From joachim.pries.hansen at regionh.dk Fri Jan 6 05:49:34 2017 From: joachim.pries.hansen at regionh.dk (Joachim Pries Hansen) Date: Fri, 6 Jan 2017 10:49:34 +0000 Subject: [MINC-users] MINC Mail list Message-ID: <1483699773901.26018@regionh.dk> Hello, >From the last email i got in subscribing to the MINC email list. I were told to email my mail to this adress so here goes: Joachim.Pries.Hansen at regionh.dk Thanks! ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den. From jp at biospective.com Fri Jan 6 16:49:22 2017 From: jp at biospective.com (Jean-Philippe Coutu) Date: Fri, 6 Jan 2017 16:49:22 -0500 Subject: [MINC-users] mincbbox Message-ID: Dear MINC users, There seems to be a few problems with the current implementation of mincbbox ( https://github.com/BIC-MNI/mni_autoreg/blob/develop/mincbbox/mincbbox.c). Right now, it seems to work only on volumes with a step of 1mm. 1) The first issue is with the option -mincresample, where it will print a step of 1.0 regardless of the actual step of the volume: print ("-step 1.0 1.0 1.0 -start %f %f %f -nelements %d %d %d\n", minx, miny, minz, VIO_ROUND(maxx-minx)+1, VIO_ROUND(maxy-miny)+1, VIO_ROUND(maxz-minz)+1); The step should probably be (max{x,y,z}-min{x,y,z})/(v_max{x,y,z}-v_min{x,y,z}). 2) Also, it seems to report the wrong -nelements (should probably be v_max{x,y,z}-v_min{x,y,z}+1 like above for -mincreshape). 3) Another issue is that it returns by default the wrong extent if the step is not 1mm: if (two_lines) print ("%f %f %f\n%f %f %f\n",minx, miny, minz, maxx-minx+1, maxy-miny+1, maxz-minz+1); else print ("%f %f %f %f %f %f\n",minx, miny, minz, maxx-minx+1, maxy-miny+1, maxz-minz+1); "max{x,y,z}-min{x,y,z}+1" should probably be replaced by "max{x,y,z}-min{x,y,z}+step{x,y,z}" to report the extent of the voxel dimensions (edge to edge) in world coordinates as I think is intended or simply "max{x,y,z}-min{x,y,z}" to report the extent between the voxel centers. I am unclear on which one is intended to be returned for this one though, thoughts? Best regards, JP From joachim.pries.hansen at regionh.dk Sat Jan 7 07:29:15 2017 From: joachim.pries.hansen at regionh.dk (Joachim Pries Hansen) Date: Sat, 7 Jan 2017 12:29:15 +0000 Subject: [MINC-users] How to read DICOM-RT with MINC? Message-ID: <1483792158552.51851@regionh.dk> Hello, I'm interested in being able to convert a DICOM-RT file into MINC format so that it would be possible to use the RT file as a label when viewing with MINC. I have a hard time figuring out the proper way to go ahead with this problem, since the DICOM image sets must be together with the RT file for the RT file to be valid. Have anyone come across this problem before and would like to share their process or code? Kind Regards, Joachim? ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den. From robert.d.vincent at mcgill.ca Sat Jan 7 09:21:42 2017 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Sat, 7 Jan 2017 09:21:42 -0500 Subject: [MINC-users] How to read DICOM-RT with MINC? In-Reply-To: <1483792158552.51851@regionh.dk> References: <1483792158552.51851@regionh.dk> Message-ID: Hi, I'm not really familiar with the DICOM-RT format, but I see that some effort has been made with this here: https://github.com/ulrikls/dicomrt2matlab I'd be happy to take a look at how this might be accomplished in other environments if you can point me to some sample data. -bert On Sat, Jan 7, 2017 at 7:29 AM, Joachim Pries Hansen < joachim.pries.hansen at regionh.dk> wrote: > Hello, > > > I'm interested in being able to convert a DICOM-RT file into MINC format > so that it would be possible to use the RT file as a label when viewing > with MINC. > > I have a hard time figuring out the proper way to go ahead with this > problem, since the DICOM image sets must be together with the RT file for > the RT file to be valid. > > Have anyone come across this problem before and would like to share their > process or code? > > > Kind Regards, > > Joachim? > > > > ________________________________ > > > Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette > modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, > beder vi dig venligst informere afsender om fejlen ved at bruge > svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at > videresende eller kopiere den. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Mon Jan 9 09:50:44 2017 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Mon, 9 Jan 2017 09:50:44 -0500 Subject: [MINC-users] mincbbox In-Reply-To: References: Message-ID: <942152e8-1bfe-e152-2c8a-5d7ee877a034@gmail.com> Hello, thank you for the bug report, Gabriel included this in the list of issues : https://github.com/BIC-MNI/mni_autoreg/issues Let's see who has time to fix this. On 2017-01-06 04:49 PM, Jean-Philippe Coutu wrote: > Dear MINC users, > > There seems to be a few problems with the current implementation of > mincbbox ( > https://github.com/BIC-MNI/mni_autoreg/blob/develop/mincbbox/mincbbox.c). > Right now, it seems to work only on volumes with a step of 1mm. > > 1) The first issue is with the option -mincresample, where it will print a > step of 1.0 regardless of the actual step of the volume: > > print ("-step 1.0 1.0 1.0 -start %f %f %f -nelements %d %d %d\n", > minx, miny, minz, VIO_ROUND(maxx-minx)+1, VIO_ROUND(maxy-miny)+1, > VIO_ROUND(maxz-minz)+1); > > The step should probably be > (max{x,y,z}-min{x,y,z})/(v_max{x,y,z}-v_min{x,y,z}). > > 2) Also, it seems to report the wrong -nelements (should probably be > v_max{x,y,z}-v_min{x,y,z}+1 like above for -mincreshape). > > 3) Another issue is that it returns by default the wrong extent if the step > is not 1mm: > > if (two_lines) > print ("%f %f %f\n%f %f %f\n",minx, miny, minz, maxx-minx+1, maxy-miny+1, > maxz-minz+1); > else > print ("%f %f %f %f %f %f\n",minx, miny, minz, maxx-minx+1, maxy-miny+1, > maxz-minz+1); > > "max{x,y,z}-min{x,y,z}+1" should probably be replaced by > "max{x,y,z}-min{x,y,z}+step{x,y,z}" to report the extent of the voxel > dimensions (edge to edge) in world coordinates as I think is intended or > simply "max{x,y,z}-min{x,y,z}" to report the extent between the voxel > centers. > > I am unclear on which one is intended to be returned for this one though, > thoughts? > > Best regards, > JP > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From zijdenbos at gmail.com Mon Jan 9 10:29:18 2017 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Mon, 9 Jan 2017 10:29:18 -0500 Subject: [MINC-users] mincbbox In-Reply-To: <942152e8-1bfe-e152-2c8a-5d7ee877a034@gmail.com> References: <942152e8-1bfe-e152-2c8a-5d7ee877a034@gmail.com> Message-ID: Hello, What is the answer to the conceptual question though - should mincbbox report a bounding box to the voxel centers, or voxel edges (0.5 step larger on each end of a dimension)? From the way it is implemented I would say the original intent was the latter. Or, perhaps it would make sense to add an option an option for the user to choose, making sure the default behaviour (on 1mm isotropic volumes) doesn't change? -- A On Mon, Jan 9, 2017 at 9:50 AM, Vladimir S. Fonov wrote: > Hello, > > thank you for the bug report, Gabriel included this in the list of issues > : https://github.com/BIC-MNI/mni_autoreg/issues > > Let's see who has time to fix this. > > > On 2017-01-06 04:49 PM, Jean-Philippe Coutu wrote: > >> Dear MINC users, >> >> There seems to be a few problems with the current implementation of >> mincbbox ( >> https://github.com/BIC-MNI/mni_autoreg/blob/develop/mincbbox/mincbbox.c). >> Right now, it seems to work only on volumes with a step of 1mm. >> >> 1) The first issue is with the option -mincresample, where it will print a >> step of 1.0 regardless of the actual step of the volume: >> >> print ("-step 1.0 1.0 1.0 -start %f %f %f -nelements %d %d %d\n", >> minx, miny, minz, VIO_ROUND(maxx-minx)+1, VIO_ROUND(maxy-miny)+1, >> VIO_ROUND(maxz-minz)+1); >> >> The step should probably be >> (max{x,y,z}-min{x,y,z})/(v_max{x,y,z}-v_min{x,y,z}). >> >> 2) Also, it seems to report the wrong -nelements (should probably be >> v_max{x,y,z}-v_min{x,y,z}+1 like above for -mincreshape). >> >> 3) Another issue is that it returns by default the wrong extent if the >> step >> is not 1mm: >> >> if (two_lines) >> print ("%f %f %f\n%f %f %f\n",minx, miny, minz, maxx-minx+1, maxy-miny+1, >> maxz-minz+1); >> else >> print ("%f %f %f %f %f %f\n",minx, miny, minz, maxx-minx+1, maxy-miny+1, >> maxz-minz+1); >> >> "max{x,y,z}-min{x,y,z}+1" should probably be replaced by >> "max{x,y,z}-min{x,y,z}+step{x,y,z}" to report the extent of the voxel >> dimensions (edge to edge) in world coordinates as I think is intended or >> simply "max{x,y,z}-min{x,y,z}" to report the extent between the voxel >> centers. >> >> I am unclear on which one is intended to be returned for this one though, >> thoughts? >> >> Best regards, >> JP >> _______________________________________________ >> 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 pgravel at bic.mni.mcgill.ca Thu Jan 12 13:50:50 2017 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 