From a.janke at gmail.com Thu Oct 4 22:51:23 2007 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 5 Oct 2007 12:51:23 +1000 Subject: [MINC-users] MINC 2.0.13 In-Reply-To: <20070919031520.GF6592@sumost.ca> References: <20070919031520.GF6592@sumost.ca> Message-ID: > > http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.13.tar.gz > > > > I would be willing to say that this is our first stable release of > > MINC2 (or at least more stable than previous versions!) > > That's good news. I'd like to package this version for Debian, either > alongside the current Debian minc package (version 1.5) or replacing > it. Good good. I guess I should start naming my packages on packages.bic.mni.mcgill.ca slightly differently to save collisions then.. > The library versioning, however, remains a problem. Packagers such as > Debian prefer to ship shared libraries. For this to work > successfully, the software must correctly version the shared libraries. > Since you're using libtool, you need only follow the rules outlined > in http://www.gnu.org/software/libtool/manual.html#Versioning, > specifically section 6.3. > > It would be helpful if the MINC maintainers would commit to following > this procedure. Is this possible? Possible, although I suspect the more deep-seated problem is that minc really needs to be split into libminc and minc-tools within CVS to make life easier I guess? I had thought that we were following libtool style versioning though? (from what I can read of that page you mention) or am I missing something? (likely). The other note of contention is that I presume you will be building shared versions of libminc whereas typically in the past everything has been static. Then to add another cat into the mix I have been working on a CMake (shudder) build of MINC for the ITK integration stuff and suffice to say I have found no easy way to sync the two build processes. :( It's hard enough to find any documentation on CMake out there without buying the book as it is so getting the thing to behave as I expect has proved problematic (make install,dist,distcheck etc). Do you have any thoughts on CMake steve? All those who use it seem to crow its praises over autoconf/make but from what I have seen of it so far it is easy(ish) to use but the lack of documentation and worked examples of how things should be done is slowing me up a lot. a a From atsuko at bic.mni.mcgill.ca Fri Oct 5 10:59:24 2007 From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano) Date: Fri, 5 Oct 2007 10:59:24 -0400 Subject: [MINC-users] transfer integer from MNI to native space Message-ID: <16761c140710050759p4d28a7fdi3b06d34ee080ee47@mail.gmail.com> Hello all, I have several ROIs with integers on one MNI space. Then I transferred the ROI.mnc into native space for each subject. However, all integer changed into several values. eg. MNI space: ROI A has the value of 33, Native space: ROI A has the value between 9 to 33. I guess it is because of smoothing. How can I get same value for each ROI in native space? Thank you, Atsuko From jason at bic.mni.mcgill.ca Fri Oct 5 10:52:20 2007 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Fri, 5 Oct 2007 10:52:20 -0400 Subject: [MINC-users] transfer integer from MNI to native space In-Reply-To: <16761c140710050759p4d28a7fdi3b06d34ee080ee47@mail.gmail.com> References: <16761c140710050759p4d28a7fdi3b06d34ee080ee47@mail.gmail.com> Message-ID: <47064FA4.30901@bic.mni.mcgill.ca> If you are using mincresample to transfer the values back into native space, try using 'mincresample -nearest_neighbour' Otherwise there was a discussion on the minc-development list a while back about label volumes, which I suspect applies. I've pasted one message (from Claude Lepage) below in case it helps. Jason ==== Hi, > > Correct, the way I have always done this is do a mincreshape to files > > that are misbehaving.. > > > > mincreshape -image_range 0 255 -valid_range 0 255 ... > This does not correct the problem if the min/max are set per slice and that they vary for each slice. Once a label file has been "decimalized" by the ranges, there is no way to recover the original values by the above operation. For example: Take a label = 10, with voxel value of 10 if there is a one-to-one correspondence with voxel range and image real. Now assume that the slice has a min=0 and a max=61. That's 62 values over a 256 range, so each bin has a value of 62/256=0.2421875. The label 10 will be best approximated by the 41th bin with value 41*0.2421 = 9.9297. (There might be some ajustment to do if the values are range-centered, but my argument is still valid.) Setting back max=255 for the slice will not recover the original label 10. Now keep doing this repeatedly (minccalc, mincmath, etc) and some labels will change value (10 drifts to 9, for example). The option -keep_real_range in mincresample does the trick as the global min/max of the image are applied to each slice, thus not changing the internal voxel values. minccalc (which uses voxel_loop as AJ pointed out) does not. Despite being ugly, I also think that working in floats might be the best compromise (on the temporary files, of course). Claude Atsuko Nagano wrote: > Hello all, > > I have several ROIs with integers on one MNI space. > Then I transferred the ROI.mnc into native space for each subject. > > However, all integer changed into several values. > eg. MNI space: ROI A has the value of 33, Native space: ROI A has the > value between 9 to 33. > > I guess it is because of smoothing. > How can I get same value for each ROI in native space? > > Thank you, > Atsuko > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From atsuko at bic.mni.mcgill.ca Fri Oct 5 11:34:00 2007 From: atsuko at bic.mni.mcgill.ca (Atsuko Nagano) Date: Fri, 5 Oct 2007 11:34:00 -0400 Subject: [MINC-users] transfer integer from MNI to native space In-Reply-To: <47064FA4.30901@bic.mni.mcgill.ca> References: <16761c140710050759p4d28a7fdi3b06d34ee080ee47@mail.gmail.com> <47064FA4.30901@bic.mni.mcgill.ca> Message-ID: <16761c140710050834k72924bf5jff63d8d470e7ae74@mail.gmail.com> Thank you Jason, It works well, and the value of each ROI is homogeneous now. However the value changes into integer to real number. eg. form 20 to 20.058 It occurs when I added -byte. Can I change all the values into integers again? Regards, Atsuko On 10/5/07, Jason Lerch wrote: > If you are using mincresample to transfer the values back into native > space, try using 'mincresample -nearest_neighbour' > > Otherwise there was a discussion on the minc-development list a while > back about label volumes, which I suspect applies. I've pasted one > message (from Claude Lepage) below in case it helps. > > Jason > > ==== > > Hi, > > > > > Correct, the way I have always done this is do a mincreshape to files > > > that are misbehaving.. > > > > > > mincreshape -image_range 0 255 -valid_range 0 255 ... > > > > This does not correct the problem if the min/max are set per slice and that > they vary for each slice. Once a label file has been "decimalized" by the > ranges, there is no way to recover the original values by the above > operation. > > For example: > Take a label = 10, with voxel value of 10 if there is a one-to-one > correspondence with voxel range and image real. Now assume that the slice > has a min=0 and a max=61. That's 62 values over a 256 range, so each bin > has a value of 62/256=0.2421875. The label 10 will be best approximated > by the 41th bin with value 41*0.2421 = 9.9297. (There might be some > ajustment to do if the values are range-centered, but my argument is still > valid.) Setting back max=255 for the slice will not recover the original > label 10. Now keep doing this repeatedly (minccalc, mincmath, etc) and > some labels will change value (10 drifts to 9, for example). > > The option -keep_real_range in mincresample does the trick as the global > min/max of the image are applied to each slice, thus not changing the > internal voxel values. minccalc (which uses voxel_loop as AJ pointed out) > does not. > > Despite being ugly, I also think that working in floats might be the best > compromise (on the temporary files, of course). > > Claude > > > > Atsuko Nagano wrote: > > Hello all, > > > > I have several ROIs with integers on one MNI space. > > Then I transferred the ROI.mnc into native space for each subject. > > > > However, all integer changed into several values. > > eg. MNI space: ROI A has the value of 33, Native space: ROI A has the > > value between 9 to 33. > > > > I guess it is because of smoothing. > > How can I get same value for each ROI in native space? > > > > Thank you, > > Atsuko > > _______________________________________________ > > 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 dfwang at cse.cuhk.edu.hk Mon Oct 8 04:35:02 2007 From: dfwang at cse.cuhk.edu.hk (Defeng WANG) Date: Mon, 8 Oct 2007 16:35:02 +0800 Subject: [MINC-users] convert mesh from VTK to .obj References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> Message-ID: <00a501c80986$22f86170$a459bd89@PC89164> Dear MINC Users, I have one mesh in VTK format at hand, and would like to convert it into the .obj format in MINC. Which tool can do this? Or any suggestions on the way to convert it? Many thanks! Defeng From se at hst.aau.dk Mon Oct 8 05:03:25 2007 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Mon, 08 Oct 2007 11:03:25 +0200 Subject: [MINC-users] convert mesh from VTK to .obj In-Reply-To: <00a501c80986$22f86170$a459bd89@PC89164> References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> Message-ID: <4709F25D.5030500@hst.aau.dk> Hi Defeng, If you're dealing with triangular mesh and pure ascii, you can try my small parser found here: 32bit linux: http://www.hst.aau.dk/~se/software/parse.bin 64bit linux: http://www.hst.aau.dk/~se/software/parse.bin64 Also, more information about the .obj format can be found here: http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles Simon Defeng WANG wrote: > Dear MINC Users, > > I have one mesh in VTK format at hand, and would like to convert it into the > .obj format in MINC. Which tool can do this? Or any suggestions on the way > to convert it? > > Many thanks! > Defeng > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From dfwang at cse.cuhk.edu.hk Mon Oct 8 05:20:16 2007 From: dfwang at cse.cuhk.edu.hk (dfwang@cse.cuhk.edu.hk) Date: Mon, 8 Oct 2007 17:20:16 +0800 Subject: [MINC-users] convert mesh from VTK to .obj In-Reply-To: <4709F25D.5030500@hst.aau.dk> References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> Message-ID: <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> Hi, Simon, Thanks for your reply. Yes, my VTK mesh is in triangular. My linux system is CentOS 4.4. I downloaded your small parser just now, and changed the mode by chmod a+x parse.bin then run parse.bin, I got the following error, Floating point exception Could you please tell me how I can run it successfully? Best wishes, Defeng Quoting Simon Fristed Eskildsen : > Hi Defeng, > > If you're dealing with triangular mesh and pure ascii, you can try my > small parser found here: > 32bit linux: http://www.hst.aau.dk/~se/software/parse.bin > 64bit linux: http://www.hst.aau.dk/~se/software/parse.bin64 > > Also, more information about the .obj format can be found here: > http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles > > Simon > > Defeng WANG wrote: > > Dear MINC Users, > > > > I have one mesh in VTK format at hand, and would like to convert it into > the > > .obj format in MINC. Which tool can do this? Or any suggestions on the way > > to convert it? > > > > Many thanks! > > Defeng > > > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From se at hst.aau.dk Mon Oct 8 08:54:07 2007 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Mon, 08 Oct 2007 14:54:07 +0200 Subject: [MINC-users] convert mesh from VTK to .obj In-Reply-To: <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> Message-ID: <470A286F.2020206@hst.aau.dk> Hi Defeng, parse.bin is compiled on a pentium4, and it works also on pentiumM. What CPU are you using? What is the output of cat /proc/cpuinfo uname -a strace ./parse.bin I have