From ocustom at gmail.com Fri Oct 8 10:05:39 2010 From: ocustom at gmail.com (=?ISO-8859-1?Q?Cl=E1udio_Vin=EDcius?=) Date: Fri, 8 Oct 2010 11:05:39 -0300 Subject: [MINC-users] Automatic converting .tag to .obj Message-ID: Hello everyone! I'm been using Minc for a couple weeks, and I have a doubt: Is there a way to convert the a .tag file from a segmented region directly to a .obj polygon, without using the "Display" interface(create surface)? I have lots of .tags and it would take me too much time to convert them all manually. Thanks! Claudio V.C From laurence at bic.mni.mcgill.ca Fri Oct 8 10:13:45 2010 From: laurence at bic.mni.mcgill.ca (Laurence Mercier) Date: Fri, 08 Oct 2010 10:13:45 -0400 Subject: [MINC-users] Automatic converting .tag to .obj In-Reply-To: References: Message-ID: <4CAF2719.2080409@bic.mni.mcgill.ca> Do you mean labels? Tags are just point coordinates. To transform a label (.mnc) into a 3D surface (.obj) you can use marching_cubes Laurence On 10/8/2010 10:05 AM, Cl?udio Vin?cius wrote: > Hello everyone! I'm been using Minc for a couple weeks, and I have a doubt: > Is there a way to convert the a .tag file from a segmented region directly > to a .obj polygon, without using the "Display" interface(create surface)? I > have lots of .tags and it would take me too much time to convert them all > manually. > Thanks! > Claudio V.C > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- Laurence Mercier McConnell Brain Imaging Center Montreal Neurological Institute, room: WB-320 3801 University St Montreal (QC), H3A 2B4 CANADA Office Phone: +1 514.398.1573 Office FAX: +1 514.398.2975 Web: http://www.bic.mni.mcgill.ca/~laurence From ocustom at gmail.com Fri Oct 8 13:31:22 2010 From: ocustom at gmail.com (=?ISO-8859-1?Q?Cl=E1udio_Vin=EDcius?=) Date: Fri, 8 Oct 2010 14:31:22 -0300 Subject: [MINC-users] Automatic converting .tag to .obj In-Reply-To: <4CAF2719.2080409@bic.mni.mcgill.ca> References: <4CAF2719.2080409@bic.mni.mcgill.ca> Message-ID: Thanks Laurence! Yes, i meant the .mnc files. But i can't find the marching_cubes....i'm running Ubuntu 10.04, and installed the ".deb" packages from the site, but there's no marching cubes files. Did i do something wrong, or do I need something else? Thanks again. Claudio 2010/10/8 Laurence Mercier > Do you mean labels? Tags are just point coordinates. > > To transform a label (.mnc) into a 3D surface (.obj) you can use > marching_cubes > > Laurence > > > On 10/8/2010 10:05 AM, Cl?udio Vin?cius wrote: > >> Hello everyone! I'm been using Minc for a couple weeks, and I have a >> doubt: >> Is there a way to convert the a .tag file from a segmented region directly >> to a .obj polygon, without using the "Display" interface(create surface)? >> I >> have lots of .tags and it would take me too much time to convert them all >> manually. >> Thanks! >> Claudio V.C >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > -- > Laurence Mercier > McConnell Brain Imaging Center > Montreal Neurological Institute, room: WB-320 > 3801 University St > Montreal (QC), H3A 2B4 > CANADA > > Office Phone: +1 514.398.1573 > Office FAX: +1 514.398.2975 > Web: http://www.bic.mni.mcgill.ca/~laurence > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From laurence at bic.mni.mcgill.ca Fri Oct 8 13:37:30 2010 From: laurence at bic.mni.mcgill.ca (Laurence Mercier) Date: Fri, 08 Oct 2010 13:37:30 -0400 Subject: [MINC-users] Automatic converting .tag to .obj In-Reply-To: References: <4CAF2719.2080409@bic.mni.mcgill.ca> Message-ID: <4CAF56DA.70806@bic.mni.mcgill.ca> marching_cubes seems to be in the standard minc package, but I am sorry I can't help you with that, I never installed the minc package myself. I am sure others will have the answer to this though. Laurence On 10/8/2010 1:31 PM, Cl?udio Vin?cius wrote: > Thanks Laurence! Yes, i meant the .mnc files. > But i can't find the marching_cubes....i'm running Ubuntu 10.04, and > installed the ".deb" packages from the site, but there's no marching cubes > files. Did i do something wrong, or do I need something else? > Thanks again. > Claudio > > 2010/10/8 Laurence Mercier > >> Do you mean labels? Tags are just point coordinates. >> >> To transform a label (.mnc) into a 3D surface (.obj) you can use >> marching_cubes >> >> Laurence >> >> >> On 10/8/2010 10:05 AM, Cl?udio Vin?cius wrote: >> >>> Hello everyone! I'm been using Minc for a couple weeks, and I have a >>> doubt: >>> Is there a way to convert the a .tag file from a segmented region directly >>> to a .obj polygon, without using the "Display" interface(create surface)? >>> I >>> have lots of .tags and it would take me too much time to convert them all >>> manually. >>> Thanks! >>> Claudio V.C >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >> >> >> -- >> Laurence Mercier >> McConnell Brain Imaging Center >> Montreal Neurological Institute, room: WB-320 >> 3801 University St >> Montreal (QC), H3A 2B4 >> CANADA >> >> Office Phone: +1 514.398.1573 >> Office FAX: +1 514.398.2975 >> Web: http://www.bic.mni.mcgill.ca/~laurence >> >> _______________________________________________ >> 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 -- Laurence Mercier McConnell Brain Imaging Center Montreal Neurological Institute, room: WB-320 3801 University St Montreal (QC), H3A 2B4 CANADA Office Phone: +1 514.398.1573 Office FAX: +1 514.398.2975 Web: http://www.bic.mni.mcgill.ca/~laurence From laurence at bic.mni.mcgill.ca Fri Oct 8 14:15:25 2010 From: laurence at bic.mni.mcgill.ca (Laurence Mercier) Date: Fri, 08 Oct 2010 14:15:25 -0400 Subject: [MINC-users] Automatic converting .tag to .obj In-Reply-To: References: <4CAF2719.2080409@bic.mni.mcgill.ca> Message-ID: <4CAF5FBD.7080808@bic.mni.mcgill.ca> Claudio, Vlad just gave the answer you were looking for: to have marching_cubes you need to install the minc package called: conglomerate. Laurence On 10/8/2010 1:31 PM, Cl?udio Vin?cius wrote: > Thanks Laurence! Yes, i meant the .mnc files. > But i can't find the marching_cubes....i'm running Ubuntu 10.04, and > installed the ".deb" packages from the site, but there's no marching cubes > files. Did i do something wrong, or do I need something else? > Thanks again. > Claudio > > 2010/10/8 Laurence Mercier > >> Do you mean labels? Tags are just point coordinates. >> >> To transform a label (.mnc) into a 3D surface (.obj) you can use >> marching_cubes >> >> Laurence >> >> >> On 10/8/2010 10:05 AM, Cl?udio Vin?cius wrote: >> >>> Hello everyone! I'm been using Minc for a couple weeks, and I have a >>> doubt: >>> Is there a way to convert the a .tag file from a segmented region directly >>> to a .obj polygon, without using the "Display" interface(create surface)? >>> I >>> have lots of .tags and it would take me too much time to convert them all >>> manually. >>> Thanks! >>> Claudio V.C >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >> >> >> -- >> Laurence Mercier >> McConnell Brain Imaging Center >> Montreal Neurological Institute, room: WB-320 >> 3801 University St >> Montreal (QC), H3A 2B4 >> CANADA >> >> Office Phone: +1 514.398.1573 >> Office FAX: +1 514.398.2975 >> Web: http://www.bic.mni.mcgill.ca/~laurence >> >> _______________________________________________ >> 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 -- Laurence Mercier McConnell Brain Imaging Center Montreal Neurological Institute, room: WB-320 3801 University St Montreal (QC), H3A 2B4 CANADA Office Phone: +1 514.398.1573 Office FAX: +1 514.398.2975 Web: http://www.bic.mni.mcgill.ca/~laurence From sylvain at bic.mni.mcgill.ca Fri Oct 8 14:18:43 2010 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Fri, 8 Oct 2010 14:18:43 -0400 (EDT) Subject: [MINC-users] Automatic converting .tag to .obj In-Reply-To: <4CAF56DA.70806@bic.mni.mcgill.ca> References: <4CAF2719.2080409@bic.mni.mcgill.ca> <4CAF56DA.70806@bic.mni.mcgill.ca> Message-ID: it is part of the conglomerate package. On Fri, 8 Oct 2010, Laurence Mercier wrote: > marching_cubes seems to be in the standard minc package, but I am sorry I > can't help you with that, I never installed the minc package myself. > > I am sure others will have the answer to this though. > > Laurence > > On 10/8/2010 1:31 PM, Cl?udio Vin?cius wrote: >> Thanks Laurence! Yes, i meant the .mnc files. >> But i can't find the marching_cubes....i'm running Ubuntu 10.04, and >> installed the ".deb" packages from the site, but there's no marching cubes >> files. Did i do something wrong, or do I need something else? >> Thanks again. >> Claudio >> >> 2010/10/8 Laurence Mercier >> >>> Do you mean labels? Tags are just point coordinates. >>> >>> To transform a label (.mnc) into a 3D surface (.obj) you can use >>> marching_cubes >>> >>> Laurence >>> >>> >>> On 10/8/2010 10:05 AM, Cl?udio Vin?cius wrote: >>> >>>> Hello everyone! I'm been using Minc for a couple weeks, and I have a >>>> doubt: >>>> Is there a way to convert the a .tag file from a segmented region >>>> directly >>>> to a .obj polygon, without using the "Display" interface(create surface)? >>>> I >>>> have lots of .tags and it would take me too much time to convert them all >>>> manually. >>>> Thanks! >>>> Claudio V.C >>>> _______________________________________________ >>>> MINC-users at bic.mni.mcgill.ca >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>> >>> >>> >>> -- >>> Laurence