From andrew at biospective.com Tue Apr 14 17:36:20 2015 From: andrew at biospective.com (Andrew Wood) Date: Tue, 14 Apr 2015 17:36:20 -0400 Subject: [MINC-users] Building minc-toolkit for debugging Message-ID: Hi all, I'm having trouble getting the minc-toolkit built with debugging symbols (specifically trying to dive into minctracc). I've tried setting CMAKE_BUILD_TYPE to Debug and DEBUG. Am I missing something obvious? Thanks, Andrew From vladimir.fonov at gmail.com Wed Apr 15 00:31:33 2015 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Wed, 15 Apr 2015 00:31:33 -0400 Subject: [MINC-users] Building minc-toolkit for debugging In-Reply-To: References: Message-ID: <552DE9A5.7010109@gmail.com> Hello, I noticed that URL of netcdf library changed - I updated it in the repository. Otherwise it compiles fine with the following settings: BUILD_TESTING:BOOL=ON CMAKE_BUILD_TYPE:STRING=Debug CMAKE_INSTALL_PREFIX:PATH=/opt/minc GLUT_X11_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libX11.so GLUT_Xi_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXi.so GLUT_Xmu_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXmu.so MNI_AUTOREG_OLD_AMOEBA_INIT:BOOL=ON MT_BUILD_C3D:BOOL=ON MT_BUILD_ITK_TOOLS:BOOL=ON MT_BUILD_LITE:BOOL=OFF MT_BUILD_MINC_ANTS:BOOL=ON MT_BUILD_SHARED_LIBS:BOOL=ON MT_BUILD_VISUAL_TOOLS:BOOL=ON MT_USE_OPENMP:BOOL=ON USE_SYSTEM_FFTW3F:BOOL=OFF USE_SYSTEM_GLUT:BOOL=OFF USE_SYSTEM_GSL:BOOL=OFF USE_SYSTEM_HDF5:BOOL=OFF USE_SYSTEM_ITK:BOOL=OFF USE_SYSTEM_NETCDF:BOOL=OFF USE_SYSTEM_PCRE:BOOL=OFF USE_SYSTEM_ZLIB:BOOL=OFF On 15-04-14 05:36 PM, Andrew Wood wrote: > Hi all, > > I'm having trouble getting the minc-toolkit built with debugging symbols > (specifically trying to dive into minctracc). > > I've tried setting CMAKE_BUILD_TYPE to Debug and DEBUG. > > Am I missing something obvious? > > Thanks, > Andrew > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From andrew at biospective.com Wed Apr 15 11:22:26 2015 From: andrew at biospective.com (Andrew Wood) Date: Wed, 15 Apr 2015 11:22:26 -0400 Subject: [MINC-users] Building minc-toolkit for debugging In-Reply-To: <552DE9A5.7010109@gmail.com> References: <552DE9A5.7010109@gmail.com> Message-ID: Hi Vlad, My issue wasn't with the missing netcdf library (I already had a copy lying around that I dropped into where the download was supposed to go) but rather getting executables suitable for use in gdb. I'm less than a CMake novice, so I'm still confused.. I normally specify cmake variables on the command like "-MCMAKE_BUILD_TYPE=Debug" but you're suggesting a lot of options, so I'm trying to drop them in a config file. If I understand CMake correctly, I should drop these settings at the end of the CMakeLists.txt file in the root directory. To satisfy CMake syntax, I copy/pasted from your email then translated everything to SET calls: SET( BUILD_TESTING ON ) SET( CMAKE_BUILD_TYPE Debug ) etc... Then I did the standard `mkdir build; cd build; cmake ..` and everything happily built (the netcdf download worked this time - thanks!). The executables still aren't suited for gdb though: $ gdb build_debug/mni_autoreg/minctracc/minctracc ... Reading symbols from build_debug/mni_autoreg/minctracc/minctracc...(no debugging symbols found)...done. (gdb) I must have put those settings in the wrong place? Thanks, Andrew On Wed, Apr 15, 2015 at 12:31 AM, Vladimir S. Fonov < vladimir.fonov at gmail.com> wrote: > Hello, > > I noticed that URL of netcdf library changed - I updated it in the > repository. > Otherwise it compiles fine with the following settings: > > > BUILD_TESTING:BOOL=ON > CMAKE_BUILD_TYPE:STRING=Debug > CMAKE_INSTALL_PREFIX:PATH=/opt/minc > GLUT_X11_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libX11.so > GLUT_Xi_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXi.so > GLUT_Xmu_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXmu.so > MNI_AUTOREG_OLD_AMOEBA_INIT:BOOL=ON > MT_BUILD_C3D:BOOL=ON > MT_BUILD_ITK_TOOLS:BOOL=ON > MT_BUILD_LITE:BOOL=OFF > MT_BUILD_MINC_ANTS:BOOL=ON > MT_BUILD_SHARED_LIBS:BOOL=ON > MT_BUILD_VISUAL_TOOLS:BOOL=ON > MT_USE_OPENMP:BOOL=ON > USE_SYSTEM_FFTW3F:BOOL=OFF > USE_SYSTEM_GLUT:BOOL=OFF > USE_SYSTEM_GSL:BOOL=OFF > USE_SYSTEM_HDF5:BOOL=OFF > USE_SYSTEM_ITK:BOOL=OFF > USE_SYSTEM_NETCDF:BOOL=OFF > USE_SYSTEM_PCRE:BOOL=OFF > USE_SYSTEM_ZLIB:BOOL=OFF > > > > > On 15-04-14 05:36 PM, Andrew Wood wrote: > >> Hi all, >> >> I'm having trouble getting the minc-toolkit built with debugging symbols >> (specifically trying to dive into minctracc). >> >> I've tried setting CMAKE_BUILD_TYPE to Debug and DEBUG. >> >> Am I missing something obvious? >> >> Thanks, >> Andrew >> _______________________________________________ >> 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 andrew at biospective.com Wed Apr 15 14:09:47 2015 From: andrew at biospective.com (Andrew Wood) Date: Wed, 15 Apr 2015 14:09:47 -0400 Subject: [MINC-users] Building minc-toolkit for debugging In-Reply-To: References: <552DE9A5.7010109@gmail.com> Message-ID: Hi again, I think I figured out the answer to my own question - the configuration settings from the above email belong in CMakeCache.txt in the build directory. I did come across another though when I used your configuration options though: [ 1%] Built target NETCDF make[2]: *** No rule to make target `external/opt/minc/lib/libz.a', needed by `libminc/libminc2.so.2.3.00'. Stop. make[1]: *** [libminc/CMakeFiles/minc2.dir/all] Error 2 make: *** [all] Error 2 I got around this by setting USE_SYSTEM_ZLIB:BOOL=OFF, but is this a generic problem that others might come across? On somewhat a different topic, I'm curious about your suggestion to force the old amoeba initialization with MNI_AUTOREG_OLD_AMOEBA_INIT:BOOL=ON. It's my understanding that the new initialization is an improvement (removing a directional bias). Have you found that it actually creates its own sort of problems? Thanks, Andrew On Wed, Apr 15, 2015 at 11:22 AM, Andrew Wood wrote: > Hi Vlad, > > My issue wasn't with the missing netcdf library (I already had a copy > lying around that I dropped into where the download was supposed to go) but > rather getting executables suitable for use in gdb. > > I'm less than a CMake novice, so I'm still confused.. I normally specify > cmake variables on the command like "-MCMAKE_BUILD_TYPE=Debug" but you're > suggesting a lot of options, so I'm trying to drop them in a config file. > > If I understand CMake correctly, I should drop these settings at the end > of the CMakeLists.txt file in the root directory. To satisfy CMake syntax, > I copy/pasted from your email then translated everything to SET calls: > > SET( BUILD_TESTING ON ) > SET( CMAKE_BUILD_TYPE Debug ) > etc... > > Then I did the standard `mkdir build; cd build; cmake ..` and everything > happily built (the netcdf download worked this time - thanks!). The > executables still aren't suited for gdb though: > > $ gdb build_debug/mni_autoreg/minctracc/minctracc > ... > Reading symbols from build_debug/mni_autoreg/minctracc/minctracc...(no > debugging symbols found)...done. > (gdb) > > I must have put those settings in the wrong place? > > Thanks, > Andrew > > > > > > > On Wed, Apr 15, 2015 at 12:31 AM, Vladimir S. Fonov < > vladimir.fonov at gmail.com> wrote: > >> Hello, >> >> I noticed that URL of netcdf library changed - I updated it in the >> repository. >> Otherwise it compiles fine with the following settings: >> >> >> BUILD_TESTING:BOOL=ON >> CMAKE_BUILD_TYPE:STRING=Debug >> CMAKE_INSTALL_PREFIX:PATH=/opt/minc >> GLUT_X11_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libX11.so >> GLUT_Xi_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXi.so >> GLUT_Xmu_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXmu.so >> MNI_AUTOREG_OLD_AMOEBA_INIT:BOOL=ON >> MT_BUILD_C3D:BOOL=ON >> MT_BUILD_ITK_TOOLS:BOOL=ON >> MT_BUILD_LITE:BOOL=OFF >> MT_BUILD_MINC_ANTS:BOOL=ON >> MT_BUILD_SHARED_LIBS:BOOL=ON >> MT_BUILD_VISUAL_TOOLS:BOOL=ON >> MT_USE_OPENMP:BOOL=ON >> USE_SYSTEM_FFTW3F:BOOL=OFF >> USE_SYSTEM_GLUT:BOOL=OFF >> USE_SYSTEM_GSL:BOOL=OFF >> USE_SYSTEM_HDF5:BOOL=OFF >> USE_SYSTEM_ITK:BOOL=OFF >> USE_SYSTEM_NETCDF:BOOL=OFF >> USE_SYSTEM_PCRE:BOOL=OFF >> USE_SYSTEM_ZLIB:BOOL=OFF >> >> >> >> >> On 15-04-14 05:36 PM, Andrew Wood wrote: >> >>> Hi all, >>> >>> I'm having trouble getting the minc-toolkit built with debugging symbols >>> (specifically trying to dive into minctracc). >>> >>> I've tried setting CMAKE_BUILD_TYPE to Debug and DEBUG. >>> >>> Am I missing something obvious? >>> >>> Thanks, >>> Andrew >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >>> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > From gdevenyi at gmail.com Wed Apr 15 14:46:34 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Wed, 15 Apr 2015 14:46:34 -0400 Subject: [MINC-users] RGB-style combinations in Display Message-ID: Hi All, Jurgen(CC'd) and I were discussing the fact that many times we have T1/T2/PD images of the same brain, and it would be interesting to use that for RGB layering in Display (after appropriate registration). We could set individual colours, but we couldn't find a setting to make Display "add" the colours where they overlap. This would be similar to the colour overlay available in register, but we'd like the other features Display offers. Is this possible? Can anyone provide some hints? Thanks! -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com From vladimir.fonov at gmail.com Wed Apr 15 15:25:05 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 15 Apr 2015 15:25:05 -0400 Subject: [MINC-users] RGB-style combinations in Display In-Reply-To: References: Message-ID: <552EBB11.3050205@gmail.com> You can create an RGB minc file ( i.e 4D volume - x,y,z + vector dimension) , Display will display it properly, but you will not be able to adjust contrast dynamically. P.S. Components will have to be in the [0,1] range. On 15-04-15 02:46 PM, Gabriel A. Devenyi wrote: > Hi All, > > Jurgen(CC'd) and I were discussing the fact that many times we have > T1/T2/PD images of the same brain, and it would be interesting to use that > for RGB layering in Display (after appropriate registration). We could set > individual colours, but we couldn't find a setting to make Display "add" > the colours where they overlap. This would be similar to the colour overlay > available in register, but we'd like the other features Display offers. > > Is this possible? Can anyone provide some hints? Thanks! > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From vladimir.fonov at gmail.com Wed Apr 15 15:26:12 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 15 Apr 2015 15:26:12 -0400 Subject: [MINC-users] Building minc-toolkit for debugging In-Reply-To: References: <552DE9A5.7010109@gmail.com> Message-ID: <552EBB54.7000703@gmail.com> Hello, I prefer to build all the underlying libraries instead of relying on the system ones. On 15-04-15 02:09 PM, Andrew Wood wrote: > I think I figured out the answer to my own question - the configuration > settings from the above email belong in CMakeCache.txt in the build > directory. > > > I did come across another though when I used your configuration options > though: > > [ 1%] Built target NETCDF > make[2]: *** No rule to make target `external/opt/minc/lib/libz.a', needed > by `libminc/libminc2.so.2.3.00'. Stop. > make[1]: *** [libminc/CMakeFiles/minc2.dir/all] Error 2 > make: *** [all] Error 2 > > I got around this by setting USE_SYSTEM_ZLIB:BOOL=OFF, but is this a > generic problem that others might come across? > > > On somewhat a different topic, I'm curious about your suggestion to force > the old amoeba initialization with MNI_AUTOREG_OLD_AMOEBA_INIT:BOOL=ON. > It's my understanding that the new initialization is an improvement > (removing a directional bias). Have you found that it actually creates its > own sort of problems? Just for compatibility. > > Thanks, > Andrew > > On Wed, Apr 15, 2015 at 11:22 AM, Andrew Wood > wrote: > >> Hi Vlad, >> >> My issue wasn't with the missing netcdf library (I already had a copy >> lying around that I dropped into where the download was supposed to go) but >> rather getting executables suitable for use in gdb. >> >> I'm less than a CMake novice, so I'm still confused.. I normally specify >> cmake variables on the command like "-MCMAKE_BUILD_TYPE=Debug" but you're >> suggesting a lot of options, so I'm trying to drop them in a config file. >> >> If I understand CMake correctly, I should drop these settings at the end >> of the CMakeLists.txt file in the root directory. To satisfy CMake syntax, >> I copy/pasted from your email then translated everything to SET calls: >> >> SET( BUILD_TESTING ON ) >> SET( CMAKE_BUILD_TYPE Debug ) >> etc... >> >> Then I did the standard `mkdir build; cd build; cmake ..` and everything >> happily built (the netcdf download worked this time - thanks!). The >> executables still aren't suited for gdb though: >> >> $ gdb build_debug/mni_autoreg/minctracc/minctracc >> ... >> Reading symbols from build_debug/mni_autoreg/minctracc/minctracc...(no >> debugging symbols found)...done. >> (gdb) >> >> I must have put those settings in the wrong place? >> >> Thanks, >> Andrew >> >> >> >> >> >> >> On Wed, Apr 15, 2015 at 12:31 AM, Vladimir S. Fonov < >> vladimir.fonov at gmail.com> wrote: >> >>> Hello, >>> >>> I noticed that URL of netcdf library changed - I updated it in the >>> repository. >>> Otherwise it compiles fine with the following settings: >>> >>> >>> BUILD_TESTING:BOOL=ON >>> CMAKE_BUILD_TYPE:STRING=Debug >>> CMAKE_INSTALL_PREFIX:PATH=/opt/minc >>> GLUT_X11_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libX11.so >>> GLUT_Xi_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXi.so >>> GLUT_Xmu_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libXmu.so >>> MNI_AUTOREG_OLD_AMOEBA_INIT:BOOL=ON >>> MT_BUILD_C3D:BOOL=ON >>> MT_BUILD_ITK_TOOLS:BOOL=ON >>> MT_BUILD_LITE:BOOL=OFF >>> MT_BUILD_MINC_ANTS:BOOL=ON >>> MT_BUILD_SHARED_LIBS:BOOL=ON >>> MT_BUILD_VISUAL_TOOLS:BOOL=ON >>> MT_USE_OPENMP:BOOL=ON >>> USE_SYSTEM_FFTW3F:BOOL=OFF >>> USE_SYSTEM_GLUT:BOOL=OFF >>> USE_SYSTEM_GSL:BOOL=OFF >>> USE_SYSTEM_HDF5:BOOL=OFF >>> USE_SYSTEM_ITK:BOOL=OFF >>> USE_SYSTEM_NETCDF:BOOL=OFF >>> USE_SYSTEM_PCRE:BOOL=OFF >>> USE_SYSTEM_ZLIB:BOOL=OFF >>> >>> >>> >>> >>> On 15-04-14 05:36 PM, Andrew Wood wrote: >>> >>>> Hi all, >>>> >>>> I'm having trouble getting the minc-toolkit built with debugging symbols >>>> (specifically trying to dive into minctracc). >>>> >>>> I've tried setting CMAKE_BUILD_TYPE to Debug and DEBUG. >>>> >>>> Am I missing something obvious? >>>> >>>> Thanks, >>>> Andrew >>>> _______________________________________________ >>>> 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 pgravel at bic.mni.mcgill.ca Tue Apr 21 16:35:40 2015 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Tue, 21 Apr 2015 16:35:40 -0400 (EDT) Subject: [MINC-users] MINC Support and Documentation In-Reply-To: <552EBB11.3050205@gmail.com> References: <552EBB11.3050205@gmail.com> Message-ID: Dear All, Out of curiosity, is there still an interest (and a need) in having someone supporting the MINC tools, e.g. continuing to write the documentation (and maybe more...), because I know a good software developer that could be interested? Could you please let me know if you would be interested in hiring such a person (even part-time)? Best Regards, Paul From matthijs at mouseimaging.ca Wed Apr 22 12:09:54 2015 From: matthijs at mouseimaging.ca (Matthijs van Eede) Date: Wed, 22 Apr 2015 12:09:54 -0400 (EDT) Subject: [MINC-users] Surface Object Correction In-Reply-To: References: Message-ID: <1914513311.514562.1429718994219.JavaMail.zimbra@mouseimaging.ca> Hi Raihaan, This is a bit of a late reply, so probably this is more for future reference, but there is another way that might do what you want. There is a program that can convert mesh files between obj (BIC), stl, and vtk formats. By default the program runs a "clean" operation on the mesh which run: vtkCleanPolyData() According to the vtk documentation, this: "merge duplicate points, and/or remove unused points and/or remove degenerate cells". You need to have vtk installed which can be done using: sudo apt-get install libvtk5-dev python-vtk The program is here: https://github.com/jan-scholz/minc-scripts And you could run it like so: vtk_meshconvert.py -i input_mesh.obj -o output_mesh_clean.obj (alternatively convert to stl and open with blender) vtk_meshconvert.py -i input_mesh.obj -o output_mesh_clean.stl Cheers, Matthijs ----- Original Message ----- From: "Raihaan Patel" To: "MINC users mailing list" Sent: Wednesday, March 25, 2015 12:20:27 PM Subject: Re: [MINC-users] Surface Object Correction Hi Alex and Simon, Thank you both for your replies. Alex - a quick look at the Meshlab docs looks promising and I will certainly give it a try. Simon - the object was created using a label.mnc file and Display, then downsampled using Amira. 1. Display label.mnc 2. In Create Surface menu (G), use Volume Bin-Isosurf (S) to isolate ROI and extract surface 3. In Polygons menu (Z), perform one iteration of Smooth Polygon (C) 4. Save as .obj file 5. Downsampled the .obj file using Amira software, reducing the number of faces The downsampled .obj file is a triangular mesh. Raihaan On Wed, Mar 25, 2015 at 9:01 AM, Alex Zijdenbos wrote: > Hi Raihaan, > > Agreeing with Simon - probably better to avoid these in the first place; > but for editing meshes, you may want to take a look at Meshlab, it has a > variety of options for cleaning/remeshing/etc. > > -- A > > On Wed, Mar 25, 2015 at 6:16 AM, Simon Eskildsen wrote: > > > Hi Raihaan, > > > > What you're asking for is far from trivial. Can you provide more details? > > How did you create the object - how did the intersections happen? Are we > > talking about a triangular mesh? > > In general, the best strategy is to prevent these unwanted features to > > happen in the first place. > > > > Simon > > > > On Mon, Mar 23, 2015 at 3:33 PM, Raihaan Patel > > wrote: > > > > > Hi All, > > > > > > I'm looking for any advice/input on correcting a surface object (.obj). > > > Specifically, I am wondering how to: > > > > > > - remove/correct any intersecting faces > > > - remove/correct any faces that have an area of 0 > > > > > > Thanks very much, > > > Raihaan > > > _______________________________________________ > > > 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 From andrew at biospective.com Tue Apr 28 15:48:26 2015 From: andrew at biospective.com (Andrew Wood) Date: Tue, 28 Apr 2015 15:48:26 -0400 Subject: [MINC-users] Latest stable version of packages Message-ID: Hi all, This question refers specifically to mni_autoreg, but it's about minc packages in general. The latest release of mni_autoreg is 0.99.60 (according to the tags in BIC-MNI/mni_autoreg on github), but there have been many minc-toolkit releases using commits from after the 0.99.60 tag. I'm wondering how to determine the most recent blessed version of minc packages. It appears that the tags in the packages themselves shouldn't be trusted (or perhaps this is unique to mni_autoreg). It looks to me like the packages all released in lockstep, each time minc-toolkit is tagged. Could someone please confirm? Thanks, Andrew From vladimir.fonov at gmail.com Tue Apr 28 15:59:36 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Tue, 28 Apr 2015 15:59:36 -0400 Subject: [MINC-users] Latest stable version of packages In-Reply-To: References: Message-ID: <553FE6A8.8040008@gmail.com> Hello, The most reliable way currently, would be to take master branch of minc-toolkit and use underlying packages. On 15-04-28 03:48 PM, Andrew Wood wrote: > Hi all, > > This question refers specifically to mni_autoreg, but it's about minc > packages in general. > > The latest release of mni_autoreg is 0.99.60 (according to the tags in > BIC-MNI/mni_autoreg on github), but there have been many minc-toolkit > releases using commits from after the 0.99.60 tag. > > I'm wondering how to determine the most recent blessed version of minc > packages. It appears that the tags in the packages themselves shouldn't be > trusted (or perhaps this is unique to mni_autoreg). > > It looks to me like the packages all released in lockstep, each time > minc-toolkit is tagged. Could someone please confirm? -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From gdevenyi at gmail.com Tue Apr 28 16:12:35 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Tue, 28 Apr 2015 16:12:35 -0400 Subject: [MINC-users] Latest stable version of packages In-Reply-To: <553FE6A8.8040008@gmail.com> References: <553FE6A8.8040008@gmail.com> Message-ID: Hi Vlad? How often are there "releases" of minc-toolkit? We prefer to quarantine our software versions (a la SciNet with environment-modules). As such, we usually want to build versioned releases. I could do it via git tags, but that will result in a proliferation of a large number of different versions. How many commits have happened since 1.0.04? -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Tue, Apr 28, 2015 at 3:59 PM, Vladimir S. FONOV wrote: > Hello, > > The most reliable way currently, would be to take master branch of > minc-toolkit and use underlying packages. > > > On 15-04-28 03:48 PM, Andrew Wood wrote: > >> Hi all, >> >> This question refers specifically to mni_autoreg, but it's about minc >> packages in general. >> >> The latest release of mni_autoreg is 0.99.60 (according to the tags in >> BIC-MNI/mni_autoreg on github), but there have been many minc-toolkit >> releases using commits from after the 0.99.60 tag. >> >> I'm wondering how to determine the most recent blessed version of minc >> packages. It appears that the tags in the packages themselves shouldn't be >> trusted (or perhaps this is unique to mni_autoreg). >> >> It looks to me like the packages all released in lockstep, each time >> minc-toolkit is tagged. Could someone please confirm? >> > > > -- > 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 gdevenyi at gmail.com Wed Apr 29 13:06:42 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Wed, 29 Apr 2015 13:06:42 -0400 Subject: [MINC-users] RGB-style combinations in Display In-Reply-To: <552EBB11.3050205@gmail.com> References: <552EBB11.3050205@gmail.com> Message-ID: Thanks Vlad, Can you offer some example steps on how we might do that if we had three co-registered images? -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Wed, Apr 15, 2015 at 3:25 PM, Vladimir S. FONOV wrote: > You can create an RGB minc file ( i.e 4D volume - x,y,z + vector > dimension) , Display will display it properly, but you will not be able to > adjust contrast dynamically. > > P.S. Components will have to be in the [0,1] range. > > On 15-04-15 02:46 PM, Gabriel A. Devenyi wrote: > >> Hi All, >> >> Jurgen(CC'd) and I were discussing the fact that many times we have >> T1/T2/PD images of the same brain, and it would be interesting to use that >> for RGB layering in Display (after appropriate registration). We could set >> individual colours, but we couldn't find a setting to make Display "add" >> the colours where they overlap. This would be similar to the colour >> overlay >> available in register, but we'd like the other features Display offers. >> >> Is this possible? Can anyone provide some hints? Thanks! >> >> > > -- > Best regards, > > Vladimir S. FONOV ~ vladimir.fonov gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Wed Apr 29 14:07:17 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 29 Apr 2015 14:07:17 -0400 Subject: [MINC-users] RGB-style combinations in Display In-Reply-To: References: <552EBB11.3050205@gmail.com> Message-ID: <55411DD5.4040606@gmail.com> mincconcat -concat_dimension vector_dimension r.mnc g.mnc b.mnc rgb_.mnc mincreshape -dimorder xspace,yspace,zspace,vector_dimension rgb_.mnc rgb.mnc On 15-04-29 01:06 PM, Gabriel A. Devenyi wrote: > Thanks Vlad, > > Can you offer some example steps on how we might do that if we had three > co-registered images? > -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From joanna.glazer at utoronto.ca Thu Apr 30 14:14:32 2015 From: joanna.glazer at utoronto.ca (joanna.glazer at utoronto.ca) Date: Thu, 30 Apr 2015 14:14:32 -0400 Subject: [MINC-users] Dicom to minc conversion Message-ID: <20150430141432.0bjye0xfkw8s4osc@webmail.utoronto.ca> Dear All, I am having a problem converting dicom files into minc using dicom3_to_minc. The message I am getting is: Reading headers from file "445/IM000000" Negative length at /research/lib/perl5/5.8.5/DICOM/Element.pm line 88. I have tried to convert some older data and that worked fine. Would you have any idea what could be wrong? Thank you very much for your help. Joanna From robert.d.vincent at mcgill.ca Thu Apr 30 14:40:48 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Thu, 30 Apr 2015 14:40:48 -0400 Subject: [MINC-users] Dicom to minc conversion In-Reply-To: <13377_1430417731_55427143_13377_145_3_20150430141432.0bjye0xfkw8s4osc@webmail.utoronto.ca> References: <13377_1430417731_55427143_13377_145_3_20150430141432.0bjye0xfkw8s4osc@webmail.utoronto.ca> Message-ID: Hi Joanna, I can't offer much advice on dicom3_to_minc, as we no longer really support it. Our other tool, dcm2mnc, is still supported, and might be worth a try if you have it installed. If it doesn't work, I can provide you with an updated version that might. What type of system are you working with (Linux, Mac, etc.)? -bert On Thu, Apr 30, 2015 at 2:14 PM, wrote: > Dear All, > > I am having a problem converting dicom files into minc using > dicom3_to_minc. The message I am getting is: > Reading headers from file "445/IM000000" > Negative length at /research/lib/perl5/5.8.5/DICOM/Element.pm line 88. > > I have tried to convert some older data and that worked fine. > Would you have any idea what could be wrong? > > Thank you very much for your help. > > Joanna > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From najma at bic.mni.mcgill.ca Thu Apr 30 17:18:20 2015 From: najma at bic.mni.mcgill.ca (Najmeh Khalili-Mahani) Date: Thu, 30 Apr 2015 17:18:20 -0400 (EDT) Subject: [MINC-users] glim_image Message-ID: Hi, Is Glim_image totally extinct? I cannot find the documentation in Jon Taylor's site and my memory of the command syntax has faded! I am looking for a way to do VBM, using surfstat-like design matrices. Thank you for sugegstions. Naj From gdevenyi at gmail.com Thu Apr 30 17:38:19 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Thu, 30 Apr 2015 17:38:19 -0400 Subject: [MINC-users] Extracting/Elimintating Time Dimension in minc files Message-ID: Hi all, I'm having trouble with some minc files generated by pvconv.pl, they seem to have a time dimension even though they're a single scan. Is there a way to either fix pvconv.pl so it doesn't do this, or eliminate/extract the single 3D object from the 4D minc volume? Thanks for your help! -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com From gdevenyi at gmail.com Thu Apr 30 17:43:27 2015 From: gdevenyi at gmail.com (Gabriel A. Devenyi) Date: Thu, 30 Apr 2015 17:43:27 -0400 Subject: [MINC-users] glim_image In-Reply-To: References: Message-ID: Najmeh, I think we've moved on to doing such statistics with RMINC https://wiki.mouseimaging.ca/display/MICePub/RMINC -- Gabriel A. Devenyi B.Eng. Ph.D. Research Computing Associate Computational Brain Anatomy Laboratory Cerebral Imaging Center Douglas Mental Health University Institute McGill University t: 514.761.6131x4781 e: gdevenyi at gmail.com On Thu, Apr 30, 2015 at 5:18 PM, Najmeh Khalili-Mahani < najma at bic.mni.mcgill.ca> wrote: > Hi, > > Is Glim_image totally extinct? I cannot find the documentation in Jon > Taylor's site and my memory of the command syntax has faded! > > I am looking for a way to do VBM, using surfstat-like design matrices. > > Thank you for sugegstions. > > Naj > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sorench at gmail.com Thu Apr 30 17:49:09 2015 From: sorench at gmail.com (Soren Christensen) Date: Thu, 30 Apr 2015 14:49:09 -0700 Subject: [MINC-users] Extracting/Elimintating Time Dimension in minc files In-Reply-To: References: Message-ID: Hi Gabriel, mincreshape -dimrange time=0,0 in.mnc out.mnc will eliminate the time dimension Soren On Thu, Apr 30, 2015 at 2:38 PM, Gabriel A. Devenyi wrote: > Hi all, > > I'm having trouble with some minc files generated by pvconv.pl, they seem > to have a time dimension even though they're a single scan. Is there a way > to either fix pvconv.pl so it doesn't do this, or eliminate/extract the > single 3D object from the 4D minc volume? > > Thanks for your help! > > -- > Gabriel A. Devenyi B.Eng. Ph.D. > Research Computing Associate > Computational Brain Anatomy Laboratory > Cerebral Imaging Center > Douglas Mental Health University Institute > McGill University > t: 514.761.6131x4781 > e: gdevenyi at gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Apr 30 17:49:44 2015 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 1 May 2015 07:49:44 +1000 Subject: [MINC-users] Extracting/Elimintating Time Dimension in minc files In-Reply-To: References: Message-ID: Hi Gabriel, This is a common problem with pvconv.pl and it's to do with how paravision defines files. The simple fix is to do this after the conversion: mincreshape -dimrange time=0,0 in.mnc out.mnc a On 1 May 2015 at 07:38, Gabriel A. Devenyi wrote: > Hi all, > > I'm having trouble with some minc files generated by pvconv.pl, they seem > to have a time dimension even though they're a single scan. Is there a way > to either fix pvconv.pl so it doesn't do this, or eliminate/extract the > single 3D object from the 4D minc volume? > > Thanks for your help! > > -- > Gabriel A. Devenyi B.Eng. Ph.D. > Research Computing Associate > Computational Brain Anatomy Laboratory > Cerebral Imaging Center > Douglas Mental Health University Institute > McGill University > t: 514.761.6131x4781 > e: gdevenyi at gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Thu Apr 30 18:18:46 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 30 Apr 2015 18:18:46 -0400 Subject: [MINC-users] glim_image In-Reply-To: References: Message-ID: <5542AA46.70405@gmail.com> Hello, there is a little bit here: https://github.com/BIC-MNI/glim_image/tree/develop On 15-04-30 05:18 PM, Najmeh Khalili-Mahani wrote: > Hi, > > Is Glim_image totally extinct? I cannot find the documentation in Jon > Taylor's site and my memory of the command syntax has faded! > > I am looking for a way to do VBM, using surfstat-like design matrices. > > Thank you for sugegstions. > > Naj > > _______________________________________________ > 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 Thu Apr 30 18:21:26 2015 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 1 May 2015 08:21:26 +1000 Subject: [MINC-users] glim_image In-Reply-To: <5542AA46.70405@gmail.com> References: <5542AA46.70405@gmail.com> Message-ID: This looks like a dump from -help which is this: EXAMPLE - group comparison glim_image -max_num_row 350 \ -t_stat glim_t1-2_groupAB-10mm.mnc t_stat voxel column 2 \ glim_t1-2_groupAB-10mm EXAMPLE - pairwise subtraction Pfizer_Part2 Command-specific options: Stats options: Common options: -family: Specify exponential family for GLM. -link: Specify link function for GLM. -var_func: Specify variance function for GLM. -t_stat: Defines t-statistics wanted for output T-statistics are defined as follows: -t_stat type (one of t_stat, stdev, corr, beta) stdev_type (one of pool or voxel) intype (one of matrix, column or file) string (string defining contrast depends on intype) For example, the following: -t_stat out.mnc corr pool column 4 defines an output file that will be a partial correlation testing column 4 of the design matrix -t_stat out.mnc beta voxel matrix '0 1.5 0 -2.3' defines an output file that will have the of 1.5*beta2 - 2.3*beta4 where the betas are the parameters estimated in the regression. -t_stat out.mnc stdev pool file contrast1.txt defines an output file that will be the stdev of the t_stat defined in the textfile contrast1.txt with a pooled stdev. This doesn't make sense because we would not use a pooled stdev to look at the stdev as it varies over the image, so glim_image spits this out as a warning. -f_stat: Defines F-statistics wanted for output F_statistics are defined in the same way as t_statistics except there is no type, this is because the variance of an F-stat is a matrix, as is the numerator. For this reason, column is also not an intype for F_statistics because a matrix with more than two rows is needed for an F_stat. For example: -f_stat out.mnc pool matrix '0 1 2 0 ; 1 2 3 0' defines an output file that is an F-stat testing whether beta2 + 2*beta3 = 0 and beta1 + beta2 + beta3 = 0 simultaneously. This comes into play for anova designs when there are factors with multiple levels. -est_scale: Use estimated scale (for binomial and poisson families) -scale_par: Set scale parameter, (default: estimate it) Default value: -1 -max_iter: Maximum iterations for Fisher scoring. Default value: 10 -tolerance: Tolerance for convergence of fitted parameters. Default value: 0.0001 -eps_sing: Epsilon added to repsonse values that would cause singularities. Default value: 0.0001 -maxVoxelSdBasedValue: Maximum absolute value of t_statistic image. Default value: 99 -avg: File name for means (missing values not skipped. Needs sd_type and out_type. Avg is used for comparison of means at the same time as fitting a design file, the output types are t_stat, beta, corr and stdev; stdev types are voxel or pool. -deviance: Output an image of deviances (default: FALSE) -avg_deviance: Output image of deviances for avg. -scale: Output image of scale estimate (default: FALSE) -errfile: Output convergence error codes. -use_mu: Use previous fitted values instead of response for initial values. -pool_sd: Mask file for region over which to pool s.d. -fwhm: Calculate FWHM estimate to be used for assessing significance. -fwhm_gauss: Output fwhm image for gaussian fit. -fwhm_simple: Output non-weight corrected FWHM estimate for non-Gaussian data. -fwhm_avg: Output fwhm image for comparison of means fit. -search: Mask file for search region. -fit_all: Fit GLM at all voxels with no missing values, not just search region. -fit_missing: Fit GLM at all voxels, even with missing values. Must provide name for degrees of freedom volume. -max_num_row: Maximum number of rows for design_file. Should be increased for large files. Default value: 300 -max_num_col: Maximum number of rows for design_file. Should be increased for large files. Default value: 100 -scylla: Flag to see if computer is at neuro or math dept. General options: -path: Path for input files and design_matrix file. -clobber: Overwrite existing file. -noclobber: Don't overwrite existing file (default). -verbose: Print out log messages (default). -quiet: Do not print out log messages. -copy_header: Copy all of the header from the first file. -nocopy_header: Do not copy all of the header from the first file. -filetype: Use data type of first file (default). -byte: Write out byte data. -short: Write out short integer data. -long: Write out long integer data. -float: Write out single-precision floating-point data. -double: Write out double-precision floating-point data. -signed: Write signed integer data. -unsigned: Write unsigned integer data (default if type specified). -range: Valid range for output data. Default value: 0 0 -max_buffer_size_in_kb: Specify the maximum size of the internal buffers (in kbytes). Default value: 10240 -check_dimensions: Check that files have matching dimensions (default). -nocheck_dimensions: Do not check that files have matching dimensions. Generic options for all commands: -help: Print summary of command-line options and abort Usage: glim_image [options] glim_image -help Your command line was (after parsing): glim_image -help Use '-' as des.file to read from stdin. Last line should end with 'END'. I am sure I cached jon's help page somewhere but can't find it right now. If anyone can find it please point me to it (even in archive.org) and I'll put it up on the MINC wikibooks pages. a On 1 May 2015 at 08:18, Vladimir S. FONOV wrote: > Hello, > > > there is a little bit here: > https://github.com/BIC-MNI/glim_image/tree/develop > > > On 15-04-30 05:18 PM, Najmeh Khalili-Mahani wrote: > >> Hi, >> >> Is Glim_image totally extinct? I cannot find the documentation in Jon >> Taylor's site and my memory of the command syntax has faded! >> >> I am looking for a way to do VBM, using surfstat-like design matrices. >> >> Thank you for sugegstions. >> >> Naj >> >> _______________________________________________ >> 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 >