compiled it on a pentium3 as well. Maybe that works for you: http://www.hst.aau.dk/~se/software/parse.p3fc2 Simon dfwang at cse.cuhk.edu.hk wrote: > Hi, Simon, > > Thanks for your reply. Yes, my VTK mesh is in triangular. > > My linux system is CentOS 4.4. I downloaded your small parser just now, and > changed the mode by > > chmod a+x parse.bin > > then run parse.bin, I got the following error, > > Floating point exception > > Could you please tell me how I can run it successfully? > > Best wishes, > Defeng > Quoting Simon Fristed Eskildsen : > >> Hi Defeng, >> >> If you're dealing with triangular mesh and pure ascii, you can try my >> small parser found here: >> 32bit linux: http://www.hst.aau.dk/~se/software/parse.bin >> 64bit linux: http://www.hst.aau.dk/~se/software/parse.bin64 >> >> Also, more information about the .obj format can be found here: >> http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles >> >> Simon >> >> Defeng WANG wrote: >>> Dear MINC Users, >>> >>> I have one mesh in VTK format at hand, and would like to convert it into >> the >>> .obj format in MINC. Which tool can do this? Or any suggestions on the way >>> to convert it? >>> >>> Many thanks! >>> Defeng >>> >>> >>> _______________________________________________ >>> 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 dfwang at cse.cuhk.edu.hk Mon Oct 8 09:40:10 2007 From: dfwang at cse.cuhk.edu.hk (dfwang@cse.cuhk.edu.hk) Date: Mon, 8 Oct 2007 21:40:10 +0800 Subject: [MINC-users] convert mesh from VTK to .obj In-Reply-To: <470A286F.2020206@hst.aau.dk> References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> <470A286F.2020206@hst.aau.dk> Message-ID: <1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> Hi, Simon, My computer information is as follows, [dfwang at pc89164 ~]$ cat /proc/cpuinfo processor : 0 vendor_id : GenuineIntel cpu family : 15 model : 4 model name : Intel(R) Xeon(TM) CPU 3.00GHz stepping : 3 cpu MHz : 3001.815 cache size : 2048 KB fdiv_bug : no hlt_bug : no f00f_bug : no coma_bug : no fpu : yes fpu_exception : yes cpuid level : 5 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni monito r ds_cpl cid xtpr bogomips : 6004.11 processor : 1 vendor_id : GenuineIntel cpu family : 15 model : 4 model name : Intel(R) Xeon(TM) CPU 3.00GHz stepping : 3 cpu MHz : 3001.815 cache size : 2048 KB fdiv_bug : no hlt_bug : no f00f_bug : no coma_bug : no fpu : yes fpu_exception : yes cpuid level : 5 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni monito r ds_cpl cid xtpr bogomips : 5999.43 [dfwang at pc89164 data]$ uname -a Linux pc89164.cse.cuhk.edu.hk 2.6.9-55.0.9.ELsmp #1 SMP Thu Sep 27 18:27:41 EDT 2007 i686 i686 i386 GNU/Linux [dfwang at pc89164 data]$ strace ./parse.bin execve("./parse.bin", ["./parse.bin"], [/* 64 vars */]) = 0 uname({sys="Linux", node="pc89164.cse.cuhk.edu.hk", ...}) = 0 brk(0) = 0x9b99000 --- SIGFPE (Floating point exception) @ 0 (0) --- +++ killed by SIGFPE +++ Process 5227 detached Thanks a lot! Best wishes, Defeng Quoting Simon Fristed Eskildsen : > Hi Defeng, > > parse.bin is compiled on a pentium4, and it works also on pentiumM. > What CPU are you using? > What is the output of > cat /proc/cpuinfo > uname -a > strace ./parse.bin > > I have compiled it on a pentium3 as well. Maybe that works for you: > http://www.hst.aau.dk/~se/software/parse.p3fc2 > > Simon > > dfwang at cse.cuhk.edu.hk wrote: > > Hi, Simon, > > > > Thanks for your reply. Yes, my VTK mesh is in triangular. > > > > My linux system is CentOS 4.4. I downloaded your small parser just now, and > > changed the mode by > > > > chmod a+x parse.bin > > > > then run parse.bin, I got the following error, > > > > Floating point exception > > > > Could you please tell me how I can run it successfully? > > > > Best wishes, > > Defeng > > Quoting Simon Fristed Eskildsen : > > > >> Hi Defeng, > >> > >> If you're dealing with triangular mesh and pure ascii, you can try my > >> small parser found here: > >> 32bit linux: http://www.hst.aau.dk/~se/software/parse.bin > >> 64bit linux: http://www.hst.aau.dk/~se/software/parse.bin64 > >> > >> Also, more information about the .obj format can be found here: > >> http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles > >> > >> Simon > >> > >> Defeng WANG wrote: > >>> Dear MINC Users, > >>> > >>> I have one mesh in VTK format at hand, and would like to convert it into > >> the > >>> .obj format in MINC. Which tool can do this? Or any suggestions on the > way > >>> to convert it? > >>> > >>> Many thanks! > >>> Defeng > >>> > >>> > >>> _______________________________________________ > >>> 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 se at hst.aau.dk Tue Oct 9 04:52:13 2007 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Tue, 09 Oct 2007 10:52:13 +0200 Subject: [MINC-users] convert mesh from VTK to .obj In-Reply-To: <1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> <470A286F.2020206@hst.aau.dk> <1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> Message-ID: <470B413D.9030102@hst.aau.dk> Ok, you have a xeon cpu. Try my opteron version: http://www.hst.aau.dk/~se/software/parse.opteron_ub I think the binary should be compatible with the xeon architecture. But I'm wondering why the 32bit versions doesn't work on xeon. My P4 and P3 binaries work on opteron. Simon dfwang at cse.cuhk.edu.hk wrote: > Hi, Simon, > > My computer information is as follows, > > [dfwang at pc89164 ~]$ cat /proc/cpuinfo > processor : 0 > vendor_id : GenuineIntel > cpu family : 15 > model : 4 > model name : Intel(R) Xeon(TM) CPU 3.00GHz > stepping : 3 > cpu MHz : 3001.815 > cache size : 2048 KB > fdiv_bug : no > hlt_bug : no > f00f_bug : no > coma_bug : no > fpu : yes > fpu_exception : yes > cpuid level : 5 > wp : yes > flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat > pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni > monito r ds_cpl cid xtpr > bogomips : 6004.11 > > processor : 1 > vendor_id : GenuineIntel > cpu family : 15 > model : 4 > model name : Intel(R) Xeon(TM) CPU 3.00GHz > stepping : 3 > cpu MHz : 3001.815 > cache size : 2048 KB > fdiv_bug : no > hlt_bug : no > f00f_bug : no > coma_bug : no > fpu : yes > fpu_exception : yes > cpuid level : 5 > wp : yes > flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat > pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni > monito r ds_cpl cid xtpr > bogomips : 5999.43 > > [dfwang at pc89164 data]$ uname -a > Linux pc89164.cse.cuhk.edu.hk 2.6.9-55.0.9.ELsmp #1 SMP Thu Sep 27 18:27:41 EDT > 2007 i686 i686 i386 GNU/Linux > > > [dfwang at pc89164 data]$ strace ./parse.bin > execve("./parse.bin", ["./parse.bin"], [/* 64 vars */]) = 0 > uname({sys="Linux", node="pc89164.cse.cuhk.edu.hk", ...}) = 0 > brk(0) = 0x9b99000 > --- SIGFPE (Floating point exception) @ 0 (0) --- > +++ killed by SIGFPE +++ > Process 5227 detached > > > Thanks a lot! > > Best wishes, > Defeng > > > Quoting Simon Fristed Eskildsen : > >> Hi Defeng, >> >> parse.bin is compiled on a pentium4, and it works also on pentiumM. >> What CPU are you using? >> What is the output of >> cat /proc/cpuinfo >> uname -a >> strace ./parse.bin >> >> I have compiled it on a pentium3 as well. Maybe that works for you: >> http://www.hst.aau.dk/~se/software/parse.p3fc2 >> >> Simon >> >> dfwang at cse.cuhk.edu.hk wrote: >>> Hi, Simon, >>> >>> Thanks for your reply. Yes, my VTK mesh is in triangular. >>> >>> My linux system is CentOS 4.4. I downloaded your small parser just now, and >>> changed the mode by >>> >>> chmod a+x parse.bin >>> >>> then run parse.bin, I got the following error, >>> >>> Floating point exception >>> >>> Could you please tell me how I can run it successfully? >>> >>> Best wishes, >>> Defeng >>> Quoting Simon Fristed Eskildsen : >>> >>>> Hi Defeng, >>>> >>>> If you're dealing with triangular mesh and pure ascii, you can try my >>>> small parser found here: >>>> 32bit linux: http://www.hst.aau.dk/~se/software/parse.bin >>>> 64bit linux: http://www.hst.aau.dk/~se/software/parse.bin64 >>>> >>>> Also, more information about the .obj format can be found here: >>>> http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles >>>> >>>> Simon >>>> >>>> Defeng WANG wrote: >>>>> Dear MINC Users, >>>>> >>>>> I have one mesh in VTK format at hand, and would like to convert it into >>>> the >>>>> .obj format in MINC. Which tool can do this? Or any suggestions on the >> way >>>>> to convert it? >>>>> >>>>> Many thanks! >>>>> Defeng >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 se at hst.aau.dk Tue Oct 9 06:20:42 2007 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Tue, 09 Oct 2007 12:20:42 +0200 Subject: [MINC-users] convert mesh from VTK to .obj In-Reply-To: <1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> <470A286F.2020206@hst.aau.dk> <1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> Message-ID: <470B55FA.3060606@hst.aau.dk> Did you try the P3 version? http://www.hst.aau.dk/~se/software/parse.p3fc2 It should be compatible whether you run 32 or 64 bit xeon. Simon dfwang at cse.cuhk.edu.hk wrote: > Hi, Simon, > > My computer information is as follows, > > [dfwang at pc89164 ~]$ cat /proc/cpuinfo > processor : 0 > vendor_id : GenuineIntel > cpu family : 15 > model : 4 > model name : Intel(R) Xeon(TM) CPU 3.00GHz > stepping : 3 > cpu MHz : 3001.815 > cache size : 2048 KB > fdiv_bug : no > hlt_bug : no > f00f_bug : no > coma_bug : no > fpu : yes > fpu_exception : yes > cpuid level : 5 > wp : yes > flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat > pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni > monito r ds_cpl cid xtpr > bogomips : 6004.11 > > processor : 1 > vendor_id : GenuineIntel > cpu family : 15 > model : 4 > model name : Intel(R) Xeon(TM) CPU 3.00GHz > stepping : 3 > cpu MHz : 3001.815 > cache size : 2048 KB > fdiv_bug : no > hlt_bug : no > f00f_bug : no > coma_bug : no > fpu : yes > fpu_exception : yes > cpuid level : 5 > wp : yes > flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat > pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni > monito r ds_cpl cid xtpr > bogomips : 5999.43 > > [dfwang at pc89164 data]$ uname -a > Linux pc89164.cse.cuhk.edu.hk 2.6.9-55.0.9.ELsmp #1 SMP Thu Sep 27 18:27:41 EDT > 2007 i686 i686 i386 GNU/Linux > > > [dfwang at pc89164 data]$ strace ./parse.bin > execve("./parse.bin", ["./parse.bin"], [/* 64 vars */]) = 0 > uname({sys="Linux", node="pc89164.cse.cuhk.edu.hk", ...}) = 0 > brk(0) = 0x9b99000 > --- SIGFPE (Floating point exception) @ 0 (0) --- > +++ killed by SIGFPE +++ > Process 5227 detached > > > Thanks a lot! > > Best wishes, > Defeng > > > Quoting Simon Fristed Eskildsen : > >> Hi Defeng, >> >> parse.bin is compiled on a pentium4, and it works also on pentiumM. >> What CPU are you using? >> What is the output of >> cat /proc/cpuinfo >> uname -a >> strace ./parse.bin >> >> I have compiled it on a pentium3 as well. Maybe that works for you: >> http://www.hst.aau.dk/~se/software/parse.p3fc2 >> >> Simon >> >> dfwang at cse.cuhk.edu.hk wrote: >>> Hi, Simon, >>> >>> Thanks for your reply. Yes, my VTK mesh is in triangular. >>> >>> My linux system is CentOS 4.4. I downloaded your small parser just now, and >>> changed the mode by >>> >>> chmod a+x parse.bin >>> >>> then run parse.bin, I got the following error, >>> >>> Floating point exception >>> >>> Could you please tell me how I can run it successfully? >>> >>> Best wishes, >>> Defeng >>> Quoting Simon Fristed Eskildsen : >>> >>>> Hi Defeng, >>>> >>>> If you're dealing with triangular mesh and pure ascii, you can try my >>>> small parser found here: >>>> 32bit linux: http://www.hst.aau.dk/~se/software/parse.bin >>>> 64bit linux: http://www.hst.aau.dk/~se/software/parse.bin64 >>>> >>>> Also, more information about the .obj format can be found here: >>>> http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles >>>> >>>> Simon >>>> >>>> Defeng WANG wrote: >>>>> Dear MINC Users, >>>>> >>>>> I have one mesh in VTK format at hand, and would like to convert it into >>>> the >>>>> .obj format in MINC. Which tool can do this? Or any suggestions on the >> way >>>>> to convert it? >>>>> >>>>> Many thanks! >>>>> Defeng >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 dfwang at cse.cuhk.edu.hk Tue Oct 9 07:40:01 2007 From: dfwang at cse.cuhk.edu.hk (Defeng WANG) Date: Tue, 9 Oct 2007 19:40:01 +0800 Subject: [MINC-users] convert mesh from VTK to .obj References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> <470A286F.2020206@hst.aau.dk><1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> <470B55FA.3060606@hst.aau.dk> Message-ID: <004001c80a69$248096f0$a459bd89@PC89164> Hi, Simon, I tried and succeded. Many thanks! Best wishes, Defeng ----- Original Message ----- From: "Simon Fristed Eskildsen" To: "MINC users mailing list" Sent: Tuesday, October 09, 2007 6:20 PM Subject: Re: [MINC-users] convert mesh from VTK to .obj > Did you try the P3 version? > http://www.hst.aau.dk/~se/software/parse.p3fc2 > It should be compatible whether you run 32 or 64 bit xeon. > > Simon > dfwang at cse.cuhk.edu.hk wrote: >> Hi, Simon, >> >> My computer information is as follows, >> >> [dfwang at pc89164 ~]$ cat /proc/cpuinfo >> processor : 0 >> vendor_id : GenuineIntel >> cpu family : 15 >> model : 4 >> model name : Intel(R) Xeon(TM) CPU 3.00GHz >> stepping : 3 >> cpu MHz : 3001.815 >> cache size : 2048 KB >> fdiv_bug : no >> hlt_bug : no >> f00f_bug : no >> coma_bug : no >> fpu : yes >> fpu_exception : yes >> cpuid level : 5 >> wp : yes >> flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca >> cmov pat >> pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni >> monito r ds_cpl cid xtpr >> bogomips : 6004.11 >> >> processor : 1 >> vendor_id : GenuineIntel >> cpu family : 15 >> model : 4 >> model name : Intel(R) Xeon(TM) CPU 3.00GHz >> stepping : 3 >> cpu MHz : 3001.815 >> cache size : 2048 KB >> fdiv_bug : no >> hlt_bug : no >> f00f_bug : no >> coma_bug : no >> fpu : yes >> fpu_exception : yes >> cpuid level : 5 >> wp : yes >> flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca >> cmov pat >> pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni >> monito r ds_cpl cid xtpr >> bogomips : 5999.43 >> >> [dfwang at pc89164 data]$ uname -a >> Linux pc89164.cse.cuhk.edu.hk 2.6.9-55.0.9.ELsmp #1 SMP Thu Sep 27 >> 18:27:41 EDT >> 2007 i686 i686 i386 GNU/Linux >> >> >> [dfwang at pc89164 data]$ strace ./parse.bin >> execve("./parse.bin", ["./parse.bin"], [/* 64 vars */]) = 0 >> uname({sys="Linux", node="pc89164.cse.cuhk.edu.hk", ...}) = 0 >> brk(0) = 0x9b99000 >> --- SIGFPE (Floating point exception) @ 0 (0) --- >> +++ killed by SIGFPE +++ >> Process 5227 detached >> >> >> Thanks a lot! >> >> Best wishes, >> Defeng >> >> >> Quoting Simon Fristed Eskildsen : >> >>> Hi Defeng, >>> >>> parse.bin is compiled on a pentium4, and it works also on pentiumM. >>> What CPU are you using? >>> What is the output of >>> cat /proc/cpuinfo >>> uname -a >>> strace ./parse.bin >>> >>> I have compiled it on a pentium3 as well. Maybe that works for you: >>> http://www.hst.aau.dk/~se/software/parse.p3fc2 >>> >>> Simon >>> >>> dfwang at cse.cuhk.edu.hk wrote: >>>> Hi, Simon, >>>> >>>> Thanks for your reply. Yes, my VTK mesh is in triangular. >>>> >>>> My linux system is CentOS 4.4. I downloaded your small parser just now, >>>> and >>>> changed the mode by >>>> >>>> chmod a+x parse.bin >>>> >>>> then run parse.bin, I got the following error, >>>> >>>> Floating point exception >>>> >>>> Could you please tell me how I can run it successfully? >>>> >>>> Best wishes, >>>> Defeng >>>> Quoting Simon Fristed Eskildsen : >>>> >>>>> Hi Defeng, >>>>> >>>>> If you're dealing with triangular mesh and pure ascii, you can try my >>>>> small parser found here: >>>>> 32bit linux: http://www.hst.aau.dk/~se/software/parse.bin >>>>> 64bit linux: http://www.hst.aau.dk/~se/software/parse.bin64 >>>>> >>>>> Also, more information about the .obj format can be found here: >>>>> http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles >>>>> >>>>> Simon >>>>> >>>>> Defeng WANG wrote: >>>>>> Dear MINC Users, >>>>>> >>>>>> I have one mesh in VTK format at hand, and would like to convert it >>>>>> into >>>>> the >>>>>> .obj format in MINC. Which tool can do this? Or any suggestions on >>>>>> the >>> way >>>>>> to convert it? >>>>>> >>>>>> Many thanks! >>>>>> Defeng >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 rupe.brooks at gmail.com Wed Oct 10 10:03:56 2007 From: rupe.brooks at gmail.com (Rupert Brooks) Date: Wed, 10 Oct 2007 10:03:56 -0400 Subject: [MINC-users] MINC 2.0.13 - windows Message-ID: hi people, I've been using Leila Bagdadis Windows binaries of minc 2.0.09 for a while now. Its high time for me to upgrade, mainly for compatibility with the MINC reader in ITK3.4 (in the Review section). What is particularly important to me is to be able to link against it with Visual C++. It doesnt seem easy to get cygwin or mingw to take me down this road. Has anyone done this? My main questions are - how were these binaries built? They seem to have been built with VC++7, and i suppose that means that Microsoft's Posix compatibility layer was used. But this is a total guess based on running strings against the binary. Does anyone plan to build a set of these soon (Leila??) ? Anyway, if no one has plans to build a set, I don't mind building it, but a few pointers as to where to start would be very helpful. cheers Rupert B. -- -------------------------------------------------------------- Rupert Brooks McGill Centre for Intelligent Machines (www.cim.mcgill.ca) Ph.D Student, Electrical and Computer Engineering http://www.cyberus.ca/~rbrooks From penhunelab at gmail.com Wed Oct 10 10:34:20 2007 From: penhunelab at gmail.com (Penhune Lab) Date: Wed, 10 Oct 2007 10:34:20 -0400 Subject: [MINC-users] MINC 2.0.13 - windows In-Reply-To: References: Message-ID: i already compiled minc 2.0.13 using visual studio 2003. the thing is i only compiled the main library (minc2.dll), mincinfo, mincresample and mincreshape If you need any of those let me know. if you need anything else i don't think i have the time to set that up right now. I'm writing instructions on how to run a basic fmri analysis under windows natively (i don't like cygwin) so i still have to port a couple more things (like mritotal). i finished porting fmr_preprocess and the mni_autoreg tools just in case you need them too. I will we posting a website on how to install everything under windows hopefully sooner rather than later. ps. i think i wrote a document for myself about the necessary settings (trial and error + a little intuition) to compile minc in visual studio. let me know if you're interested on that too Alejandro Endo On 10/10/07, Rupert Brooks wrote: > hi people, > > I've been using Leila Bagdadis Windows binaries of minc 2.0.09 for a > while now. Its high time for me to upgrade, mainly for compatibility > with the MINC reader in ITK3.4 (in the Review section). > > What is particularly important to me is to be able to link against it > with Visual C++. It doesnt seem easy to get cygwin or mingw to take > me down this road. Has anyone done this? > > My main questions are - how were these binaries built? They seem to > have been built with VC++7, and i suppose that means that Microsoft's > Posix compatibility layer was used. But this is a total guess based > on running strings against the binary. Does anyone plan to build a > set of these soon (Leila??) ? > > Anyway, if no one has plans to build a set, I don't mind building it, > but a few pointers as to where to start would be very helpful. > > cheers > Rupert B. > > -- > -------------------------------------------------------------- > Rupert Brooks > McGill Centre for Intelligent Machines (www.cim.mcgill.ca) > Ph.D Student, Electrical and Computer Engineering > http://www.cyberus.ca/~rbrooks > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Laboratory for Motor Learning and Neural Plasticity Directed by Dr. Virginia Penhune Department of Psychology, Concordia University SP-A 244, 7141 Sherbrooke St. W Montreal, QC H4B 1R6 Canada (514)848-2424 ext. 7567 http://psychology.concordia.ca/fac/penhune/winindex.html From rupe.brooks at gmail.com Wed Oct 10 12:35:47 2007 From: rupe.brooks at gmail.com (Rupert Brooks) Date: Wed, 10 Oct 2007 12:35:47 -0400 Subject: [MINC-users] MINC 2.0.13 - windows In-Reply-To: References: Message-ID: Cool, sounds like exactly what i wanted to hear :-) Ultimately where i want to get to is to have binarys for all the basic minctools, and ideally register as well, maybe display. Since it sounds like I need more than what you have compiled so far, i guess i would be most interested in the "how you did it" document. That would probably save me having to ask you again on the next release and so forth. Failing that, i'll take the minc2.dll and the tools you have built. Thanks! Rupert On 10/10/07, Penhune Lab wrote: > i already compiled minc 2.0.13 using visual studio 2003. the thing is i only > compiled the main library (minc2.dll), mincinfo, mincresample and > mincreshape > > If you need any of those let me know. if you need anything else i don't > think i have the time to set that up right now. I'm writing instructions on > how to run a basic fmri analysis under windows natively (i don't like > cygwin) so i still have to port a couple more things (like mritotal). i > finished porting fmr_preprocess and the mni_autoreg tools just in case you > need them too. > > I will we posting a website on how to install everything under windows > hopefully sooner rather than later. > > ps. i think i wrote a document for myself about the necessary settings > (trial and error + a little intuition) to compile minc in visual studio. let > me know if you're interested on that too > > Alejandro Endo > > On 10/10/07, Rupert Brooks wrote: > > hi people, > > > > I've been using Leila Bagdadis Windows binaries of minc 2.0.09 for a > > while now. Its high time for me to upgrade, mainly for compatibility > > with the MINC reader in ITK3.4 (in the Review section). > > > > What is particularly important to me is to be able to link against it > > with Visual C++. It doesnt seem easy to get cygwin or mingw to take > > me down this road. Has anyone done this? > > > > My main questions are - how were these binaries built? They seem to > > have been built with VC++7, and i suppose that means that Microsoft's > > Posix compatibility layer was used. But this is a total guess based > > on running strings against the binary. Does anyone plan to build a > > set of these soon (Leila??) ? > > > > Anyway, if no one has plans to build a set, I don't mind building it, > > but a few pointers as to where to start would be very helpful. > > > > cheers > > Rupert B. > > > > -- > > -------------------------------------------------------------- > > Rupert Brooks > > McGill Centre for Intelligent Machines (www.cim.mcgill.ca) > > Ph.D Student, Electrical and Computer Engineering > > http://www.cyberus.ca/~rbrooks > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > -- > Laboratory for Motor Learning and Neural Plasticity > Directed by Dr. Virginia Penhune > Department of Psychology, Concordia University > SP-A 244, 7141 Sherbrooke St. W > Montreal, QC H4B 1R6 Canada > (514)848-2424 ext. 7567 > http://psychology.concordia.ca/fac/penhune/winindex.html > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- -------------------------------------------------------------- Rupert Brooks McGill Centre for Intelligent Machines (www.cim.mcgill.ca) Ph.D Student, Electrical and Computer Engineering http://www.cyberus.ca/~rbrooks From penhunelab at gmail.com Wed Oct 10 13:51:46 2007 From: penhunelab at gmail.com (Penhune Lab) Date: Wed, 10 Oct 2007 13:51:46 -0400 Subject: [MINC-users] MINC 2.0.13 - windows In-Reply-To: References: Message-ID: oh i forgot to mention i have a version of register and display that work in windows (XP) . i got it from Dr. Jorge Armony, i don't really know where he got it from but it IS different to the version that's around online I'm pretty sure you need to have the source code of mni_autoreg too because minc2 needs volume_io2. i guess you can use the one that comes with the package available online and use the volume_io2.lib (static?) library let me know how it goes, Alejandro Endo On 10/10/07, Rupert Brooks wrote: > > Cool, sounds like exactly what i wanted to hear :-) > > Ultimately where i want to get to is to have binarys for all the basic > minctools, and ideally register as well, maybe display. > > Since it sounds like I need more than what you have compiled so far, i > guess i would be most interested in the "how you did it" document. > That would probably save me having to ask you again on the next > release and so forth. Failing that, i'll take the minc2.dll and the > tools you have built. > > Thanks! > Rupert > > > On 10/10/07, Penhune Lab wrote: > > i already compiled minc 2.0.13 using visual studio 2003. the thing is i > only > > compiled the main library (minc2.dll), mincinfo, mincresample and > > mincreshape > > > > If you need any of those let me know. if you need anything else i don't > > think i have the time to set that up right now. I'm writing instructions > on > > how to run a basic fmri analysis under windows natively (i don't like > > cygwin) so i still have to port a couple more things (like mritotal). i > > finished porting fmr_preprocess and the mni_autoreg tools just in case > you > > need them too. > > > > I will we posting a website on how to install everything under windows > > hopefully sooner rather than later. > > > > ps. i think i wrote a document for myself about the necessary settings > > (trial and error + a little intuition) to compile minc in visual studio. > let > > me know if you're interested on that too > > > > Alejandro Endo > > > > On 10/10/07, Rupert Brooks < rupe.brooks at gmail.com> wrote: > > > hi people, > > > > > > I've been using Leila Bagdadis Windows binaries of minc 2.0.09 for a > > > while now. Its high time for me to upgrade, mainly for compatibility > > > with the MINC reader in ITK3.4 (in the Review section). > > > > > > What is particularly important to me is to be able to link against it > > > with Visual C++. It doesnt seem easy to get cygwin or mingw to take > > > me down this road. Has anyone done this? > > > > > > My main questions are - how were these binaries built? They seem to > > > have been built with VC++7, and i suppose that means that Microsoft's > > > Posix compatibility layer was used. But this is a total guess based > > > on running strings against the binary. Does anyone plan to build a > > > set of these soon (Leila??) ? > > > > > > Anyway, if no one has plans to build a set, I don't mind building it, > > > but a few pointers as to where to start would be very helpful. > > > > > > cheers > > > Rupert B. > > > > > > -- > > > -------------------------------------------------------------- > > > Rupert Brooks > > > McGill Centre for Intelligent Machines (www.cim.mcgill.ca ) > > > Ph.D Student, Electrical and Computer Engineering > > > http://www.cyberus.ca/~rbrooks > > > _______________________________________________ > > > MINC-users at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > > -- > > Laboratory for Motor Learning and Neural Plasticity > > Directed by Dr. Virginia Penhune > > Department of Psychology, Concordia University > > SP-A 244, 7141 Sherbrooke St. W > > Montreal, QC H4B 1R6 Canada > > (514)848-2424 ext. 7567 > > http://psychology.concordia.ca/fac/penhune/winindex.html > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > -- > -------------------------------------------------------------- > Rupert Brooks > McGill Centre for Intelligent Machines (www.cim.mcgill.ca) > Ph.D Student, Electrical and Computer Engineering > http://www.cyberus.ca/~rbrooks > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Laboratory for Motor Learning and Neural Plasticity Directed by Dr. Virginia Penhune Department of Psychology, Concordia University SP-A 244, 7141 Sherbrooke St. W Montreal, QC H4B 1R6 Canada (514)848-2424 ext. 7567 http://psychology.concordia.ca/fac/penhune/winindex.html From sorench at gmail.com Mon Oct 15 03:42:25 2007 From: sorench at gmail.com (Soren Christensen) Date: Mon, 15 Oct 2007 17:42:25 +1000 Subject: [MINC-users] mnc2nii Message-ID: Hi, I noticed that FSL 4.0 complains over the .nii files created by mnc2nii. ++ WARNING: nifti_read_buffer(tmp.nii): data bytes needed = 2097152 data bytes input = 2097148 number missing = 4 (set to 0) Apparently it is triggered by the use of a new nifti library in the FSL package. Does anyone know if there is a bug (in FSL or mnc2nii) and if it has any consequences (a pixel or 2 are nulled pherhaps)? Soren From a.janke at gmail.com Mon Oct 15 04:03:33 2007 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 15 Oct 2007 18:03:33 +1000 Subject: [MINC-users] mnc2nii In-Reply-To: References: Message-ID: On 10/15/07, Soren Christensen wrote: > Hi, > I noticed that FSL 4.0 complains over the .nii files created by mnc2nii. > ++ WARNING: nifti_read_buffer(tmp.nii): > data bytes needed = 2097152 > data bytes input = 2097148 > number missing = 4 (set to 0) > > Apparently it is triggered by the use of a new nifti library in the > FSL package. Does anyone know if there is a bug (in FSL or mnc2nii) > and if it has any consequences (a pixel or 2 are nulled pherhaps)? Hi Soren, Yes this is correct from what I understand. The new version of MINC (in the 2.X chain) fixes this by linking with the new niftilib as well. The simple fix is to use .hdr/.img files instead of a .nii from what I understand it is because of a ambiguity in the spec WRT NifTI/Analyze. a From najma at bic.mni.mcgill.ca Mon Oct 15 08:00:07 2007 From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.) Date: Mon, 15 Oct 2007 08:00:07 -0400 Subject: [MINC-users] mnc2nii In-Reply-To: References: Message-ID: Soren, You can use FSL's "correctheader" command to fix that. But ONLT if you have 4 missing bytes and get the warning message you posted. Without this correction, your data might be shifted by one voxel. Cheers Naj On Mon, 15 Oct 2007, Andrew Janke wrote: > On 10/15/07, Soren Christensen wrote: > > Hi, > > I noticed that FSL 4.0 complains over the .nii files created by mnc2nii. > > ++ WARNING: nifti_read_buffer(tmp.nii): > > data bytes needed = 2097152 > > data bytes input = 2097148 > > number missing = 4 (set to 0) > > > > Apparently it is triggered by the use of a new nifti library in the > > FSL package. Does anyone know if there is a bug (in FSL or mnc2nii) > > and if it has any consequences (a pixel or 2 are nulled pherhaps)? > > Hi Soren, > > Yes this is correct from what I understand. The new version of MINC > (in the 2.X chain) fixes this by linking with the new niftilib as > well. > > The simple fix is to use .hdr/.img files instead of a .nii from what I > understand it is because of a ambiguity in the spec WRT NifTI/Analyze. > > > a > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sorench at gmail.com Mon Oct 15 18:30:49 2007 From: sorench at gmail.com (Soren Christensen) Date: Tue, 16 Oct 2007 08:30:49 +1000 Subject: [MINC-users] mnc2nii In-Reply-To: References: Message-ID: Thanks for the fast help Naj and Andrew - used the correctheader for a quick fix and seems to work fine. Cheers Soren On 10/15/07, Najmeh Khalili M. wrote: > > Soren, > > You can use FSL's "correctheader" command to fix that. But ONLT > if you have 4 missing bytes and get the warning message you > posted. > > Without this correction, your data might be shifted by one voxel. > > Cheers > Naj > > On Mon, 15 Oct 2007, Andrew Janke wrote: > > > On 10/15/07, Soren Christensen wrote: > > > Hi, > > > I noticed that FSL 4.0 complains over the .nii files created by mnc2nii. > > > ++ WARNING: nifti_read_buffer(tmp.nii): > > > data bytes needed = 2097152 > > > data bytes input = 2097148 > > > number missing = 4 (set to 0) > > > > > > Apparently it is triggered by the use of a new nifti library in the > > > FSL package. Does anyone know if there is a bug (in FSL or mnc2nii) > > > and if it has any consequences (a pixel or 2 are nulled pherhaps)? > > > > Hi Soren, > > > > Yes this is correct from what I understand. The new version of MINC > > (in the 2.X chain) fixes this by linking with the new niftilib as > > well. > > > > The simple fix is to use .hdr/.img files instead of a .nii from what I > > understand it is because of a ambiguity in the spec WRT NifTI/Analyze. > > > > > > a > > _______________________________________________ > > 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 Mon Oct 15 20:07:47 2007 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 16 Oct 2007 10:07:47 +1000 Subject: [MINC-users] Display and slice plane rendering In-Reply-To: References: Message-ID: Hi Soren, Not sure if anyone posted a reply to this so here is how I do this (when I have to) Display does not have the best documentation! First place the cross hairs in the 3D view on a place that you want in your oblique view. then.. 1. Press 's' for Slice View 2. Press 'r' to make sure things are visible 3. Press 'e' (Pick slice Angle). Then click somewhere else in the image that you want in your oblique view. after a few hacks at this (#3 only) you will get the hang of it. a On 9/10/07, Soren Christensen wrote: > Hi, > I am trying to create a 3D sliceplane rendering from an arbitrary > slice plane but have problems doing this in Display. > I: > 1) turn on the "fourth window" in Display (S-S) > 2) Toggle on the cut plane in the 3D window (S-Q) and orient it as I want. > 3) Try to do S-A from the fourth window in order to render the > arbitrary slice-cut to the 3D window. > > Step 3 is where I have the problem. I cannot render the arbitrary > slice-cut to the 3D window. The other standard view planes render > fine. > > If this functionality is not available using the approach above, is > there pherhaps another way to achieve it? eg. resampling volume > differently or so? > > Thanks > Soren > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From a.janke at gmail.com Tue Oct 16 02:09:40 2007 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 16 Oct 2007 16:09:40 +1000 Subject: [MINC-users] EMMA for MINC 2.x In-Reply-To: <46EED29A.7060907@pet.ubc.ca> References: <46EED29A.7060907@pet.ubc.ca> Message-ID: Hi Dan, Not sure if anyone replied to this, so here goes. This is certainly something that is on my big list of things to do but unfortunately it is not all that high up as of yet. I realise that good MATLAB integration is a big hole in MINC but I dont have much time to work on it as I dont have a machine with MATLAB on it at my disposal. What I did plan instead was a Octave MINC interface but would need a show of support before embarking on such a project. a On 9/18/07, Dan Nesbitt wrote: > I was wondering if anyone is working on porting EMMA to MINC 2.x? > > It looks like from the source code that EMMA uses some NetCDF > definitions and library calls that would require some effort to port to > MINC 2.x (w/HDF5). From rupe.brooks at gmail.com Tue Oct 16 08:49:00 2007 From: rupe.brooks at gmail.com (Rupert Brooks) Date: Tue, 16 Oct 2007 08:49:00 -0400 Subject: [MINC-users] getting a specific voxel value from a minc file Message-ID: Hi, I really hope im not missing something too obvious here.. but im stuck. In the process of checking some data importing, im trying to retrieve the actual value of a specific voxel in a minc file. I am using register - i enter a specific world coordinate or voxel coordinate in the appropriate fields and read off the value stored there from the field below (beside the "Filter" button) According to my understanding, to do what i want, i should set the filter to "Nearest". Unfortunately the reported value seems off - it seems to be always filtered. In fact, no matter what i set the filter to, the value is the same. The minc volume was created by hand, and contains only integer values. Register is reporting values that are non integer. I'm using the build of register from here. http://packages.bic.mni.mcgill.ca/cygwin/ So, my questions are - am i using the tool wrong? Is there another, easier way to do this (A command line solution would be ideal)? If i rebuild a newer version of register - no small project because i am on Windows - will this problem go away? Thanks Rupert B. -- -------------------------------------------------------------- Rupert Brooks McGill Centre for Intelligent Machines (www.cim.mcgill.ca) Ph.D Student, Electrical and Computer Engineering http://www.cyberus.ca/~rbrooks From louis.collins at mcgill.ca Tue Oct 16 09:06:21 2007 From: louis.collins at mcgill.ca (D. Louis Collins) Date: Tue, 16 Oct 2007 09:06:21 -0400 Subject: [MINC-users] getting a specific voxel value from a minc file In-Reply-To: References: Message-ID: <6AF25FF6-4944-4FE4-A251-B0856DDF53BD@mcgill.ca> Rupert, register (and Display) load in data as bytes. if your original data was short, then the value will be truncated to the discrete range of a byte. If you want a specific value, try: mincextract -start 10,20,30 -count 1,1,1 volume.mnc By default, it will spit out the value of the voxel as a double. check the options for other possibilities. -Louis On Oct 16, 2007, at 8:49 AM, Rupert Brooks wrote: > Hi, > > I really hope im not missing something too obvious here.. but im > stuck. > > In the process of checking some data importing, im trying to retrieve > the actual value of a specific voxel in a minc file. I am using > register - i enter a specific world coordinate or voxel coordinate in > the appropriate fields and read off the value stored there from the > field below (beside the "Filter" button) > > According to my understanding, to do what i want, i should set the > filter to "Nearest". > > Unfortunately the reported value seems off - it seems to be always > filtered. In fact, no matter what i set the filter to, the value is > the same. The minc volume was created by hand, and contains only > integer values. Register is reporting values that are non integer. > > I'm using the build of register from here. > http://packages.bic.mni.mcgill.ca/cygwin/ > > So, my questions are - am i using the tool wrong? Is there another, > easier way to do this (A command line solution would be ideal)? If i > rebuild a newer version of register - no small project because i am on > Windows - will this problem go away? > > Thanks > Rupert B. > -- > -------------------------------------------------------------- > Rupert Brooks > McGill Centre for Intelligent Machines (www.cim.mcgill.ca) > Ph.D Student, Electrical and Computer Engineering > http://www.cyberus.ca/~rbrooks > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From rupe.brooks at gmail.com Tue Oct 16 09:39:36 2007 From: rupe.brooks at gmail.com (Rupert Brooks) Date: Tue, 16 Oct 2007 09:39:36 -0400 Subject: [MINC-users] getting a specific voxel value from a minc file In-Reply-To: <6AF25FF6-4944-4FE4-A251-B0856DDF53BD@mcgill.ca> References: <6AF25FF6-4944-4FE4-A251-B0856DDF53BD@mcgill.ca> Message-ID: Works like a charm, thanks Rupert On 10/16/07, D. Louis Collins wrote: > Rupert, > > register (and Display) load in data as bytes. if your original data > was short, then the value will be truncated to the discrete range of > a byte. > > If you want a specific value, try: > > mincextract -start 10,20,30 -count 1,1,1 volume.mnc > > By default, it will spit out the value of the voxel as a double. > check the options for other possibilities. > > -Louis > > On Oct 16, 2007, at 8:49 AM, Rupert Brooks wrote: > > > Hi, > > > > I really hope im not missing something too obvious here.. but im > > stuck. > > > > In the process of checking some data importing, im trying to retrieve > > the actual value of a specific voxel in a minc file. I am using > > register - i enter a specific world coordinate or voxel coordinate in > > the appropriate fields and read off the value stored there from the > > field below (beside the "Filter" button) > > > > According to my understanding, to do what i want, i should set the > > filter to "Nearest". > > > > Unfortunately the reported value seems off - it seems to be always > > filtered. In fact, no matter what i set the filter to, the value is > > the same. The minc volume was created by hand, and contains only > > integer values. Register is reporting values that are non integer. > > > > I'm using the build of register from here. > > http://packages.bic.mni.mcgill.ca/cygwin/ > > > > So, my questions are - am i using the tool wrong? Is there another, > > easier way to do this (A command line solution would be ideal)? If i > > rebuild a newer version of register - no small project because i am on > > Windows - will this problem go away? > > > > Thanks > > Rupert B. > > -- > > -------------------------------------------------------------- > > Rupert Brooks > > McGill Centre for Intelligent Machines (www.cim.mcgill.ca) > > Ph.D Student, Electrical and Computer Engineering > > http://www.cyberus.ca/~rbrooks > > _______________________________________________ > > 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 > -- -------------------------------------------------------------- Rupert Brooks McGill Centre for Intelligent Machines (www.cim.mcgill.ca) Ph.D Student, Electrical and Computer Engineering http://www.cyberus.ca/~rbrooks From rupe.brooks at gmail.com Tue Oct 16 09:49:50 2007 From: rupe.brooks at gmail.com (Rupert Brooks) Date: Tue, 16 Oct 2007 09:49:50 -0400 Subject: [MINC-users] getting a specific voxel value from a minc file In-Reply-To: References: <6AF25FF6-4944-4FE4-A251-B0856DDF53BD@mcgill.ca> Message-ID: For anyone that googles this later, i will just point out that mincextract takes input in dimension order. So its not -start xpixel,ypixel,zpixel they have to be in the dimension order that appears in your file, which in my case was -start zpixel,ypixel,xpixel. Just trying to save the next person the puzzlement :-) Rupert On 10/16/07, Rupert Brooks wrote: > Works like a charm, > > thanks > Rupert > > On 10/16/07, D. Louis Collins wrote: > > Rupert, > > > > register (and Display) load in data as bytes. if your original data > > was short, then the value will be truncated to the discrete range of > > a byte. > > > > If you want a specific value, try: > > > > mincextract -start 10,20,30 -count 1,1,1 volume.mnc > > > > By default, it will spit out the value of the voxel as a double. > > check the options for other possibilities. > > > > -Louis > > > > On Oct 16, 2007, at 8:49 AM, Rupert Brooks wrote: > > > > > Hi, > > > > > > I really hope im not missing something too obvious here.. but im > > > stuck. > > > > > > In the process of checking some data importing, im trying to retrieve > > > the actual value of a specific voxel in a minc file. I am using > > > register - i enter a specific world coordinate or voxel coordinate in > > > the appropriate fields and read off the value stored there from the > > > field below (beside the "Filter" button) > > > > > > According to my understanding, to do what i want, i should set the > > > filter to "Nearest". > > > > > > Unfortunately the reported value seems off - it seems to be always > > > filtered. In fact, no matter what i set the filter to, the value is > > > the same. The minc volume was created by hand, and contains only > > > integer values. Register is reporting values that are non integer. > > > > > > I'm using the build of register from here. > > > http://packages.bic.mni.mcgill.ca/cygwin/ > > > > > > So, my questions are - am i using the tool wrong? Is there another, > > > easier way to do this (A command line solution would be ideal)? If i > > > rebuild a newer version of register - no small project because i am on > > > Windows - will this problem go away? > > > > > > Thanks > > > Rupert B. > > > -- > > > -------------------------------------------------------------- > > > Rupert Brooks > > > McGill Centre for Intelligent Machines (www.cim.mcgill.ca) > > > Ph.D Student, Electrical and Computer Engineering > > > http://www.cyberus.ca/~rbrooks > > > _______________________________________________ > > > 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 > > > > > -- > -------------------------------------------------------------- > Rupert Brooks > McGill Centre for Intelligent Machines (www.cim.mcgill.ca) > Ph.D Student, Electrical and Computer Engineering > http://www.cyberus.ca/~rbrooks > -- -------------------------------------------------------------- Rupert Brooks McGill Centre for Intelligent Machines (www.cim.mcgill.ca) Ph.D Student, Electrical and Computer Engineering http://www.cyberus.ca/~rbrooks From nikelski at bic.mni.mcgill.ca Tue Oct 16 10:51:14 2007 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Tue, 16 Oct 2007 10:51:14 -0400 Subject: [MINC-users] EMMA for MINC 2.x In-Reply-To: References: <46EED29A.7060907@pet.ubc.ca> Message-ID: Hi Andrew (and List), I would very much support the move away from Matlab, however in the past I have found Octave project development to be very inconsistent. The R-project, on the other hand, is under extremely active development. Would R not be a reasonable replacement? -Jim > Hi Dan, > > Not sure if anyone replied to this, so here goes. > > This is certainly something that is on my big list of things to do but > unfortunately it is not all that high up as of yet. > > I realise that good MATLAB integration is a big hole in MINC but I > dont have much time to work on it as I dont have a machine with MATLAB > on it at my disposal. > > What I did plan instead was a Octave MINC interface but would need a > show of support before embarking on such a project. > > > a > > On 9/18/07, Dan Nesbitt wrote: > > I was wondering if anyone is working on porting EMMA to MINC 2.x? > > > > It looks like from the source code that EMMA uses some NetCDF > > definitions and library calls that would require some effort to port to > > MINC 2.x (w/HDF5). > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University Tel: (514) 340-8222 x 2298 Fax: (514) 340-8295 From jason at bic.mni.mcgill.ca Tue Oct 16 13:45:06 2007 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Tue, 16 Oct 2007 13:45:06 -0400 Subject: [MINC-users] EMMA for MINC 2.x In-Reply-To: References: <46EED29A.7060907@pet.ubc.ca> Message-ID: <4714F8A2.2000109@bic.mni.mcgill.ca> Doing matrix work in R can be a bit tedious - so if I have my K space data and want to fourier transform it, matlab will be a lot friendlier, I think. So I don't know if R can ever replace matlab for some things. That being said, there is a MINC interface in R already, and it too is under active development. Jason EJ Nikelski wrote: > Hi Andrew (and List), > > I would very much support the move away from Matlab, however in the > past I have found Octave project development to be very inconsistent. > The R-project, on the other hand, is under extremely active > development. Would R not be a reasonable replacement? > > -Jim > > > >> Hi Dan, >> >> Not sure if anyone replied to this, so here goes. >> >> This is certainly something that is on my big list of things to do but >> unfortunately it is not all that high up as of yet. >> >> I realise that good MATLAB integration is a big hole in MINC but I >> dont have much time to work on it as I dont have a machine with MATLAB >> on it at my disposal. >> >> What I did plan instead was a Octave MINC interface but would need a >> show of support before embarking on such a project. >> >> >> a >> >> On 9/18/07, Dan Nesbitt wrote: >> >>> I was wondering if anyone is working on porting EMMA to MINC 2.x? >>> >>> It looks like from the source code that EMMA uses some NetCDF >>> definitions and library calls that would require some effort to port to >>> MINC 2.x (w/HDF5). >>> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> > > > From nikelski at bic.mni.mcgill.ca Tue Oct 16 16:37:05 2007 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Tue, 16 Oct 2007 16:37:05 -0400 Subject: [MINC-users] mritotal nonlinear fitting problem Message-ID: Hi all, I'm attempting to use mritotal to do a nonlinear fit and, after a certain amount of processing, am greeted with the following error: -------------------------------------- special pre-processing for high-resolution nonlinear fits: making /usr/tmp/mritotal_1554//chertLab_0001_t1_final_8_nlcrop.xfm [mritotal] [nikelski at owen:/data/aces/aces1/nikelski/nlfit_test] [2007-10-16 14:44:54] /usr/local/mni/bin/xfmtool 'extract(1):/usr/tmp/mritotal_1554//chertLab_0001_t1_final_8_nl.xfm' /usr/tmp/mritotal_1554//chertLab_0001_t1_final_lin.xfm Undefined subroutine &main::parse_num_list called at /usr/local/mni/bin/xfmtool line 399, line 11. mritotal: crashed while running xfmtool (termination status=65280) -------------------------------------- So, it looks like xfmtool is looking for perl subroutine parse_num_list. Does anyone know where this thing lives? Might it be package TransformFile? If so, where is it, and do I need to add something to my PATH/PERL5LIB? Any help would be appreciated. Thanks, -Jim From a.janke at gmail.com Tue Oct 16 20:42:30 2007 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 17 Oct 2007 10:42:30 +1000 Subject: [MINC-users] mritotal nonlinear fitting problem In-Reply-To: References: Message-ID: Hi Jim, > I'm attempting to use mritotal to do a nonlinear fit and, after a > certain amount of processing, am greeted with the following error: > > special pre-processing for high-resolution nonlinear fits: making > Undefined subroutine &main::parse_num_list called at > /usr/local/mni/bin/xfmtool line 399, line 11. > mritotal: crashed while running xfmtool (termination status=65280) > > So, it looks like xfmtool is looking for perl subroutine > parse_num_list. Does anyone know where this thing lives? You are correct! Seems that when I converted xfmtool to using MNI:: perllib things that I missed one function. In the end it turns out that this function only seems to be used in xfmtool so I have added it to xfmtool itself. Try this patched version: http://mavis.anu.edu.au/minc/xfmtool You will have to replace your current version of xfmtool with this so that the other tools use it in deference to the old one. This should make it into the next release of mni-autoreg. a From sorench at gmail.com Wed Oct 17 23:21:40 2007 From: sorench at gmail.com (Soren Christensen) Date: Thu, 18 Oct 2007 13:21:40 +1000 Subject: [MINC-users] strange mnc2nii behaviour Message-ID: Hi, Thanks for the help with mnc2nii earlier in the week. Used correct_header and still use MINC 1.5 for now so apologies if this is not a bug in MINC 2.0: I Had mnc2nii crash on a long filename - here's and example (with a filename to illustrate the point): mnc2nii -signed -float t.mnc 0123456789012345678901234567890123456789.nii ... The usual header output MINC type 5 signed 1 Segmentation fault When making the filename shorter or longer: mnc2nii -signed -float t.mnc 01234567890123456789012345678901234567890.nii ... The usual header output MINC type 5 signed 1 0: 256 0 1 1: 124 1 1 2: 256 2 1 bytes per voxel 4 # of voxels 8126464 0 0 0 => -105.570312 -105.400002 -90.670311 10 0 0 => -96.976562 -105.400002 -90.670311 0 10 0 => -105.570312 -90.400002 -90.670311 0 0 10 => -105.570312 -105.400002 -82.076561 10 10 10 => -96.976562 -90.400002 -82.076561 = no errors Is there something going on with a string pointer somewhere in nii2mnc? Cheers Soren From najma at bic.mni.mcgill.ca Thu Oct 18 08:15:12 2007 From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.) Date: Thu, 18 Oct 2007 08:15:12 -0400 Subject: [MINC-users] strange mnc2nii behaviour In-Reply-To: References: Message-ID: Hi Soren, I had that problem too. But Andrew tested nii2mnc it with even a longer file name and it worked. Naj On Thu, 18 Oct 2007, Soren Christensen wrote: > Hi, > Thanks for the help with mnc2nii earlier in the week. Used > correct_header and still use MINC 1.5 for now so apologies if this is > not a bug in MINC 2.0: > I Had mnc2nii crash on a long filename - here's and example (with a > filename to illustrate the point): > mnc2nii -signed -float t.mnc 0123456789012345678901234567890123456789.nii > ... The usual header output > MINC type 5 signed 1 > Segmentation fault > > > When making the filename shorter or longer: > mnc2nii -signed -float t.mnc 01234567890123456789012345678901234567890.nii > ... The usual header output > MINC type 5 signed 1 > 0: 256 0 1 > 1: 124 1 1 > 2: 256 2 1 > bytes per voxel 4 > # of voxels 8126464 > 0 0 0 => -105.570312 -105.400002 -90.670311 > 10 0 0 => -96.976562 -105.400002 -90.670311 > 0 10 0 => -105.570312 -90.400002 -90.670311 > 0 0 10 => -105.570312 -105.400002 -82.076561 > 10 10 10 => -96.976562 -90.400002 -82.076561 > > = no errors > > > Is there something going on with a string pointer somewhere in nii2mnc? > > Cheers > Soren > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sorench at gmail.com Thu Oct 18 08:44:47 2007 From: sorench at gmail.com (Soren Christensen) Date: Thu, 18 Oct 2007 22:44:47 +1000 Subject: [MINC-users] strange mnc2nii behaviour In-Reply-To: References: Message-ID: Hi Naj, Yes it seems to only be a problem for that particular length. I am running on Linux but tested it on Mac today where it works without problems. Any ideas as to where to locate that error are appriciated. Cheers Soren On 10/18/07, Najmeh Khalili M. wrote: > > Hi Soren, > > I had that problem too. But Andrew tested nii2mnc > it with even a longer file name and it worked. > > Naj > > > On Thu, 18 Oct 2007, Soren Christensen wrote: > > > Hi, > > Thanks for the help with mnc2nii earlier in the week. Used > > correct_header and still use MINC 1.5 for now so apologies if this is > > not a bug in MINC 2.0: > > I Had mnc2nii crash on a long filename - here's and example (with a > > filename to illustrate the point): > > mnc2nii -signed -float t.mnc 0123456789012345678901234567890123456789.nii > > ... The usual header output > > MINC type 5 signed 1 > > Segmentation fault > > > > > > When making the filename shorter or longer: > > mnc2nii -signed -float t.mnc 01234567890123456789012345678901234567890.nii > > ... The usual header output > > MINC type 5 signed 1 > > 0: 256 0 1 > > 1: 124 1 1 > > 2: 256 2 1 > > bytes per voxel 4 > > # of voxels 8126464 > > 0 0 0 => -105.570312 -105.400002 -90.670311 > > 10 0 0 => -96.976562 -105.400002 -90.670311 > > 0 10 0 => -105.570312 -90.400002 -90.670311 > > 0 0 10 => -105.570312 -105.400002 -82.076561 > > 10 10 10 => -96.976562 -90.400002 -82.076561 > > > > = no errors > > > > > > Is there something going on with a string pointer somewhere in nii2mnc? > > > > Cheers > > Soren > > _______________________________________________ > > 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 Sun Oct 21 21:16:52 2007 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 22 Oct 2007 11:16:52 +1000 Subject: [MINC-users] strange mnc2nii behaviour In-Reply-To: References: Message-ID: > > > I Had mnc2nii crash on a long filename - here's and example (with a > > > filename to illustrate the point): > > > mnc2nii -signed -float t.mnc 0123456789012345678901234567890123456789.nii > > > ... The usual header output > > > MINC type 5 signed 1 > > > Segmentation fault > Yes it seems to only be a problem for that particular length. I am > running on Linux but tested it on Mac today where it works without > problems. Any ideas as to where to locate that error are appreciated.\ Hi Soren, I had a bit of a quick hunt for this bug and I can say that it does happen in MINC 2.0.9 but not in 2.0.13. What did change in between these versions is the niftilib version. However I am not entirely sure that this is the problem. What I do know however is that there is a limit to the filename size that can be put into the nifti header (although I think that field is no longer used in deference to the filename itself). I think the limit was 14 ascii characters in the db_name field? In any case the bug (Whatever it was) is squashed! I like problems that are fixed already, perhaps the answer is to "Backport" the 2.X changes to 1.5. Although in this case it means little more than just relinking against the new nifti libs (and one small change to nii2mnc and mnc2nii IIRC). a From claude at bic.mni.mcgill.ca Sun Oct 21 22:30:50 2007 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Sun, 21 Oct 2007 22:30:50 -0400 (EDT) Subject: [MINC-users] strange mnc2nii behaviour References: Message-ID: <200710220230.l9M2UoLE19477529@yorick.bic.mni.mcgill.ca> Andrew, In my case, nii2mnc a la minc-2.0.13 crashes with a segmentation fault in all cases I have tried so far, on Linux. So I am using the minc-1.5 version instead. I haven't had time to investigate the bug, but maybe you can try on your side first. Haven't tried mnc2nii though. Claude From a.janke at gmail.com Mon Oct 22 21:33:49 2007 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 23 Oct 2007 11:33:49 +1000 Subject: [MINC-users] strange mnc2nii behaviour In-Reply-To: <200710220230.l9M2UoLE19477529@yorick.bic.mni.mcgill.ca> References: <200710220230.l9M2UoLE19477529@yorick.bic.mni.mcgill.ca> Message-ID: OK, I think I have managed to track this down to a linking error with niftilib. In any case it is high time for another patched MINC2 release, so here we go: http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.14.tar.gz This version also includes support for a CMake build (for linking with ITK) so I will be most interested to hear reports from users as to whether this works or not. I suspect there will be problems with the CMake build but then I might just get lucky to. To build with cmake, do this: 1. Get Cmake (and configure it with autoconf/automake amusingly -- they may have fixed this though...) 2. untar; cd minc-xx 3. cmake . (or ccmake . for a pretty version) 4. make install Or do it the supported way using configure and make. a On 10/22/07, Claude LEPAGE wrote: > Andrew, > > In my case, nii2mnc a la minc-2.0.13 crashes with a segmentation > fault in all cases I have tried so far, on Linux. So I am using > the minc-1.5 version instead. I haven't had time to investigate > the bug, but maybe you can try on your side first. Haven't tried > mnc2nii though. > > Claude > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From fachkar at mrs.mni.mcgill.ca Tue Oct 23 09:59:47 2007 From: fachkar at mrs.mni.mcgill.ca (Firas Aschkar) Date: Tue, 23 Oct 2007 09:59:47 -0400 Subject: [MINC-users] volume data structure Message-ID: <471DFE53.70400@mrs.mni.mcgill.ca> greetings, I want to create and allocate custom buffers for specific non-subsequent slices of a minc volume. However, it is not clear to me how the *volume data* is store in memory, i.e. given a 3D volume: Volume data1; float v1 = data1->array.data[1][1][1]; flaot v2 = *( data1->array.data + (1 * data1->array.sizes[0]) + (1 * data1->array.sizes[1]) + 1 ); They produce different values given that : static char *default_dim_names[3] = { MIzspace, MIxspace, MIyspace }; thks, firas From Kent.Conover at concordia.ca Tue Oct 23 10:00:55 2007 From: Kent.Conover at concordia.ca (conover) Date: Tue, 23 Oct 2007 10:00:55 -0400 Subject: [MINC-users] MINC Configure error Message-ID: <285F3DDE-1F1A-47CA-A55B-E4B58B9E8E68@concordia.ca> Hi Andrew, I am inspired by the flurry of MINC updates to endeavor to install the MINC tools from source, and so free my self from my binary dependancy. However, when I run "./configure" I get the message: "configure: error: cannot find required library netcdf" Where should I put the netcdf tools so ./configure can find them? Regards, -Kent From sean at rogue-research.com Tue Oct 23 10:13:07 2007 From: sean at rogue-research.com (Sean McBride) Date: Tue, 23 Oct 2007 10:13:07 -0400 Subject: [MINC-users] strange mnc2nii behaviour In-Reply-To: References: <200710220230.l9M2UoLE19477529@yorick.bic.mni.mcgill.ca> Message-ID: <20071023141307.1096622718@smtp1.sympatico.ca> On 10/23/07 11:33 AM, Andrew Janke said: >To build with cmake, do this: > > 1. Get Cmake (and configure it with autoconf/automake amusingly -- > they may have fixed this though...) No need to actually build CMake itself in most cases, there are binaries for many OSes here: -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From jason at bic.mni.mcgill.ca Tue Oct 23 10:31:14 2007 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Tue, 23 Oct 2007 10:31:14 -0400 Subject: [MINC-users] volume data structure In-Reply-To: <471DFE53.70400@mrs.mni.mcgill.ca> References: <471DFE53.70400@mrs.mni.mcgill.ca> Message-ID: <471E05B2.2090301@bic.mni.mcgill.ca> If you are working with minc2 see here: http://en.wikibooks.org/wiki/MINC/Tutorials/Programming05 Jason Firas Aschkar wrote: > greetings, > I want to create and allocate custom buffers for specific non-subsequent > slices of a minc volume. However, it is not clear to me how the *volume > data* is store in memory, i.e. given a 3D volume: > > Volume data1; > float v1 = data1->array.data[1][1][1]; > flaot v2 = *( data1->array.data + (1 * data1->array.sizes[0]) + (1 * > data1->array.sizes[1]) + 1 ); > > They produce different values given that : > > static char *default_dim_names[3] = > { > MIzspace, MIxspace, MIyspace > }; > > thks, > firas > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From jason at bic.mni.mcgill.ca Tue Oct 23 10:32:23 2007 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Tue, 23 Oct 2007 10:32:23 -0400 Subject: [MINC-users] MINC Configure error In-Reply-To: <285F3DDE-1F1A-47CA-A55B-E4B58B9E8E68@concordia.ca> References: <285F3DDE-1F1A-47CA-A55B-E4B58B9E8E68@concordia.ca> Message-ID: <471E05F7.3030507@bic.mni.mcgill.ca> It doesn't matter where you put it - just specify the --with-build-path argument, i.e. if you put netcdf in /usr/local/minc, do ./configure --with-build-path=/usr/local/minc Jason conover wrote: > Hi Andrew, > > I am inspired by the flurry of MINC updates to endeavor to install > the MINC tools from source, and so free my self from my binary > dependancy. However, when I run "./configure" I get the message: > > "configure: error: cannot find required library netcdf" > > Where should I put the netcdf tools so ./configure can find them? > > Regards, > > -Kent > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From luis.ibanez at kitware.com Tue Oct 23 11:01:37 2007 From: luis.ibanez at kitware.com (Luis Ibanez) Date: Tue, 23 Oct 2007 11:01:37 -0400 Subject: [MINC-users] strange mnc2nii behaviour In-Reply-To: <20071023141307.1096622718@smtp1.sympatico.ca> References: <200710220230.l9M2UoLE19477529@yorick.bic.mni.mcgill.ca> <20071023141307.1096622718@smtp1.sympatico.ca> Message-ID: <471E0CD1.4010309@kitware.com> Sean McBride wrote: > On 10/23/07 11:33 AM, Andrew Janke said: > > >>To build with cmake, do this: >> >> 1. Get Cmake (and configure it with autoconf/automake amusingly -- >> they may have fixed this though...) > > > No need to actually build CMake itself in most cases, there are binaries > for many OSes here: > > Just FYI: CMake is not really configured with autoconf/automake. It does have a "configure" shell script that simply calls a "bootstrap" shell script. You will find this script in the file "CMake/bootstrap". An initial Makefile is generated from this script, and then CMake configures itself during its own build process. It is a chicken-egg problem, like trying to build a compiler without having a compiler :-) In any case: As Sean pointed out, you can simply use a binary-installed CMake. Note also that CMake is already available as a package with most GNU/Linux distributions, as well as Cygwin and MinGW. If you are running GNU/Linux, chances are that you already have a cmake installed. Luis From sorench at gmail.com Tue Oct 23 19:42:16 2007 From: sorench at gmail.com (Soren Christensen) Date: Wed, 24 Oct 2007 09:42:16 +1000 Subject: [MINC-users] strange mnc2nii behaviour In-Reply-To: References: <200710220230.l9M2UoLE19477529@yorick.bic.mni.mcgill.ca> Message-ID: Many thanks Andrew, I will switch to MINC 2 ASAP. Cheers Soren On 10/23/07, Andrew Janke wrote: > > OK, I think I have managed to track this down to a linking error with > niftilib. In any case it is high time for another patched MINC2 > release, so here we go: > > http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.14.tar.gz > > This version also includes support for a CMake build (for linking with > ITK) so I will be most interested to hear reports from users as to > whether this works or not. I suspect there will be problems with the > CMake build but then I might just get lucky to. > > To build with cmake, do this: > > 1. Get Cmake (and configure it with autoconf/automake amusingly -- > they may have fixed this though...) > > 2. untar; cd minc-xx > > 3. cmake . (or ccmake . for a pretty version) > > 4. make install > > Or do it the supported way using configure and make. > > > a > > On 10/22/07, Claude LEPAGE wrote: > > Andrew, > > > > In my case, nii2mnc a la minc-2.0.13 crashes with a segmentation > > fault in all cases I have tried so far, on Linux. So I am using > > the minc-1.5 version instead. I haven't had time to investigate > > the bug, but maybe you can try on your side first. Haven't tried > > mnc2nii though. > > > > Claude > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > -- > Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia +61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.t.reid at science.ru.nl Wed Oct 24 04:55:42 2007 From: a.t.reid at science.ru.nl (andrew) Date: Wed, 24 Oct 2007 10:55:42 +0200 Subject: [MINC-users] Building minc2 problems Message-ID: <1193216142.5523.6.camel@typically-desktop> Hi, I have a good of output I've generated with Minc-2 at the BIC and now I want to work with it from abroad, as well as generate more. This means I have to install Minc-2 on my Ubuntu workstation here (Minc-1 won't read my volumes). I've run into the following error, when running make or make check on either the minc-2.0.13 or minc-2.0.14 source distributions. Configure runs fine with no errors. I'm relatively new to compiling in Linux, so any insights are more than welcome. Cheers, Andrew Reid make all-recursive make[1]: Entering directory `/home/typically/minc-2.0.14' Making all in . make[2]: Entering directory `/home/typically/minc-2.0.14' /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -o vff2mnc conversion/vff2mnc/vff2mnc.o libvolume_io2.la libminc2.la -lnetcdf -lm gcc -g -O2 -o vff2mnc conversion/vff2mnc/vff2mnc.o ./.libs/libvolume_io2.a ./.libs/libminc2.a -lnetcdf -lm conversion/vff2mnc/vff2mnc.o: In function `add_vff_attribute_to_file': /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:954: undefined reference to `miset_attr_values' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:960: undefined reference to `miset_attr_values' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:966: undefined reference to `miset_attr_values' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:972: undefined reference to `miset_attr_values' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:978: undefined reference to `miset_attr_values' conversion/vff2mnc/vff2mnc.o:/home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:984: more undefined references to `miset_attr_values' follow conversion/vff2mnc/vff2mnc.o: In function `read_3Dvff_file_image': /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:910: undefined reference to `miset_voxel_value_hyperslab' conversion/vff2mnc/vff2mnc.o: In function `read_2Dvff_files_image': /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:658: undefined reference to `miset_voxel_value_hyperslab' conversion/vff2mnc/vff2mnc.o: In function `main': /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:238: undefined reference to `micreate_dimension' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:244: undefined reference to `micreate_dimension' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:250: undefined reference to `micreate_dimension' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:257: undefined reference to `miset_dimension_start' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:262: undefined reference to `miset_dimension_start' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:268: undefined reference to `miset_dimension_start' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:274: undefined reference to `miset_dimension_separation' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:280: undefined reference to `miset_dimension_separation' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:286: undefined reference to `miset_dimension_separation' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:292: undefined reference to `micreate_volume' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:299: undefined reference to `micreate_volume_image' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:314: undefined reference to `miset_volume_valid_range' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:322: undefined reference to `miset_volume_range' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:359: undefined reference to `miadd_history_attr' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:369: undefined reference to `miclose_volume' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:339: undefined reference to `miset_attr_values' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:345: undefined reference to `miset_attr_values' /home/typically/minc-2.0.14/conversion/vff2mnc/vff2mnc.c:351: undefined reference to `miset_attr_values' collect2: ld returned 1 exit status make[2]: *** [vff2mnc] Error 1 make[2]: Leaving directory `/home/typically/minc-2.0.14' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/typically/minc-2.0.14' make: *** [all] Error 2 From claude at bic.mni.mcgill.ca Wed Oct 24 09:23:27 2007 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Wed, 24 Oct 2007 09:23:27 -0400 (EDT) Subject: [MINC-users] Building minc2 problems Message-ID: <200710241323.l9ODNRUO20051156@yorick.bic.mni.mcgill.ca> Andrew, You have to take care of dependencies when you compile minc (hdf5, netcdf, etc). I compiled 2.0.14 yesterday without any problem. Since you are at the BIC, why don't you drop by my office after lunch so that I can show you how to install the software "easily". Claude From acaroli at fatebenefratelli.it Fri Oct 26 04:41:02 2007 From: acaroli at fatebenefratelli.it (Anna Caroli) Date: Fri, 26 Oct 2007 10:41:02 +0200 Subject: [MINC-users] Problems in installing display on Mac OS X Message-ID: <001b01c817ab$f1349260$ce005b0a@fbfplv.it> Dear MINC list, I'm trying to install Display on Mac OS X. I first installed Netcdf, Minc and Bicpl as required, and than Display (using display-1.4.1.pkg.tar, downloaded from the MNI website). The strangeness is that, despite all the installations seem to work fine, I can't find any of the programs installed anywhere (neither searching by myself nor using the finder) ... Did anybody of you have the same problem? Do you have any suggestion about what is wrong with it? In the Display installation instructions I saw that openGL is also required. Could anybody of you give me a link where I can download it for Mac OSX? Thanks a lot for your help! Anna Laboratory of Epidemiology, Neuroimaging & Telemedicine IRCCS San Giovanni di Dio FBF - The National Center for Research and Care of Alzheimer's Disease via Pilastroni 4, 25125 - Brescia, Italy Tel: +39 030 3501 361, Fax: +39 02 700 435 727 http://www.irccs-fatebenefratelli.it/ From ed.gronenschild at mi.unimaas.nl Fri Oct 26 07:55:27 2007 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Fri, 26 Oct 2007 13:55:27 +0200 Subject: [MINC-users] Intracranial volume Message-ID: Hi, The problem with skullstripping tools (e.g. FSL BET) is that not only the skull is removed but also the dura and the cerebrospinal fluid exterior to the brain. So, skullstripping is in fact brain extraction. However, I want to know the volume just inside the skull, the so-called intracranial volume (ICV). Is there a MINC tool available to derive the ICV? Ed From claude at bic.mni.mcgill.ca Fri Oct 26 10:37:15 2007 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Fri, 26 Oct 2007 10:37:15 -0400 (EDT) Subject: [MINC-users] Intracranial volume Message-ID: <200710261437.l9QEbFQp20549891@yorick.bic.mni.mcgill.ca> Hi Ed, I'm not aware of any tool to compute ICV at the BIC (maybe there is one but I don't know). Anyone here knows? I would suggest to try the -s option in FSL BET: -s : generate approximate skull image I've never tried it, but maybe you can use it for ICV. My guess is that it probably finds the external boundary of the skull as opposed to the inner boundary. Worth trying if you are curious. > The problem with skullstripping tools (e.g. FSL BET) is > that not only the skull is removed but also the dura and > the cerebrospinal fluid exterior to the brain. So, > skullstripping is in fact brain extraction. However, I > want to know the volume just inside the skull, the > so-called intracranial volume (ICV). Is there a MINC tool > available to derive the ICV? > > Ed From mhough at fmrib.ox.ac.uk Fri Oct 26 10:45:50 2007 From: mhough at fmrib.ox.ac.uk (Morgan Hough) Date: Fri, 26 Oct 2007 15:45:50 +0100 Subject: [MINC-users] Intracranial volume In-Reply-To: <200710261437.l9QEbFQp20549891@yorick.bic.mni.mcgill.ca> References: <200710261437.l9QEbFQp20549891@yorick.bic.mni.mcgill.ca> Message-ID: <4721FD9E.1000506@fmrib.ox.ac.uk> Hi there, Which version of FSL are you using? You might check if you have betsurf available (its certainly in the latest stable). It will give you inner and outer skull and you can improve the estimate with a T2 volume if you have that available as well. Cheers, -Morgan Claude LEPAGE wrote: > Hi Ed, > > I'm not aware of any tool to compute ICV at the BIC (maybe there > is one but I don't know). Anyone here knows? > > I would suggest to try the -s option in FSL BET: > > -s : generate approximate skull image > > I've never tried it, but maybe you can use it for ICV. My guess is > that it probably finds the external boundary of the skull as opposed > to the inner boundary. Worth trying if you are curious. > > >> The problem with skullstripping tools (e.g. FSL BET) is >> that not only the skull is removed but also the dura and >> the cerebrospinal fluid exterior to the brain. So, >> skullstripping is in fact brain extraction. However, I >> want to know the volume just inside the skull, the >> so-called intracranial volume (ICV). Is there a MINC tool >> available to derive the ICV? >> >> Ed >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From Wolfgang.Bogner at gmx.net Sun Oct 28 11:32:36 2007 From: Wolfgang.Bogner at gmx.net (Wolfgang Bogner) Date: Sun, 28 Oct 2007 16:32:36 +0100 Subject: [MINC-users] mnc2nii conversion problem Message-ID: <20071028153236.46340@gmx.net> Hello, I have some 3D minc images and want to work with them in matlab. Therefore i thought i could use mnc2nii first and then read the resulting files with "load_nii"-command and write back the result to a different *.nii file and convert them back to mnc. Unfortunately i cannot make mnc2nii conversion work properly. For a test i simply tried to convert a single pixel using mnc2nii and then back with nii2mnc. syntax: rm comp_image.nii comp_image_back.mnc ;mnc2nii -short comp_image.mnc comp_image.nii; nii2mnc comp_image.nii comp_image_back.mnc; register comp_image_back.mnc comp_image.mnc & --> the result: before conversion values (before -> after) are 654 -> 672 in one point. If i take a different points its for example 232 -> 116 and so on. There is no real pattern but if one looks at the images with register both seems to be "quite" similar. Any suggestions what i did wrong? Thanks a lot!!! Wolfgang P.S.: I tried to install minc 2.0.13 and 2.0.14 with the following error when i type "make" after ./configure Xan:/home/bow/Desktop/MINC_binaries/minc-2.0.14 # make make all-recursive make[1]: Entering directory `/home/bow/Desktop/MINC_binaries/minc-2.0.14' Making all in . make[2]: Entering directory `/home/bow/Desktop/MINC_binaries/minc-2.0.14' depbase=`echo conversion/nifti1/mnc2nii.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ gcc -DHAVE_CONFIG_H -I. -I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib -I./conversion/Acr_nema -g -O2 -MT conversion/nifti1/mnc2nii.o -MD -MP -MF $depbase.Tpo -c -o conversion/nifti1/mnc2nii.o conversion/nifti1/mnc2nii.c &&\ mv -f $depbase.Tpo $depbase.Po conversion/nifti1/mnc2nii.c:1:19: error: minc2.h: No such file or directory make[2]: *** [conversion/nifti1/mnc2nii.o] Error 1 make[2]: Leaving directory `/home/bow/Desktop/MINC_binaries/minc-2.0.14' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/bow/Desktop/MINC_binaries/minc-2.0.14' make: *** [all] Error 2 -- Psssst! Schon vom neuen GMX MultiMessenger geh?rt? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail From claude at bic.mni.mcgill.ca Sun Oct 28 12:12:04 2007 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Sun, 28 Oct 2007 12:12:04 -0400 (EDT) Subject: [MINC-users] mnc2nii conversion problem Message-ID: <200710281612.l9SGC4xX20881507@yorick.bic.mni.mcgill.ca> Hello, > --> the result: before conversion values (before -> after) are 654 -> 672 in one point. If i take a different points its for example 232 -> 116 and so on. There is no real pattern but if one looks at the images with register both seems to be "quite" similar. > > Any suggestions what i did wrong? This looks like the way minc stores integer data with ranges. Try -float instead of -short. Is this better? > P.S.: I tried to install minc 2.0.13 and 2.0.14 with the following error when i type "make" after ./configure You have to tell configure that you are building minc2. Try the following: ./configure --enable-minc2 --with-minc2 I think one of the two minc2 flags is obsolete, but it does work with both. You also need --with-build-path=... for the path of hdf5 and netcdf. Hopefully, the INSTALL notes will be updated by next release. Claude From ed.gronenschild at mi.unimaas.nl Tue Oct 30 12:33:55 2007 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Tue, 30 Oct 2007 17:33:55 +0100 Subject: [MINC-users] Build error Message-ID: <520BEFE0-F894-4213-9577-760FBFA90AF1@mi.unimaas.nl> Hi, I'm developing an application using the minc libraries (in that order) libbicpl.a libminc.a libnetcdf.a libvolume_io.a libEBTKS.a. When I use some routines from the libbicpl.a library I get the following link errors: /../libbicpl.a(object.o) reference to undefined _sprintf$LDBLStub /../libbicpl.a(colours.o) reference to undefined _sprintf$LDBLStub /../libbicpl.a(colours.o) reference to undefined _sscanf$LDBLStub I dont know how to solve this as it seems that "sprintf" and "sscanf" are unknown whereas these are part of the StdIO library and used frequently throughout my application without any linking error. Do I miss a specific library? My platform is a Macintosh ( OSX 10.4.10) and I'm using Xcode 2.4.1. The minc software is the OSX 10.3 version and bicpl is version 1.4.2. Ed From a.janke at gmail.com Tue Oct 30 18:07:42 2007 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 31 Oct 2007 09:07:42 +1100 Subject: [MINC-users] mnc2nii conversion problem In-Reply-To: <200710281612.l9SGC4xX20881507@yorick.bic.mni.mcgill.ca> References: <200710281612.l9SGC4xX20881507@yorick.bic.mni.mcgill.ca> Message-ID: > > --> the result: before conversion values (before -> after) are 654 -> 672 in one point. If i take a different points its for example 232 -> 116 and so on. There is no real pattern but if one looks at the images with register both seems to be "quite" similar. > > > > Any suggestions what i did wrong? > > This looks like the way minc stores integer data with ranges. Try -float instead > of -short. Is this better? Claude is correct, there is always going to be rescaling going on with short/byte/int MINC images unless you pull a bunch of tricks with the nii2mnc and mnc2nii conversion. Given that you seem to want to preserve the real values in your data and not the voxel values what Claude is suggesting (using float) is the best alternative. a simple: mincreshape -float short.mnc out.mnc before the conversion to nii should solve the problem. > > P.S.: I tried to install minc 2.0.13 and 2.0.14 with the following error when i type "make" after ./configure > > You have to tell configure that you are building minc2. Try the following: > > ./configure --enable-minc2 --with-minc2 > > I think one of the two minc2 flags is obsolete, but it does work with both. You > also need --with-build-path=... for the path of hdf5 and netcdf. The correct configure flag for minc2 itself is --enable-minc2 and for the other programs when linked against minc2 is --with-minc2. I dont agree with the ambiguity but I didnt write that bit! (this is my excuse) I subsequently added --with-minc2 to the minc library build to save on some confusion and left the old --enable-minc2 flag in there for backwards compatibility. a From a.janke at gmail.com Tue Oct 30 18:09:51 2007 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 31 Oct 2007 09:09:51 +1100 Subject: [MINC-users] Intracranial volume In-Reply-To: <200710261437.l9QEbFQp20549891@yorick.bic.mni.mcgill.ca> References: <200710261437.l9QEbFQp20549891@yorick.bic.mni.mcgill.ca> Message-ID: Well I am sure that Louis would disagree here... ;) He wrote a thing called BICCR (Brain Intra-Cranial Capacity Ratio) at one stage and published a paper on it. I am not sure where the scripts are to do it though! Perhaps email Louis Collins directly and he can point you in the direction of the code that he used to do it. Either that or the FSL route shoudl work too. a On 10/27/07, Claude LEPAGE wrote: > Hi Ed, > > I'm not aware of any tool to compute ICV at the BIC (maybe there > is one but I don't know). Anyone here knows? > > I would suggest to try the -s option in FSL BET: > > -s : generate approximate skull image > > I've never tried it, but maybe you can use it for ICV. My guess is > that it probably finds the external boundary of the skull as opposed > to the inner boundary. Worth trying if you are curious. > > > The problem with skullstripping tools (e.g. FSL BET) is > > that not only the skull is removed but also the dura and > > the cerebrospinal fluid exterior to the brain. So, > > skullstripping is in fact brain extraction. However, I > > want to know the volume just inside the skull, the > > so-called intracranial volume (ICV). Is there a MINC tool > > available to derive the ICV? > > > > Ed > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From a.janke at gmail.com Tue Oct 30 18:11:34 2007 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 31 Oct 2007 09:11:34 +1100 Subject: [MINC-users] Problems in installing display on Mac OS X In-Reply-To: <001b01c817ab$f1349260$ce005b0a@fbfplv.it> References: <001b01c817ab$f1349260$ce005b0a@fbfplv.it> Message-ID: Hi Anna, You will find all the tools in /usr/local/mni/bin To use them you will have to add this to your $PATH variable in your .bashrc or .tcshrc/.cshrc in your home directory. >From memory Macs use Bash by default so adding this line to your ~/.bashrc should work: export PATH=$PATH:/usr/local/mni/bin a On 10/26/07, Anna Caroli wrote: > Dear MINC list, > I'm trying to install Display on Mac OS X. > I first installed Netcdf, Minc and Bicpl as required, and than Display > (using display-1.4.1.pkg.tar, downloaded from the MNI website). > The strangeness is that, despite all the installations seem to work fine, I > can't find any of the programs installed anywhere (neither searching by > myself nor using the finder) ... > Did anybody of you have the same problem? Do you have any suggestion about > what is wrong with it? > > In the Display installation instructions I saw that openGL is also required. > Could anybody of you give me a link where I can download it for Mac OSX? > > Thanks a lot for your help! > > Anna > > Laboratory of Epidemiology, Neuroimaging & Telemedicine > IRCCS San Giovanni di Dio FBF - The National Center for Research and Care of > Alzheimer's Disease > via Pilastroni 4, 25125 - Brescia, Italy > Tel: +39 030 3501 361, Fax: +39 02 700 435 727 > > http://www.irccs-fatebenefratelli.it/ > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From sorench at gmail.com Wed Oct 31 01:12:23 2007 From: sorench at gmail.com (Soren Christensen) Date: Wed, 31 Oct 2007 16:12:23 +1100 Subject: [MINC-users] Display - global Message-ID: Hi, Is there a good place to find documentation for how to use the Display -global option? I'd like to customize the window size and the proportion of the window allocated to the transverse section as well as the colormap windowing in order to speed up screening and QA of multiple subjects. The global_variables.h seem to contain default settings, but when I use them with the -global option it seems to have no effect. So what I am looking for is: 1) Name of the variables i need to change: (colormap min,max window position and width+hight size of transverse rendering inside window) 2) How to do this using the command line or alternatively configuration file or in another way. Cheers Soren