Mercier >>> McConnell Brain Imaging Center >>> Montreal Neurological Institute, room: WB-320 >>> 3801 University St >>> Montreal (QC), H3A 2B4 >>> CANADA >>> >>> Office Phone: +1 514.398.1573 >>> Office FAX: +1 514.398.2975 >>> Web: >>> http://www.bic.mni.mcgill.ca/~laurence >>> >>> _______________________________________________ >>> 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 > > > -- > Laurence Mercier > McConnell Brain Imaging Center > Montreal Neurological Institute, room: WB-320 > 3801 University St > Montreal (QC), H3A 2B4 > CANADA > > Office Phone: +1 514.398.1573 > Office FAX: +1 514.398.2975 > Web: http://www.bic.mni.mcgill.ca/~laurence > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (bicadmin at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 104 Montreal, Qc., H2W 1S4 From ocustom at gmail.com Fri Oct 8 17:41:04 2010 From: ocustom at gmail.com (=?ISO-8859-1?Q?Cl=E1udio_Vin=EDcius?=) Date: Fri, 8 Oct 2010 18:41:04 -0300 Subject: [MINC-users] Automatic converting .tag to .obj In-Reply-To: References: <4CAF2719.2080409@bic.mni.mcgill.ca> <4CAF56DA.70806@bic.mni.mcgill.ca> Message-ID: Thank you all really much, it worked! You saved me a lot of time =D 2010/10/8 Sylvain Milot > > > it is part of the conglomerate package. > > > > On Fri, 8 Oct 2010, Laurence Mercier wrote: > > marching_cubes seems to be in the standard minc package, but I am sorry I >> can't help you with that, I never installed the minc package myself. >> >> I am sure others will have the answer to this though. >> >> Laurence >> >> On 10/8/2010 1:31 PM, Cl?udio Vin?cius wrote: >> >>> Thanks Laurence! Yes, i meant the .mnc files. >>> But i can't find the marching_cubes....i'm running Ubuntu 10.04, and >>> installed the ".deb" packages from the site, but there's no marching >>> cubes >>> files. Did i do something wrong, or do I need something else? >>> Thanks again. >>> Claudio >>> >>> 2010/10/8 Laurence Mercier >>> >>> Do you mean labels? Tags are just point coordinates. >>>> >>>> To transform a label (.mnc) into a 3D surface (.obj) you can use >>>> marching_cubes >>>> >>>> Laurence >>>> >>>> >>>> On 10/8/2010 10:05 AM, Cl?udio Vin?cius wrote: >>>> >>>> Hello everyone! I'm been using Minc for a couple weeks, and I have a >>>>> doubt: >>>>> Is there a way to convert the a .tag file from a segmented region >>>>> directly >>>>> to a .obj polygon, without using the "Display" interface(create >>>>> surface)? >>>>> I >>>>> have lots of .tags and it would take me too much time to convert them >>>>> all >>>>> manually. >>>>> Thanks! >>>>> Claudio V.C >>>>> _______________________________________________ >>>>> MINC-users at bic.mni.mcgill.ca >>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>> >>>>> >>>> >>>> -- >>>> Laurence Mercier >>>> McConnell Brain Imaging Center >>>> Montreal Neurological Institute, room: WB-320 >>>> 3801 University St >>>> Montreal (QC), H3A 2B4 >>>> CANADA >>>> >>>> Office Phone: +1 514.398.1573 >>>> Office FAX: +1 514.398.2975 >>>> Web: http://www.bic.mni.mcgill.ca/~laurence >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >> >> >> -- >> Laurence Mercier >> McConnell Brain Imaging Center >> Montreal Neurological Institute, room: WB-320 >> 3801 University St >> Montreal (QC), H3A 2B4 >> CANADA >> >> Office Phone: +1 514.398.1573 >> Office FAX: +1 514.398.2975 >> Web: http://www.bic.mni.mcgill.ca/~laurence >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> > --- > Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (bicadmin at bic.mni.mcgill.ca) > Brain Imaging Centre > Montreal Neurological Institute > 3801 University Street > Webster 2B, Room 206 > Montreal, Qc., Canada, H3A 2B4 > Phone : (514) 398-4965, Fax: 398-8948 > Mobile : (514) 712-1768 > Office : 527 Av Des Pins O., Room 104 > Montreal, Qc., H2W 1S4 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From jason at phenogenomics.ca Mon Oct 11 09:29:03 2010 From: jason at phenogenomics.ca (Jason Lerch) Date: Mon, 11 Oct 2010 09:29:03 -0400 Subject: [MINC-users] Automatic converting .tag to .obj In-Reply-To: <4CAF2719.2080409@bic.mni.mcgill.ca> References: Message-ID: A bit of a delayed answer, but isn't the command you want 'tags_to_spheres' - that takes a tag file as an input and creates an obj file with a sphere at each tag (and you can specify the radius and number of triangles as an option). Jason On 2010-10-08, at 10:13 AM, Laurence Mercier wrote: > Do you mean labels? Tags are just point coordinates. > > To transform a label (.mnc) into a 3D surface (.obj) you can use marching_cubes > > Laurence > > On 10/8/2010 10:05 AM, Cl?udio Vin?cius wrote: >> Hello everyone! I'm been using Minc