12 Jan 2017 13:50:50 -0500 (EST) Subject: [MINC-users] MINC tools on RedHat Message-ID: Dear All, Is there a pre-compiled version of the MINC tools for RedHat? Otherwise, is there a procedure to compile the MINC tools from scratch, i.e. which packages need to be installed first (e.g. NetCDF)? And for someone that do not have Admin privileges? The version of RedHat is: $ lsb_release -a LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: RedHatEnterpriseAS Description: Red Hat Enterprise Linux AS release 6 (Update 5) Release: 6 Codename: Update5 Many thanks! Paul From vladimir.fonov at gmail.com Thu Jan 12 14:38:05 2017 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 12 Jan 2017 14:38:05 -0500 Subject: [MINC-users] MINC tools on RedHat In-Reply-To: References: Message-ID: It corresponds to CentOS 6.5. You can follow instructions for CentOS from http://bic-mni.github.io/ On Thu, Jan 12, 2017 at 1:50 PM, Paul GRAVEL wrote: > Dear All, > > Is there a pre-compiled version of the MINC tools for RedHat? > Otherwise, is there a procedure to compile the MINC tools from scratch, > i.e. which packages need to be installed first (e.g. NetCDF)? > And for someone that do not have Admin privileges? > > The version of RedHat is: > $ lsb_release -a > LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0- > noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0- > amd64:printing-4.0-noarch > Distributor ID: RedHatEnterpriseAS > Description: Red Hat Enterprise Linux AS release 6 (Update 5) > Release: 6 > Codename: Update5 > > Many thanks! > > Paul > _______________________________________________ > 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 Thu Jan 12 15:09:45 2017 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 12 Jan 2017 15:09:45 -0500 (EST) Subject: [MINC-users] MINC tools on RedHat In-Reply-To: References: Message-ID: Thanks Valdimir! Sorry for the basic question, but: Since I don't have admin privileges, is there a way to do this on my account only? Best, Paul On Thu, 12 Jan 2017, Vladimir S. FONOV wrote: > It corresponds to CentOS 6.5. You can follow instructions for CentOS from > http://bic-mni.github.io/ > > On Thu, Jan 12, 2017 at 1:50 PM, Paul GRAVEL > wrote: > >> Dear All, >> >> Is there a pre-compiled version of the MINC tools for RedHat? >> Otherwise, is there a procedure to compile the MINC tools from scratch, >> i.e. which packages need to be installed first (e.g. NetCDF)? >> And for someone that do not have Admin privileges? >> >> The version of RedHat is: >> $ lsb_release -a >> LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0- >> noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0- >> amd64:printing-4.0-noarch >> Distributor ID: RedHatEnterpriseAS >> Description: Red Hat Enterprise Linux AS release 6 (Update 5) >> Release: 6 >> Codename: Update5 >> >> Many thanks! >> >> Paul >> _______________________________________________ >> 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 Jan 12 15:47:30 2017 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 12 Jan 2017 15:47:30 -0500 Subject: [MINC-users] MINC tools on RedHat In-Reply-To: References: Message-ID: <7e105486-63b4-4918-e201-65ee28f65581@gmail.com> You will have to manually build it. Try to follow instructions from https://github.com/BIC-MNI/minc-toolkit-v2 , I recommend not to try to use any system packages (NETCDF, HDF5, etc. ) On 2017-01-12 03:09 PM, Paul GRAVEL wrote: > Thanks Valdimir! > > Sorry for the basic question, but: > Since I don't have admin privileges, is there a way to do this on my > account only? > > Best, > > Paul > > On Thu, 12 Jan 2017, Vladimir S. FONOV wrote: > >> It corresponds to CentOS 6.5. You can follow instructions for CentOS from >> http://bic-mni.github.io/ >> >> On Thu, Jan 12, 2017 at 1:50 PM, Paul GRAVEL >> wrote: >> >>> Dear All, >>> >>> Is there a pre-compiled version of the MINC tools for RedHat? >>> Otherwise, is there a procedure to compile the MINC tools from scratch, >>> i.e. which packages need to be installed first (e.g. NetCDF)? >>> And for someone that do not have Admin privileges? >>> >>> The version of RedHat is: >>> $ lsb_release -a >>> LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0- >>> noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0- >>> amd64:printing-4.0-noarch >>> Distributor ID: RedHatEnterpriseAS >>> Description: Red Hat Enterprise Linux AS release 6 (Update 5) >>> Release: 6 >>> Codename: Update5 >>> >>> Many thanks! >>> >>> Paul >>> _______________________________________________ >>> 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 -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From pgravel at bic.mni.mcgill.ca Thu Jan 12 21:47:30 2017 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Thu, 12 Jan 2017 21:47:30 -0500 (EST) Subject: [MINC-users] MINC tools on RedHat In-Reply-To: <7e105486-63b4-4918-e201-65ee28f65581@gmail.com> References: <7e105486-63b4-4918-e201-65ee28f65581@gmail.com> Message-ID: Thanks I'll give it a try! On Thu, 12 Jan 2017, Vladimir S. FONOV wrote: > You will have to manually build it. Try to follow instructions from > https://github.com/BIC-MNI/minc-toolkit-v2 , I recommend not to try to use > any system packages (NETCDF, HDF5, etc. ) > > > On 2017-01-12 03:09 PM, Paul GRAVEL wrote: >> Thanks Valdimir! >> >> Sorry for the basic question, but: >> Since I don't have admin privileges, is there a way to do this on my >> account only? >> >> Best, >> >> Paul >> >> On Thu, 12 Jan 2017, Vladimir S. FONOV wrote: >> >>> It corresponds to CentOS 6.5. You can follow instructions for CentOS from >>> http://bic-mni.github.io/ >>> >>> On Thu, Jan 12, 2017 at 1:50 PM, Paul GRAVEL >>> wrote: >>> >>>> Dear All, >>>> >>>> Is there a pre-compiled version of the MINC tools for RedHat? >>>> Otherwise, is there a procedure to compile the MINC tools from scratch, >>>> i.e. which packages need to be installed first (e.g. NetCDF)? >>>> And for someone that do not have Admin privileges? >>>> >>>> The version of RedHat is: >>>> $ lsb_release -a >>>> LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0- >>>> noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0- >>>> amd64:printing-4.0-noarch >>>> Distributor ID: RedHatEnterpriseAS >>>> Description: Red Hat Enterprise Linux AS release 6 (Update 5) >>>> Release: 6 >>>> Codename: Update5 >>>> >>>> Many thanks! >>>> >>>> Paul >>>> _______________________________________________ >>>> 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 > > > -- > 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 jp at biospective.com Fri Jan 13 14:50:08 2017 From: jp at biospective.com (Jean-Philippe Coutu) Date: Fri, 13 Jan 2017 14:50:08 -0500 Subject: [MINC-users] zlib new version Message-ID: Dear MINC-users, I was compiling the c code of minc-toolkit and noticed that zlib does not seem to have the 1.2.8 version available at the URL specified in the BuildZLIB.cmake file (http://zlib.net/zlib-1.2.8.tar.gz), which prevents the compilation. I suspect that it may not be available anymore due to the new Jan 2017 version 1.2.10 (or temporary, in which case ignore this). I was able to circumvent that using my system's zlib, but beforehand I also tried switching the URL to point to http://zlib.net/zlib-1.2.10.tar.xz instead with the appropriate md5sum, and the compilation still crashed at some point (missing libraries for mnc2nii). Unfortunately did not save the error message, but should not be hard to replicate with cloning minc-toolkit and trying to compile as indicated here: https://github.com/BIC-MNI/minc-toolkit/blob/master/README.md Just thought I should post this here in case someone is struggling to compile the toolkit. Best, JP From robert.d.vincent at mcgill.ca Fri Jan 13 14:51:50 2017 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Fri, 13 Jan 2017 14:51:50 -0500 Subject: [MINC-users] zlib new version In-Reply-To: References: Message-ID: Thanks. I believe this is now fixed in the develop branch. On Fri, Jan 13, 2017 at 2:50 PM, Jean-Philippe Coutu wrote: > Dear MINC-users, > > I was compiling the c code of minc-toolkit and noticed that zlib does not > seem to have the 1.2.8 version available at the URL specified in the > BuildZLIB.cmake file (http://zlib.net/zlib-1.2.8.tar.gz), which prevents > the compilation. I suspect that it may not be available anymore due to the > new Jan 2017 version 1.2.10 (or temporary, in which case ignore this). > > I was able to circumvent that using my system's zlib, but beforehand I also > tried switching the URL to point to http://zlib.net/zlib-1.2.10.tar.xz > instead with the appropriate md5sum, and the compilation still crashed at > some point (missing libraries for mnc2nii). Unfortunately did not save the > error message, but should not be hard to replicate with cloning > minc-toolkit and trying to compile as indicated here: > https://github.com/BIC-MNI/minc-toolkit/blob/master/README.md > > Just thought I should post this here in case someone is struggling to > compile the toolkit. > > Best, > JP > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >