAD8mN60UttvAdLxLYKtDcMha?dl=0 > > > > > > > > > > > > > > > > On 15-11-23 02:18 PM, Robert D. Vincent wrote: > >> > >> Hi Simon, > >> > >> I plan to merge many of my changes into the master branch for bicpl, > >> bicgl, > >> Display, and Register soon. However, the minc-toolkit and > minc-toolkit-v2 > >> packages pick specific commits from the submodules, so they don't > >> automatically track what is in master for a given project. In fact, > >> minc-toolkit-v2 uses commits from late June or thereabouts, so it's > >> neither > >> develop nor master. > >> > >> -bert > >> > >> On Mon, Nov 23, 2015 at 7:38 AM, Simon Eskildsen > wrote: > >> > >>> Hi Bert, > >>> > >>> Would it be possible to merge the fix into the master branch? At least > it > >>> would be good if minc-toolkit-v2 included a version of Register that > has > >>> the fix. I'm using the master branch of minc-toolkit-v2. > >>> > >>> Thanks, > >>> Simon > >>> > >>> On Mon, Oct 12, 2015 at 5:43 PM, Robert D. Vincent < > >>> robert.d.vincent at mcgill.ca> wrote: > >>> > >>>> Hi Alex, > >>>> > >>>> There is a recent commit that should fix this issue. In a nutshell, I > >>> > >>> made > >>>> > >>>> the code recognize volumes that cannot use an integral colour table, > and > >>>> use a full colour mapping instead. > >>>> On Oct 12, 2015 11:37 AM, "Alex Zijdenbos" > wrote: > >>>> > >>>>> Hi all, > >>>>> > >>>>> In the flurry of recent improvements to Display/register (thank you > >>> > >>> Bert > >>>> > >>>> et > >>>>> > >>>>> al.!), I was wondering if the problem of register not being able to > >>>> > >>>> display > >>>>> > >>>>> float volumes with a range [0,1] has been addressed? AFAIC that is > the > >>>>> single most annoying issue with register (I am keeping a register > >>> > >>> 1.3.6. > >>>>> > >>>>> build from 2009 around that still works for such volumes; or I use a > >>>>> wrapper that converts to byte/short on the fly). > >>>>> > >>>>> Thanks, > >>>>> > >>>>> -- Alex > >>>>> _______________________________________________ > >>>>> 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 > >>>> > >>> _______________________________________________ > >>> 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 > >> > > > > > > -- > > 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 robert.d.vincent at mcgill.ca Mon Nov 23 16:34:00 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Mon, 23 Nov 2015 16:34:00 -0500 Subject: [MINC-users] register and [0-1] float volumes In-Reply-To: <5653746F.4080204@gmail.com> References: <5653746F.4080204@gmail.com> Message-ID: Ok, I had hastily made a fix for Register to match what I had done for Display, but hadn't properly handled the merged volume. It should be fixed by the latest commit to develop. There will remain some situations in which the colour mapping isn't ideal for float volumes, but the latest commit should at least do something reasonable (and not crash). -bert On Mon, Nov 23, 2015 at 3:17 PM, Vladimir S. FONOV wrote: > Hello, > > > it looks like new patches are not quote ready for general use. I updated > all the subprojects in minc-toolkit-v2 to the latest develop heads and > rebuilt register. And I am getting following results: > > > 1. running register on a float volume with range 0-8.57 - i have old > behavior (i.e all the values between 0 and 1.0 are mapped to black) > > 2. running minccalc -express 'A[0]/10' test1.mnc test2.mnc (test2.mnc now > have range 0 - 0.857) , followed by register test2.mnc - works properly . > > 3. running register test2.mnc test2.mnc results in segfault, register > test1.mnc test1.mnc still works. > > 4. running minccalc -express 'A[0]*10' test2.mnc test3.mnc, > register test3.mnc - works, but with old behavior > register test3.mnc test3.mnc segfaults. > > You can download files to try it on your system: > > https://www.dropbox.com/sh/7vtg2tszawnlqyi/AAD8mN60UttvAdLxLYKtDcMha?dl=0 > > > > > > > > On 15-11-23 02:18 PM, Robert D. Vincent wrote: > >> Hi Simon, >> >> I plan to merge many of my changes into the master branch for bicpl, >> bicgl, >> Display, and Register soon. However, the minc-toolkit and minc-toolkit-v2 >> packages pick specific commits from the submodules, so they don't >> automatically track what is in master for a given project. In fact, >> minc-toolkit-v2 uses commits from late June or thereabouts, so it's >> neither >> develop nor master. >> >> -bert >> >> On Mon, Nov 23, 2015 at 7:38 AM, Simon Eskildsen >> wrote: >> >> Hi Bert, >>> >>> Would it be possible to merge the fix into the master branch? At least it >>> would be good if minc-toolkit-v2 included a version of Register that has >>> the fix. I'm using the master branch of minc-toolkit-v2. >>> >>> Thanks, >>> Simon >>> >>> On Mon, Oct 12, 2015 at 5:43 PM, Robert D. Vincent < >>> robert.d.vincent at mcgill.ca> wrote: >>> >>> Hi Alex, >>>> >>>> There is a recent commit that should fix this issue. In a nutshell, I >>>> >>> made >>> >>>> the code recognize volumes that cannot use an integral colour table, and >>>> use a full colour mapping instead. >>>> On Oct 12, 2015 11:37 AM, "Alex Zijdenbos" wrote: >>>> >>>> Hi all, >>>>> >>>>> In the flurry of recent improvements to Display/register (thank you >>>>> >>>> Bert >>> >>>> et >>>> >>>>> al.!), I was wondering if the problem of register not being able to >>>>> >>>> display >>>> >>>>> float volumes with a range [0,1] has been addressed? AFAIC that is the >>>>> single most annoying issue with register (I am keeping a register >>>>> >>>> 1.3.6. >>> >>>> build from 2009 around that still works for such volumes; or I use a >>>>> wrapper that converts to byte/short on the fly). >>>>> >>>>> Thanks, >>>>> >>>>> -- Alex >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>> 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 >> >> > > -- > 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 Mon Nov 23 16:45:51 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Mon, 23 Nov 2015 16:45:51 -0500 Subject: [MINC-users] register and [0-1] float volumes In-Reply-To: References: <5653746F.4080204@gmail.com> Message-ID: <5653890F.8010709@gmail.com> Hello, ok, I included all the latest versions of packages in the develop branch of minc-toolkit-v2, at least register doesn't crash right now. On 15-11-23 04:34 PM, Robert D. Vincent wrote: > Ok, I had hastily made a fix for Register to match what I had done for > Display, but hadn't properly handled the merged volume. It should be fixed > by the latest commit to develop. > > There will remain some situations in which the colour mapping isn't ideal > for float volumes, but the latest commit should at least do something > reasonable (and not crash). > > -bert > > On Mon, Nov 23, 2015 at 3:17 PM, Vladimir S. FONOV > wrote: > >> Hello, >> >> >> it looks like new patches are not quote ready for general use. I updated >> all the subprojects in minc-toolkit-v2 to the latest develop heads and >> rebuilt register. And I am getting following results: >> >> >> 1. running register on a float volume with range 0-8.57 - i have old >> behavior (i.e all the values between 0 and 1.0 are mapped to black) >> >> 2. running minccalc -express 'A[0]/10' test1.mnc test2.mnc (test2.mnc now >> have range 0 - 0.857) , followed by register test2.mnc - works properly . >> >> 3. running register test2.mnc test2.mnc results in segfault, register >> test1.mnc test1.mnc still works. >> >> 4. running minccalc -express 'A[0]*10' test2.mnc test3.mnc, >> register test3.mnc - works, but with old behavior >> register test3.mnc test3.mnc segfaults. >> >> You can download files to try it on your system: >> >> https://www.dropbox.com/sh/7vtg2tszawnlqyi/AAD8mN60UttvAdLxLYKtDcMha?dl=0 >> >> >> >> >> >> >> >> On 15-11-23 02:18 PM, Robert D. Vincent wrote: >> >>> Hi Simon, >>> >>> I plan to merge many of my changes into the master branch for bicpl, >>> bicgl, >>> Display, and Register soon. However, the minc-toolkit and minc-toolkit-v2 >>> packages pick specific commits from the submodules, so they don't >>> automatically track what is in master for a given project. In fact, >>> minc-toolkit-v2 uses commits from late June or thereabouts, so it's >>> neither >>> develop nor master. >>> >>> -bert >>> >>> On Mon, Nov 23, 2015 at 7:38 AM, Simon Eskildsen >>> wrote: >>> >>> Hi Bert, >>>> >>>> Would it be possible to merge the fix into the master branch? At least it >>>> would be good if minc-toolkit-v2 included a version of Register that has >>>> the fix. I'm using the master branch of minc-toolkit-v2. >>>> >>>> Thanks, >>>> Simon >>>> >>>> On Mon, Oct 12, 2015 at 5:43 PM, Robert D. Vincent < >>>> robert.d.vincent at mcgill.ca> wrote: >>>> >>>> Hi Alex, >>>>> >>>>> There is a recent commit that should fix this issue. In a nutshell, I >>>>> >>>> made >>>> >>>>> the code recognize volumes that cannot use an integral colour table, and >>>>> use a full colour mapping instead. >>>>> On Oct 12, 2015 11:37 AM, "Alex Zijdenbos" wrote: >>>>> >>>>> Hi all, >>>>>> >>>>>> In the flurry of recent improvements to Display/register (thank you >>>>>> >>>>> Bert >>>> >>>>> et >>>>> >>>>>> al.!), I was wondering if the problem of register not being able to >>>>>> >>>>> display >>>>> >>>>>> float volumes with a range [0,1] has been addressed? AFAIC that is the >>>>>> single most annoying issue with register (I am keeping a register >>>>>> >>>>> 1.3.6. >>>> >>>>> build from 2009 around that still works for such volumes; or I use a >>>>>> wrapper that converts to byte/short on the fly). >>>>>> -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From hihemanth08 at gmail.com Mon Nov 23 22:03:54 2015 From: hihemanth08 at gmail.com (Hemanth I (Hemambaradarahara Rao)) Date: Tue, 24 Nov 2015 08:33:54 +0530 Subject: [MINC-users] Small Query Message-ID: Dear mnic user, I am new to mic format images and this mnic tool kit.Can you help me with the procedure how to use these tool kit libraries to read and access mnic images. Thank you. -- Best Regards Hemanth Indlamuri From mishkind at gmail.com Tue Nov 24 02:56:24 2015 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Mon, 23 Nov 2015 21:56:24 -1000 Subject: [MINC-users] Small Query In-Reply-To: References: Message-ID: Hi, Congratulations on taking the first step! You can find lots of useful information here: https://en.wikibooks.org/wiki/MINC And there are even a few tutorials: https://en.wikibooks.org/wiki/MINC/Tutorials If you are still confused, post back to the list with what it is you want to do (e.g.,, I have two dicom images and i just want to do some simple masking, I have a program in C/vtk/matlab and I want to read in the data, do x, and output the data, etc.) and a bit about what programming background you have, and I'm sure we can help. mahalo, mishkin On Mon, Nov 23, 2015 at 5:03 PM, Hemanth I (Hemambaradarahara Rao) < hihemanth08 at gmail.com> wrote: > Dear mnic user, > I am new to mic format images and this mnic tool kit.Can you help me with > the procedure how to use these tool kit libraries to read and access mnic > images. > Thank you. > > -- > Best Regards > Hemanth Indlamuri > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Nov 26 18:29:11 2015 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 27 Nov 2015 09:29:11 +1000 Subject: [MINC-users] Power spectrum across time Message-ID: Has anyone got anything for power spectrum of the time domain for large MINC volumes? I don't think pyminc or octave are going to cut it. The files in question are ~20GB+ in size. I could chop them up but this seems counter-productive. I'm thinking mincfft + a bit of minccalc but if someone has something specific that uses voxel_loop or something similar I'm all ears. Thanks a From vladimir.fonov at gmail.com Sun Nov 29 16:51:59 2015 From: vladimir.fonov at gmail.com (vladimir.fonov at gmail.com) Date: Sun, 29 Nov 2015 16:51:59 -0500 Subject: [MINC-users] Power spectrum across time In-Reply-To: References: Message-ID: <697491A6-2F09-4A57-8401-4DD016093FD4@gmail.com> Hello, I extracted the tool from my internal repository, see https://github.com/vfonov/simple_fmri_tools the tool that you need is called time_fft ( https://github.com/vfonov/simple_fmri_tools/blob/master/src/time_fft.cpp ) - it will only work if the time_dimension is fastest varying. > On Nov 26, 2015, at 18:29, Andrew Janke wrote: > > Has anyone got anything for power spectrum of the time domain for > large MINC volumes? I don't think pyminc or octave are going to cut > it. The files in question are ~20GB+ in size. I could chop them up but > this seems counter-productive. > > I'm thinking mincfft + a bit of minccalc but if someone has something > specific that uses voxel_loop or something similar I'm all ears. > > Thanks > > > a > _______________________________________________ > 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 a.janke at gmail.com Sun Nov 29 19:33:36 2015 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 30 Nov 2015 10:33:36 +1000 Subject: [MINC-users] Power spectrum across time In-Reply-To: <697491A6-2F09-4A57-8401-4DD016093FD4@gmail.com> References: <697491A6-2F09-4A57-8401-4DD016093FD4@gmail.com> Message-ID: Thanks Vladimir, This looks pretty much akin to what I have been doing with mincfft but more straight forward. I should integrate the MINC2 bits from this into mincfft, I'm curious to know if it will be faster. I know that most of the execution time of mincfft is taken up by copying arrays to and forth due to how I was using volume_io. a On 30 November 2015 at 07:51, wrote: > Hello, > > I extracted the tool from my internal repository, see https://github.com/vfonov/simple_fmri_tools > the tool that you need is called time_fft ( https://github.com/vfonov/simple_fmri_tools/blob/master/src/time_fft.cpp ) - it will only work if the time_dimension is fastest varying. > > > >> On Nov 26, 2015, at 18:29, Andrew Janke wrote: >> >> Has anyone got anything for power spectrum of the time domain for >> large MINC volumes? I don't think pyminc or octave are going to cut >> it. The files in question are ~20GB+ in size. I could chop them up but >> this seems counter-productive. >> >> I'm thinking mincfft + a bit of minccalc but if someone has something >> specific that uses voxel_loop or something similar I'm all ears. >> >> Thanks >> >> >> a >> _______________________________________________ >> 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 > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Sun Nov 29 21:15:10 2015 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 30 Nov 2015 12:15:10 +1000 Subject: [MINC-users] Power spectrum across time In-Reply-To: References: <697491A6-2F09-4A57-8401-4DD016093FD4@gmail.com> Message-ID: For others with an interest in this, I have included most of the changes needed to do this into mincfft: https://github.com/BIC-MNI/mincfft Note that to perform my original request you will have to chop the volume up into spatial + time slices as mincfft will only handle input volumes with 3 dimensions + the vector real/imaginary dimensions if appropriate. Turns out I had to do this anyhow as the files were simply too large to work on as a whole for most tools I could get my hands on. More details in the README here: https://github.com/BIC-MNI/mincfft/blob/master/README Still have to integrate Vladimirs MINC2 version into it yet... a On 30 November 2015 at 10:33, Andrew Janke wrote: > Thanks Vladimir, > > This looks pretty much akin to what I have been doing with mincfft but > more straight forward. I should integrate the MINC2 bits from this > into mincfft, I'm curious to know if it will be faster. I know that > most of the execution time of mincfft is taken up by copying arrays to > and forth due to how I was using volume_io. > > a > > > On 30 November 2015 at 07:51, wrote: >> Hello, >> >> I extracted the tool from my internal repository, see https://github.com/vfonov/simple_fmri_tools >> the tool that you need is called time_fft ( https://github.com/vfonov/simple_fmri_tools/blob/master/src/time_fft.cpp ) - it will only work if the time_dimension is fastest varying. >> >> >> >>> On Nov 26, 2015, at 18:29, Andrew Janke wrote: >>> >>> Has anyone got anything for power spectrum of the time domain for >>> large MINC volumes? I don't think pyminc or octave are going to cut >>> it. The files in question are ~20GB+ in size. I could chop them up but >>> this seems counter-productive. >>> >>> I'm thinking mincfft + a bit of minccalc but if someone has something >>> specific that uses voxel_loop or something similar I'm all ears. >>> >>> Thanks >>> >>> >>> a >>> _______________________________________________ >>> 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 >> >> >> >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users