for a couple weeks, and I have a doubt: >> Is there a way to convert the a .tag file from a segmented region directly >> to a .obj polygon, without using the "Display" interface(create surface)? I >> have lots of .tags and it would take me too much time to convert them all >> manually. >> Thanks! >> Claudio V.C >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > -- > Laurence Mercier > McConnell Brain Imaging Center > Montreal Neurological Institute, room: WB-320 > 3801 University St > Montreal (QC), H3A 2B4 > CANADA > > Office Phone: +1 514.398.1573 > Office FAX: +1 514.398.2975 > Web: http://www.bic.mni.mcgill.ca/~laurence > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From mishkind at gmail.com Thu Oct 14 13:47:12 2010 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Thu, 14 Oct 2010 13:47:12 -0400 Subject: [MINC-users] minc tools crash in matlab In-Reply-To: References: <6fe841c71002240546u6be7050cje8e7639232bae092@mail.gmail.com> Message-ID: Just revisiting an old topic because I ran into the same problems. I can confirm that Alex's suggestion works For those with less technical skills here is what I did: cd /lab1/matlab/2009b/bin/glnxa64 mkdir bak mv libnectcdf* bak/ ln -s /usr/lib/libnetcdff.so.4.0.0 ln -s libnetcdff.so.4.0.0 libnetcdf.so.4 ln -s libnetcdf.so.4.0.0 libnetcdf.so Now things liks system('mincinfo') work fine. I still had a problem with the emma tools though, and the culprit was unix.m that came with emma 0.9.9 I changed /lab1/matlab/2009b/toolbox/emma/unix.m from function [stat,output] = unix(command) [output, stat] = system(command); To function [stat,output] = unix(command) [stat,output] = system(command); Not sure why I'm the only person to ever come across this problem.... mishkin On Sat, Feb 27, 2010 at 7:34 AM, Andrew Janke wrote: > Hi Pierre, > > I'm with Alex on this one, the fault would seem to be on the MATLAB > side as I attempt to follow the debian/ubuntu rules when making my > packages. ?I too wonder why MATLAB needs netcdf and would go with the > plan of attempting to replace MATLAB's version of netcdf with the > ubuntu version. > > Or just use octave. :) > > > -- > Andrew Janke > (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia ? ?+61 (402) 700 883 > > > On Thu, Feb 25, 2010 at 01:38, Alex Zijdenbos wrote: >> Hi Pierre, >> >> What does matlab need netcdf for? You may want to try to make matlab >> use the netcdf lib that you want, by putting a symlink in place of >> matlab's netcdf lib pointing to /usr/local/libnetcdf.so.4. A bit of a >> crude hack but hey, it might work :) > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Thu Oct 14 14:11:47 2010 From: vladimir.fonov at gmail.com (Vladimir FONOV) Date: Thu, 14 Oct 2010 14:11:47 -0400 Subject: [MINC-users] minc tools crash in matlab In-Reply-To: References: <6fe841c71002240546u6be7050cje8e7639232bae092@mail.gmail.com> Message-ID: <4CB747E3.1050109@gmail.com> Hello, Mishkin Derakhshan wrote: > > I still had a problem with the emma tools though, and the culprit was > unix.m that came with emma 0.9.9 > I changed /lab1/matlab/2009b/toolbox/emma/unix.m from > > function [stat,output] = unix(command) > [output, stat] = system(command); > > To > > function [stat,output] = unix(command) > [stat,output] = system(command); > > > Not sure why I'm the only person to ever come across this problem.... I found the problem a long time ago, but there is no official support for EMMA anymore, so my changes never made it into the official tree. Also I found that an odd behaviour of system command adding extra new lines in the output depends on the combination of Matlab version and the linux kernel somehow. > > mishkin > > On Sat, Feb 27, 2010 at 7:34 AM, Andrew Janke wrote: >> Hi Pierre, >> >> I'm with Alex on this one, the fault would seem to be on the MATLAB >> side as I attempt to follow the debian/ubuntu rules when making my >> packages. I too wonder why MATLAB needs netcdf and would go with the >> plan of attempting to replace MATLAB's version of netcdf with the >> ubuntu version. >> >> Or just use octave. :) >> >> >> -- >> Andrew Janke >> (a.janke at gmail.com || http://a.janke.googlepages.com/) >> Canberra->Australia +61 (402) 700 883 >> >> >> On Thu, Feb 25, 2010 at 01:38, Alex Zijdenbos wrote: >>> Hi Pierre, >>> >>> What does matlab need netcdf for? You may want to try to make matlab >>> use the netcdf lib that you want, by putting a symlink in place of >>> matlab's netcdf lib pointing to /usr/local/libnetcdf.so.4. A bit of a >>> crude hack but hey, it might work :) >> _______________________________________________ >> 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 ~ v.s.fonov ilmarin.info From claude at bic.mni.mcgill.ca Thu Oct 14 14:51:12 2010 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Thu, 14 Oct 2010 14:51:12 -0400 Subject: [MINC-users] minc tools crash in matlab In-Reply-To: <4CB747E3.1050109@gmail.com> Message-ID: <201010141851.o9EIpCh6013152@cassio.bic.mni.mcgill.ca> Mishkin and Vlad, I placed emma-1.0.0 in BIC packages. It's not because the package wasn't there that it didn't exist. I made those changes back in Feb 2010. The changes are also in CVS. Release 1.0.0 ------------- * Remove unix.m which is likely an obsolete and faulty implementation of a wrapper to call a unix command. Use the one provided by matlab. This was causing a segmentation fault in 64 bits. * Remove obsolete -m486 optimization compiler flag for Linux. Go for simplicity, ignore machine specific optimizations. Claude > Hello, > > Mishkin Derakhshan wrote: > > > > I still had a problem with the emma tools though, and the culprit was > > unix.m that came with emma 0.9.9 > > I changed /lab1/matlab/2009b/toolbox/emma/unix.m from > > > > function [stat,output] = unix(command) > > [output, stat] = system(command); > > > > To > > > > function [stat,output] = unix(command) > > [stat,output] = system(command); > > > > > > Not sure why I'm the only person to ever come across this problem.... > > > I found the problem a long time ago, but there is no official support > for EMMA anymore, so my changes never made it into the official tree. > Also I found that an odd behaviour of system command adding extra new > lines in the output depends on the combination of Matlab version and the > linux kernel somehow. > > > > > > mishkin > > > > On Sat, Feb 27, 2010 at 7:34 AM, Andrew Janke wrote: > >> Hi Pierre, > >> > >> I'm with Alex on this one, the fault would seem to be on the MATLAB > >> side as I attempt to follow the debian/ubuntu rules when making my > >> packages. I too wonder why MATLAB needs netcdf and would go with the > >> plan of attempting to replace MATLAB's version of netcdf with the > >> ubuntu version. > >> > >> Or just use octave. :) > >> > >> > >> -- > >> Andrew Janke > >> (a.janke at gmail.com || http://a.janke.googlepages.com/) > >> Canberra->Australia +61 (402) 700 883 > >> > >> > >> On Thu, Feb 25, 2010 at 01:38, Alex Zijdenbos wrote: > >>> Hi Pierre, > >>> > >>> What does matlab need netcdf for? You may want to try to make matlab > >>> use the netcdf lib that you want, by putting a symlink in place of > >>> matlab's netcdf lib pointing to /usr/local/libnetcdf.so.4. A bit of a > >>> crude hack but hey, it might work :) > >> _______________________________________________ > >> 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 ~ v.s.fonov ilmarin.info > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From assemlal at bic.mni.mcgill.ca Thu Oct 14 15:00:34 2010 From: assemlal at bic.mni.mcgill.ca (Haz-Edine Assemlal - L. Collins Lab) Date: Thu, 14 Oct 2010 15:00:34 -0400 (EDT) Subject: [MINC-users] Details on MINC2 data storage Message-ID: Dear MINC users, I am currently writing a plugin for the CImg library (http://cimg.sourceforge.net/) to save and load MINC2 files. It works well only under specific conditions, as it seems that the ordering of the MINC image data depends on which dimension has the biggest value. For example, an 513x512 image won't be stored the same way as a 512x513 image. Is it an expected behavior ? Best, Haz-Edine From a.janke at gmail.com Thu Oct 14 19:08:08 2010 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 15 Oct 2010 10:08:08 +1100 Subject: [MINC-users] Details on MINC2 data storage In-Reply-To: References: Message-ID: Hi, Yes, I would say this is at least not unexpected. :) Are you using the HDF5 libraries for your plugin or the MINC libraries? or are you attempting to write your own MINC reader? Andrew On Fri, Oct 15, 2010 at 06:00, Haz-Edine Assemlal - L. Collins Lab wrote: > Dear MINC users, > > I am currently writing a plugin for the CImg library > (http://cimg.sourceforge.net/) to save and load MINC2 files. It works well > only under specific conditions, as it seems that the ordering of the MINC > image data depends on which dimension has the biggest value. > > For example, an 513x512 image won't be stored the same way as a 512x513 > image. > > Is it an expected behavior ? > > Best, > Haz-Edine > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Oct 14 23:04:16 2010 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 15 Oct 2010 14:04:16 +1100 Subject: [MINC-users] mincaverage gives float numbers for integers In-Reply-To: References: Message-ID: Hi Ji, Sorry I seemed to have missed replying to this post but in case you don't have an answer to this yet, here goes. I am guessing that your original image will be either in short or byte format (use 'mincinfo' to determine this). What this means is that the entire image range of your file will be stored in byte or short format, the actual range of the image will then be mapped onto this range. So this will cause some of the issues that you are seeing. to make it more interesting, register and Display both first map your volume to byte (0-255) when reading them in so the values to read off Display and register will only have byte precision. This is the more likely cause of the discrepancy you are seeing. In order to get the real values and not just the display/register value you should use a C/L tool such as mincextract. If you really do want to preserve absolute values, your best bet is to convert the volume to float first and then back to short/byte when you are done. mincreshape -float in.mnc out.mnc Should take care of this for you. In the meantime the values you are seeing may well still be fine if you are using them with mincstats if you use the -mask_binvale option. This will assume that anything between 0.5 and 1.5 is 1 for example. Andrew On Thu, Sep 16, 2010 at 09:49, Ji Hyum KO wrote: > Hi, > > What I am trying to do is to combind masks (segmented) that are in five > seperate volume. > So, volume 1 has grey matter, volume 2 has white matter, volume 3 has > striatum, etc... > > Each volume do not have overlapping voxels. > > In order to give different integer values, I multiplied the masks with 1, 2, > 3, 4 or 5. > Then, mincaverage all volume, then mincmath -mult -const 5... > > The resulted image has weird float values such as 2.0252... > > How can I make them clean integer values like 2.000000 > > Best, > > Ji Hyun > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From alex at bic.mni.mcgill.ca Thu Oct 14 23:31:45 2010 From: alex at bic.mni.mcgill.ca (Alex Zijdenbos) Date: Thu, 14 Oct 2010 23:31:45 -0400 Subject: [MINC-users] mincaverage gives float numbers for integers In-Reply-To: References:

Message-ID: [ I had sent this reply a while ago but I don't think it made it through to the list ] On Thu, Sep 23, 2010 at 6:41 AM, Alex Zijdenbos wrote: > Hello Ji Hyun, > > I am not sure if you got an answer already, but here is one: the > floating point values you are seeing are due to the value scaling that > MINC inherently does (in order to map the voxel value to the 'real' > value), which sometimes cause trouble with discrete (label) volumes > like the ones you have. You can usually fix this by removing the value > mapping using something like > > ? mincreshape -valid_range 0 255 -image_range 0 255 > > which will set the value mapping to the identity. > > As a second suggestion, you can do what you are trying to do with a > single minccalc cal, for instance like so: create a file containing > this expression: > > result=0; > for { i in [0:len(A)) } { > ? if (A[i] > 0.5) { result = i+1 } > }; > result > > and then call > > ? minccalc -expfile > ... > > Hope this helps, > > -- A > > On Wed, Sep 15, 2010 at 6:49 PM, Ji Hyum KO wrote: >> Hi, >> >> What I am trying to do is to combind masks (segmented) that are in five >> seperate volume. >> So, volume 1 has grey matter, volume 2 has white matter, volume 3 has >> striatum, etc... >> >> Each volume do not have overlapping voxels. >> >> In order to give different integer values, I multiplied the masks with 1, 2, >> 3, 4 or 5. >> Then, mincaverage all volume, then mincmath -mult -const 5... >> >> The resulted image has weird float values such as 2.0252... >> >> How can I make them clean integer values like 2.000000 >> >> Best, >> >> Ji Hyun >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> > From sorench at gmail.com Fri Oct 15 23:10:39 2010 From: sorench at gmail.com (Soren Christensen) Date: Sat, 16 Oct 2010 14:10:39 +1100 Subject: [MINC-users] mincresample of negative zsteps Message-ID: Hi, I have trouble understanding why I get a positive zstep when resampling like a file with a negative zstep: file: template.mnc image: unsigned short 0 to 65535 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 28 -5 -149 yspace 512 -0.46875 0 xspace 512 -0.46875 0 file: to_be_resampled.mnc image: unsigned byte 0 to 255 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 28 -5 -149 yspace 512 -0.46875 0 xspace 512 -0.46875 0 mincresample -like template.mnc to_be_resampled.mnc test.mnc Transforming slices:............................Done mincinfo test.mnc file: test.mnc image: unsigned byte 0 to 255 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 28 5 -149 yspace 512 -0.46875 0 xspace 512 -0.46875 0 The effect of this seems to be that the resampling is done outside of the volume of to_be_resampled.mnc and I get an empty image as result. Can anyone see what is happening? Thanks, Soren From ocustom at gmail.com Sat Oct 16 13:29:32 2010 From: ocustom at gmail.com (=?ISO-8859-1?Q?Cl=E1udio_Vin=EDcius?=) Date: Sat, 16 Oct 2010 14:29:32 -0300 Subject: [MINC-users] Automatic converting .tag to .obj In-Reply-To: References: <4CAF2719.2080409@bic.mni.mcgill.ca> Message-ID: Hello again...I have another question,hope it is fine to use the same subject. A friend is trying to run INSECT, from classify, but we get the error: "Error while loading shared libraries: libhdf5-1.6.6.so.0: cannot open shared object file: No such file or directory" As far as I know, the latest hdf package is the libhdf5-1.8, which he has installed...does anybody know how to fix it? Thanks! Cl?udio Ps: Jason, i haven't tried tag_to_spheres yet, i'll try it later and compare with what i got. Thank you. 2010/10/11 Jason Lerch > A bit of a delayed answer, but isn't the command you want 'tags_to_spheres' > - that takes a tag file as an input and creates an obj file with a sphere at > each tag (and you can specify the radius and number of triangles as an > option). > > Jason > > On 2010-10-08, at 10:13 AM, Laurence Mercier wrote: > > > Do you mean labels? Tags are just point coordinates. > > > > To transform a label (.mnc) into a 3D surface (.obj) you can use > marching_cubes > > > > Laurence > > > > On 10/8/2010 10:05 AM, Cl?udio Vin?cius wrote: > >> Hello everyone! I'm been using Minc for a couple weeks, and I have a > doubt: > >> Is there a way to convert the a .tag file from a segmented region > directly > >> to a .obj polygon, without using the "Display" interface(create > surface)? I > >> have lots of .tags and it would take me too much time to convert them > all > >> manually. > >> Thanks! > >> Claudio V.C > >> _______________________________________________ > >> MINC-users at bic.mni.mcgill.ca > >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > -- > > Laurence Mercier > > McConnell Brain Imaging Center > > Montreal Neurological Institute, room: WB-320 > > 3801 University St > > Montreal (QC), H3A 2B4 > > CANADA > > > > Office Phone: +1 514.398.1573 > > Office FAX: +1 514.398.2975 > > Web: http://www.bic.mni.mcgill.ca/~laurence > > > > _______________________________________________ > > 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 Wed Oct 20 01:02:13 2010 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 20 Oct 2010 15:02:13 +1000 Subject: [MINC-users] mincresample of negative zsteps In-Reply-To: References: Message-ID: Hi Soren, On Sat, Oct 16, 2010 at 13:10, Soren Christensen wrote: > ?I have trouble understanding why I get a positive zstep when > resampling like a file with a negative zstep: > > The effect of this seems to be that the resampling is done outside of > the volume of to_be_resampled.mnc and I get an empty image as result. > > Can anyone see what is happening? As of right now no. My initial guess is you are being bitten by the non-image dimension behavior. (search for -1 in man mincreshape) but I am not sure if this is the case. Do the files have direction cosines? a From a.janke at gmail.com Wed Oct 20 01:50:48 2010 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 20 Oct 2010 15:50:48 +1000 Subject: [MINC-users] Debian Lenny packages now available. Message-ID: Hi all, I have had a debian lenny machine foisted upon me so decided to build some packages: http://packages.bic.mni.mcgill.ca/debian-lenny/ Have fun. Andrew From alfredojca at gmail.com Wed Oct 20 06:36:15 2010 From: alfredojca at gmail.com (alfredo jose costa abreu) Date: Wed, 20 Oct 2010 08:36:15 -0200 Subject: [MINC-users] Gray levels Message-ID: hi I wonder how do I know the levels of gray of each point of the image? I would like to have as output a file with the gray levels of each point. thanks From a.janke at gmail.com Wed Oct 20 07:53:33 2010 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 20 Oct 2010 21:53:33 +1000 Subject: [MINC-users] Gray levels In-Reply-To: References: Message-ID: Hi Alfredo, If you mean the real image values then what you want is mincextract. You can specify where you want the values to be extracted from with the -start and -count options. So, for example to extract the value at voxel position 35,60,80 in an zyx oriented file you would do this: mincextract -ascii -nonormalize -start 80,60,35 -count 1,1,1 The values will be output to STDOUT. Andrew On Wed, Oct 20, 2010 at 20:36, alfredo jose costa abreu wrote: > hi > I wonder how do I know the levels of gray of each point of the image? > I would like to have as output a file with the gray levels of each point. > > thanks > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Oct 21 02:32:17 2010 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 21 Oct 2010 16:32:17 +1000 Subject: [MINC-users] Ubuntu Maverick Packages available. Message-ID: Here: http://packages.bic.mni.mcgill.ca/ubuntu-maverick/ Note that these are the first binary release of MINC 2.1 that is linked against HDF1.8.x, a bit of a milestone and now possible given that HDF 1.8 is becoming the default in new distributions. Andrew From assemlal at bic.mni.mcgill.ca Thu Oct 21 11:05:25 2010 From: assemlal at bic.mni.mcgill.ca (Haz-Edine Assemlal - L. Collins Lab) Date: Thu, 21 Oct 2010 11:05:25 -0400 (EDT) Subject: [MINC-users] MacOS-X MINC 2.1 Message-ID: Hi everyone, I have updated the MacPort of MINC 2.1 so it compiles fine on Snow Leopard. The corresponding Portfile is attached in this email. Best, Haz-Edine -------------- next part -------------- # $Id: Portfile 56061 2009-08-24 00:33:19Z ryandesign at macports.org $ PortSystem 1.0 name minc version 2.1.00 categories science platforms darwin maintainers mac.com:mhough description This package contains tools to manipulate MINC files. long_description The Minc file format is a highly flexible medical image file format built on top of the NetCDF generalized data format. The format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. On top of the libraries is a suite of generic image-file manipulation tools. The format, libraries and tools are designed for use in a medical-imaging research environment: they are simple and powerful and make no attempt to provide a pretty interface to users. homepage http://www.bic.mni.mcgill.ca/software/ master_sites ${homepage}/distribution/packages/ \ http://packages.bic.mni.mcgill.ca/tgz/ checksums md5 1ef2402abc8f49d870d9f610eb5ad4c8 depends_lib port:netcdf port:hdf5-18 platform darwin 8 { patchfiles patch-time.c } configure.args --with-build-path="${prefix}" --mandir=${prefix}/share/man From mishkind at gmail.com Fri Oct 29 17:57:18 2010 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Fri, 29 Oct 2010 17:57:18 -0400 Subject: [MINC-users] Ubuntu Maverick Packages available. In-Reply-To: References: Message-ID: Hi Andrew, Just upgraded to 10.10 on my 32bit thinkpad, but ran into a problem when installing minc. Here are the steps I took and error msgs: 1. Added this to /etc/apt/sources.list deb http://packages.bic.mni.mcgill.ca/ubuntu-maverick ./ 2.mishkin at thinkpad:~$ sudo apt-get install minc [sudo] password for mishkin: Reading package lists... Done Building dependency tree Reading state information... Done Package minc is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source E: Package 'minc' has no installation candidate 3. mishkin at thinkpad:~$ sudo apt-get install mincbundle Reading package lists... Done Building dependency tree Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: mincbundle : Depends: minc but it is not installable Depends: glim-image but it is not installable Depends: mincblob but it is not installable Depends: mincdti but it is not installable Depends: mincfft but it is not installable Depends: mincmorph but it is not installable Depends: mincregress but it is not installable Depends: mincsample but it is not installable Depends: mrisim but it is not installable Depends: volperf but it is not installable Depends: volregrid but it is not installable Depends: mni-autoreg but it is not installable Depends: mni-models-average305-lin but it is not installable Depends: mni-models-colin27-lin but it is not installable Depends: mni-models-icbm152-lin but it is not installable Depends: mni-models-icbm152-nl-2009 but it is not installable Depends: bicpl but it is not installable Depends: postf but it is not installable Depends: display but it is not installable Depends: register but it is not installable Depends: ray-trace but it is not installable Depends: ebtks but it is not installable Depends: classify but it is not installable Depends: inormalize but it is not installable Depends: n3 but it is not installable Depends: oobicpl but it is not installable Depends: bicinventor but it is not installable E: Broken packages On Thu, Oct 21, 2010 at 2:32 AM, Andrew Janke wrote: > Here: > > ? http://packages.bic.mni.mcgill.ca/ubuntu-maverick/ > > > Note that these are the first binary release of MINC 2.1 that is > linked against HDF1.8.x, a bit of a milestone and now possible given > that HDF 1.8 is becoming the default in new distributions. > > > Andrew > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >