From cjb@pet.auh.dk Wed Dec 1 02:39:04 2004 From: cjb@pet.auh.dk (Christopher Bailey) Date: Wed Dec 1 02:39:04 2004 Subject: [MINC-users] Anatomical labelling of MINC files In-Reply-To: <848D8250-42EB-11D9-8B6E-000A95DBBFD8@bic.mni.mcgill.ca> References: <1101465471.18360.118.camel@kafka.pet.auh.dk> <5148BED6-3FC1-11D9-8B6E-000A95DBBFD8@bic.mni.mcgill.ca> <1101733507.2971.5.camel@kafka.pet.auh.dk> <848D8250-42EB-11D9-8B6E-000A95DBBFD8@bic.mni.mcgill.ca> Message-ID: <1101886708.6280.10.camel@kafka.pet.auh.dk> On Tue, 2004-11-30 at 17:18, Jason Lerch wrote: > ASP is not yet publicly available, but if all you want are rough > surfaces to use for illustration purposes, cortical_surface (available > on our web-site) should provide you with what you need. If you really > think you need high quality representation of the inner and outer > cortical surfaces, contact Alan Evans (alan@bic.mni.mcgill.ca) to plead > your case for getting the source code to ASP and/or its descendant > CLASP. > I can wait with (CL)ASP; as you said, a simple surface is sufficient for illustration purposes. However, I wasn't able to find cortical_surface. It wouldn't be the first time I miss something, but I'd appreciate a URL...? "All" I want is a simple tool (simple to help others use, anyway) for creating a cortical surface, preferrably inflated to display as much cortex as possible. I would also like to overlay 3D volumes (parametric maps, typically) on that surface. Best, -Chris -- Christopher Bailey PET Centre and Center for Functionally Integrative Neuroscience Aarhus University Hospital, Denmark http://www.cfin.au.dk/ From cjb@pet.auh.dk Wed Dec 1 02:57:09 2004 From: cjb@pet.auh.dk (Christopher Bailey) Date: Wed Dec 1 02:57:09 2004 Subject: [MINC-users] PET analysis on MINC files In-Reply-To: <1101814129.25110.126.camel@dhania.fmrib.ox.ac.uk> References: <1101465108.18360.107.camel@kafka.pet.auh.dk> <1101814129.25110.126.camel@dhania.fmrib.ox.ac.uk> Message-ID: <1101887772.6280.28.camel@kafka.pet.auh.dk> On Tue, 2004-11-30 at 12:28, Morgan Hough wrote: > Dear Chris, > > I am interested to know what it would take to do PET analysis with FSL > Tools. With the MINC support in place, what tools would need changes? I'll be bold and try to answer this question. In short: none. With proper choices of parameters, the FSL tools can be used directly for PET (blood flow) data. > McFLIRT, FLIRT - should these work as is? In principle, they should work. MCFLIRT is the motion correction script calling FLIRT, the registration program, in an EPI-optimized way. You'd probably want to consider having a look at MCFLIRT's options before using it on PET frames. FLIRT is not PET2MR-optimized, so it may not produce ideal results without some tweaking. > FUGUE, BET and FAST - is there a inhomogenity problem to deal with? > - is the intensity modeling just the kinetics > - does it help to have the tissue types? FUGUE: No, PET has no inhomogeneity issues. BET: Brain extraction (nothing to do with PET). FAST: Segmentation, also not relevant for PET. > FEAT - If GLIM is just GLM then I assume this is fine > - is everything block design in PET? > - is there an equivalent to the HRF? There are some default settings of FEAT that should be changed when using FEAT on a PET dataset. There has been info on this on the FSL mailing list. Basically, highpass filtering is out. So is FILM, a prewhitening step before FMRI model fitting. Global normalization might make more sense in PET. There's no PET HRF. PET acquisitions are blocked, yes. The GLM is exactly what's needed. > MELODIC - does anybody use ICA with PET? I don't see many papers but > there are some. MELODIC is a special case of ICA: it's "spatio-temporal". In PET, we don't have the temporal dimension of FMRI, so it's not relevant. ICA can and has been used in PET applications, but only in "spatial" mode, i.e. looking for "spatially independent components" in 3D volumetric data. So MELODIC's not relevant for PET either. > I have been reading some papers about the kinetic models and it seems > like with increasing temporal resolution there are some opportunities to > really improve analysis. Do you think this is the case? Are these kinds > of scanners common now? > Kinetic modelling of tracer kinetics using PET is an active field, yes. The temporal resolution involved, however, is on the order of 10 seconds. That is typically enough to study the kinetics of even metabolised tracers in the body. I think PET is moving into higher spatial, not temporal resolutions. Best regards, -Chris -- Christopher Bailey PET Centre and Center for Functionally Integrative Neuroscience Aarhus University Hospital, Denmark http://www.cfin.au.dk/ From m.audette@aist.go.jp Wed Dec 1 06:57:04 2004 From: m.audette@aist.go.jp (Michel Audette) Date: Wed Dec 1 06:57:04 2004 Subject: [MINC-users] biModalT option of mincstats Message-ID: <000f01c4d870$a20cc860$07751d96@surgsim5> Hi everyone, I've been trying to use mincstats just now with CT data, and the option -biModalT produces the highest value of the volume for some reason 32739. Has anyone seen this bug? Is there some kind of initialization required? Please advise, Michel Michel Audette, Ph.D., Research Fellow, Surgical Simulation, Surgical Assist Group, AIST, Namiki 1-2, Tsukuba, Japan, 305-8564 From andrew_janke@iinet.net.au Wed Dec 1 07:35:04 2004 From: andrew_janke@iinet.net.au (Andrew Janke) Date: Wed Dec 1 07:35:04 2004 Subject: [MINC-users] biModalT option of mincstats In-Reply-To: <000f01c4d870$a20cc860$07751d96@surgsim5> References: <000f01c4d870$a20cc860$07751d96@surgsim5> Message-ID: On Thu, 2 Dec 2004, Michel Audette wrote: > I've been trying to use mincstats just now with CT data, and the > option -biModalT produces the highest value of the volume for some reason > 32739. Has anyone seen this bug? Is there some kind of initialization > required? There was a bug in mincstats that would cause this behaviour on certain types of files with certain histogram properties. It has been fixed (but will still not be identical to volume_stats for other reasons) in CVS. I am not sure as to whether there has been another release of minc since then. bert? -- Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From andrew_janke@iinet.net.au Tue Dec 7 17:36:06 2004 From: andrew_janke@iinet.net.au (Andrew Janke) Date: Tue Dec 7 17:36:06 2004 Subject: [MINC-users] mincsample Message-ID: For those who want to generate (possibly) random samplings from a minc file for use in a Mixture model or the likes, the following new little tool may prove useful. http://www.bic.mni.mcgill.ca/~rotor/distro/tgz/mincsample-1.2.tar.gz If you happen to use it I'd be gratefull if you could send bug/usage reports. If you would like a feature added, I'd be more than happy to see what can be done. -- Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From beau.sapach@ualberta.ca Wed Dec 8 06:40:07 2004 From: beau.sapach@ualberta.ca (Beau Sapach) Date: Wed Dec 8 06:40:07 2004 Subject: [MINC-users] Building EBTKS Message-ID: <200412072230.iB7MUnCe018958@pilsener.srv.ualberta.ca> Hi everyone, I'm having some trouble building EBTKS 1.3. ./configure seems to run just fine but make fails. Has anyone seen this before? Any help would be much appreciated! Thanks! Beau ******** variables **************** CC=/usr/bin/gcc CXX=/usr/bin/c++ ******** configure output ********** checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for gcc... /usr/bin/gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /usr/bin/gcc accepts -g... yes checking for /usr/bin/gcc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of /usr/bin/gcc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether /usr/bin/c++ accepts -g... yes checking dependency style of /usr/bin/c++... gcc3 checking how to run the C preprocessor... /usr/bin/gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking values.h usability... yes checking values.h presence... yes checking for values.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for ld used by GCC... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking for a sed that does not truncate output... /bin/sed checking how to recognise dependent libraries... pass_all checking command to parse /usr/bin/nm -B output... ok checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for ranlib... ranlib checking for strip... strip checking for objdir... .libs checking for /usr/bin/gcc option to produce PIC... -fPIC checking if /usr/bin/gcc PIC flag -fPIC works... yes checking if /usr/bin/gcc static flag -static works... yes checking if /usr/bin/gcc supports -c -o file.o... yes checking if /usr/bin/gcc supports -c -o file.lo... yes checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions... yes checking whether the linker (/usr/bin/ld) supports shared libraries... yes checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking dynamic linker characteristics... GNU/Linux ld.so checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes creating libtool checking for finite... yes checking for isfinite... no checking for mkstemp... yes configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands ******** make output ************* make all-am make[1]: Entering directory `/root/EBTKS-1.3' if /bin/sh ./libtool --mode=compile /usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -g -O2 -MT version.lo -MD -MP -MF ".deps/version.Tpo" \ -c -o version.lo `test -f 'version.cc' || echo './'`version.cc; \ then mv ".deps/version.Tpo" ".deps/version.Plo"; \ else rm -f ".deps/version.Tpo"; exit 1; \ fi /usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -g -O2 -MT version.lo -MD -MP -MF .deps/version.Tpo -c version.cc -o version.o echo timestamp > version.lo if /bin/sh ./libtool --mode=compile /usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -g -O2 -MT FileIO.lo -MD -MP -MF ".deps/FileIO.Tpo" \ -c -o FileIO.lo `test -f 'src/FileIO.cc' || echo './'`src/FileIO.cc; \ then mv ".deps/FileIO.Tpo" ".deps/FileIO.Plo"; \ else rm -f ".deps/FileIO.Tpo"; exit 1; \ fi /usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -g -O2 -MT FileIO.lo -MD -MP -MF .deps/FileIO.Tpo -c src/FileIO.cc -o FileIO.o In file included from ./include/trivials.h:42, from ./templates/SimpleArray.h:23, from ./include/MString.h:24, from ./include/Path.h:23, from ./include/FileIO.h:26, from src/FileIO.cc:21: ./templates/miscTemplateFunc.h: In function `Histogram& add(Histogram&, const SimpleArray&)': ./templates/miscTemplateFunc.h:102: error: invalid use of undefined type `struct Histogram' ./templates/miscTemplateFunc.h:28: error: forward declaration of `struct Histogram' In file included from ./include/MString.h:24, from ./include/Path.h:23, from ./include/FileIO.h:26, from src/FileIO.cc:21: ./templates/SimpleArray.h: In member function `unsigned int SimpleArray::occurrencesOf(Type) const': ./templates/SimpleArray.h:100: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h:100: error: (Each undeclared identifier is reported only once for each function it appears in.) ./templates/SimpleArray.h: In member function `int SimpleArray::indexOf(Type, int) const': ./templates/SimpleArray.h:106: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `virtual void SimpleArray::qsort(int (*)(const void*, const void*))': ./templates/SimpleArray.h:130: error: `_contents' undeclared (first use this function) ./templates/SimpleArray.h:130: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `virtual void SimpleArray::qsortAscending()': ./templates/SimpleArray.h:132: error: `_contents' undeclared (first use this function) ./templates/SimpleArray.h:132: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `virtual void SimpleArray::qsortDescending()': ./templates/SimpleArray.h:134: error: `_contents' undeclared (first use this function) ./templates/SimpleArray.h:134: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `double SimpleArray::mean() const': ./templates/SimpleArray.h:144: error: `_size' undeclared (first use this function) ./templates/SimpleArray.h: In member function `SimpleArray SimpleArray::operator-() const': ./templates/SimpleArray.h:190: error: `_size' undeclared (first use this function) make[1]: *** [FileIO.lo] Error 1 make[1]: Leaving directory `/root/EBTKS-1.3' make: *** [all] Error 2 From andrew_janke@iinet.net.au Wed Dec 8 06:55:06 2004 From: andrew_janke@iinet.net.au (Andrew Janke) Date: Wed Dec 8 06:55:06 2004 Subject: [MINC-users] Building EBTKS In-Reply-To: <200412072230.iB7MUnCe018958@pilsener.srv.ualberta.ca> References: <200412072230.iB7MUnCe018958@pilsener.srv.ualberta.ca> Message-ID: Which version of gcc is /usr/bin/gcc? There have been a number of template problems with EBTKS and gcc, the most reliable thing to do seems to be to use at least gcc 3.3 a On Tue, 7 Dec 2004, Beau Sapach wrote: > I'm having some trouble building EBTKS 1.3. ./configure seems to run just > fine but make fails. Has anyone seen this before? Any help would be much > appreciated! Thanks! > > Beau > > ******** variables **************** > > CC=/usr/bin/gcc > CXX=/usr/bin/c++ > > > ******** configure output ********** > > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for gawk... gawk > checking whether make sets $(MAKE)... yes > checking for a BSD-compatible install... /usr/bin/install -c > checking whether ln -s works... yes > checking whether make sets $(MAKE)... (cached) yes > checking for gcc... /usr/bin/gcc > checking for C compiler default output... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether /usr/bin/gcc accepts -g... yes > checking for /usr/bin/gcc option to accept ANSI C... none needed > checking for style of include used by make... GNU > checking dependency style of /usr/bin/gcc... gcc3 > checking whether we are using the GNU C++ compiler... yes > checking whether /usr/bin/c++ accepts -g... yes > checking dependency style of /usr/bin/c++... gcc3 > checking how to run the C preprocessor... /usr/bin/gcc -E > checking for egrep... grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking values.h usability... yes > checking values.h presence... yes > checking for values.h... yes > checking malloc.h usability... yes > checking malloc.h presence... yes > checking for malloc.h... yes > checking build system type... i686-pc-linux-gnu > checking host system type... i686-pc-linux-gnu > checking for ld used by GCC... /usr/bin/ld > checking if the linker (/usr/bin/ld) is GNU ld... yes > checking for /usr/bin/ld option to reload object files... -r > checking for BSD-compatible nm... /usr/bin/nm -B > checking for a sed that does not truncate output... /bin/sed > checking how to recognise dependent libraries... pass_all > checking command to parse /usr/bin/nm -B output... ok > checking dlfcn.h usability... yes > checking dlfcn.h presence... yes > checking for dlfcn.h... yes > checking for ranlib... ranlib > checking for strip... strip > checking for objdir... .libs > checking for /usr/bin/gcc option to produce PIC... -fPIC > checking if /usr/bin/gcc PIC flag -fPIC works... yes > checking if /usr/bin/gcc static flag -static works... yes > checking if /usr/bin/gcc supports -c -o file.o... yes > checking if /usr/bin/gcc supports -c -o file.lo... yes > checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions... yes > checking whether the linker (/usr/bin/ld) supports shared libraries... yes > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking dynamic linker characteristics... GNU/Linux ld.so > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... no > checking whether to build static libraries... yes > creating libtool > checking for finite... yes > checking for isfinite... no > checking for mkstemp... yes > configure: creating ./config.status > config.status: creating Makefile > config.status: creating config.h > config.status: executing depfiles commands > > > ******** make output ************* > > make all-am > make[1]: Entering directory `/root/EBTKS-1.3' > if /bin/sh ./libtool --mode=compile /usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I. > -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -g -O2 -MT version.lo > -MD -MP -MF ".deps/version.Tpo" \ > -c -o version.lo `test -f 'version.cc' || echo './'`version.cc; \ > then mv ".deps/version.Tpo" ".deps/version.Plo"; \ > else rm -f ".deps/version.Tpo"; exit 1; \ > fi > /usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates > -DUSE_COMPMAT -DUSE_DBLMAT -g -O2 -MT version.lo -MD -MP -MF > .deps/version.Tpo -c version.cc -o version.o > echo timestamp > version.lo > if /bin/sh ./libtool --mode=compile /usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I. > -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -g -O2 -MT FileIO.lo > -MD -MP -MF ".deps/FileIO.Tpo" \ > -c -o FileIO.lo `test -f 'src/FileIO.cc' || echo './'`src/FileIO.cc; \ > then mv ".deps/FileIO.Tpo" ".deps/FileIO.Plo"; \ > else rm -f ".deps/FileIO.Tpo"; exit 1; \ > fi > /usr/bin/c++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates > -DUSE_COMPMAT -DUSE_DBLMAT -g -O2 -MT FileIO.lo -MD -MP -MF .deps/FileIO.Tpo > -c src/FileIO.cc -o FileIO.o > In file included from ./include/trivials.h:42, > from ./templates/SimpleArray.h:23, > from ./include/MString.h:24, > from ./include/Path.h:23, > from ./include/FileIO.h:26, > from src/FileIO.cc:21: > ./templates/miscTemplateFunc.h: In function `Histogram& add(Histogram&, > const SimpleArray&)': > ./templates/miscTemplateFunc.h:102: error: invalid use of undefined type > `struct Histogram' > ./templates/miscTemplateFunc.h:28: error: forward declaration of `struct > Histogram' > In file included from ./include/MString.h:24, > from ./include/Path.h:23, > from ./include/FileIO.h:26, > from src/FileIO.cc:21: > ./templates/SimpleArray.h: In member function `unsigned int > SimpleArray::occurrencesOf(Type) const': > ./templates/SimpleArray.h:100: error: `_size' undeclared (first use this > function) > ./templates/SimpleArray.h:100: error: (Each undeclared identifier is > reported only once for each function it appears in.) > ./templates/SimpleArray.h: In member function `int > SimpleArray::indexOf(Type, int) const': > ./templates/SimpleArray.h:106: error: `_size' undeclared (first use this > function) > ./templates/SimpleArray.h: In member function `virtual void > SimpleArray::qsort(int (*)(const void*, const void*))': > ./templates/SimpleArray.h:130: error: `_contents' undeclared (first use this > function) > ./templates/SimpleArray.h:130: error: `_size' undeclared (first use this > function) > ./templates/SimpleArray.h: In member function `virtual void > SimpleArray::qsortAscending()': > ./templates/SimpleArray.h:132: error: `_contents' undeclared (first use this > function) > ./templates/SimpleArray.h:132: error: `_size' undeclared (first use this > function) > ./templates/SimpleArray.h: In member function `virtual void > SimpleArray::qsortDescending()': > ./templates/SimpleArray.h:134: error: `_contents' undeclared (first use this > function) > ./templates/SimpleArray.h:134: error: `_size' undeclared (first use this > function) > ./templates/SimpleArray.h: In member function `double > SimpleArray::mean() const': > ./templates/SimpleArray.h:144: error: `_size' undeclared (first use this > function) > ./templates/SimpleArray.h: In member function `SimpleArray > SimpleArray::operator-() const': > ./templates/SimpleArray.h:190: error: `_size' undeclared (first use this > function) > make[1]: *** [FileIO.lo] Error 1 > make[1]: Leaving directory `/root/EBTKS-1.3' > make: *** [all] Error 2 > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > -- Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From cogilvie@ualberta.ca Wed Dec 8 16:31:07 2004 From: cogilvie@ualberta.ca (Catherine Ogilvie) Date: Wed Dec 8 16:31:07 2004 Subject: [MINC-users] ana2mnc problem Message-ID: <41BB9692@webmail.ualberta.ca> Hi. I'm trying to use ana2mnc for the first time. I have had a .img and .hdr pair sent to me from another lab which uses analyze. When I run ana2mnc I get this: ana2mnc: sizeof header: 1543569408 ana2mnc: Hrm, attempting byte-swapping on ANATcw.24_02_03_2.fid_001.hdr ana2mnc: No x origin info found, guessing.. ana2mnc: No y origin info found, guessing.. ana2mnc: No z origin info found, guessing.. and a very strangely pixelated output. I have read some of the archives and it seems that the byte-swapping may be the problem, if the file was moved from 1 computer to another, but I don't entirely understand this problem or how to fix it (if this is indeed what's wrong). thanks catherine ogilvie From andrew_janke@iinet.net.au Wed Dec 8 18:40:06 2004 From: andrew_janke@iinet.net.au (Andrew Janke) Date: Wed Dec 8 18:40:06 2004 Subject: [MINC-users] ana2mnc problem In-Reply-To: <41BB9692@webmail.ualberta.ca> References: <41BB9692@webmail.ualberta.ca> Message-ID: On Wed, 8 Dec 2004, Catherine Ogilvie wrote: > Hi. I'm trying to use ana2mnc for the first time. I have had a .img and .hdr > pair sent to me from another lab which uses analyze. When I run ana2mnc I get > this: > > ana2mnc: sizeof header: 1543569408 > ana2mnc: Hrm, attempting byte-swapping on ANATcw.24_02_03_2.fid_001.hdr > ana2mnc: No x origin info found, guessing.. > ana2mnc: No y origin info found, guessing.. > ana2mnc: No z origin info found, guessing.. > > and a very strangely pixelated output. I'm guessing that when you tranferred the data, the header was byte swapped and the data wasn't. Try this version of ana2mnc http://www.bic.mni.mcgill.ca/~rotor/distro/ana2mnc-1.3c using the -swap_data option. If this works, I'll add this feature into the next release of ana2mnc -- Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From cjb@pet.auh.dk Thu Dec 9 05:01:07 2004 From: cjb@pet.auh.dk (Christopher Bailey) Date: Thu Dec 9 05:01:07 2004 Subject: [MINC-users] NifTi <-> MINC ? Message-ID: <1102586427.3751.14.camel@kafka.pet.auh.dk> Dear list (not to mention Andrew ;), Has anyone out there written a NifTi <-> MINC converter? With the new analyze replacement, there's some hope of L-R consistency etc. when converting to/from MINC. I still vow to lobby inclusion of MINC I/O in FSL, but until that happens, I'm stuck with converting. Just wanted to hear if anyone had already put effort into this (re-inventing the wheel, and all that...). Cheers, Chris -- Christopher Bailey PET Centre and Center for Functionally Integrative Neuroscience Aarhus University Hospital, Denmark http://www.cfin.au.dk/ From andrew_janke@iinet.net.au Thu Dec 9 05:48:07 2004 From: andrew_janke@iinet.net.au (Andrew Janke) Date: Thu Dec 9 05:48:07 2004 Subject: [MINC-users] NifTi <-> MINC ? In-Reply-To: <1102586427.3751.14.camel@kafka.pet.auh.dk> References: <1102586427.3751.14.camel@kafka.pet.auh.dk> Message-ID: On Thu, 9 Dec 2004, Christopher Bailey wrote: > Dear list (not to mention Andrew ;), > > Has anyone out there written a NifTi <-> MINC converter? With the new > analyze replacement, there's some hope of L-R consistency etc. when > converting to/from MINC. I still vow to lobby inclusion of MINC I/O in > FSL, but until that happens, I'm stuck with converting. > > Just wanted to hear if anyone had already put effort into this > (re-inventing the wheel, and all that...). Guilty as charged. I have begun some initial work on adding another analyze "type" to ana2mnc but haven't released anyhting yet. If only because I am yet to see some example NIFTI-1 files. So if you have some and can put them on a download site somewhere I'll then have something to test what I have with! My current approach was to wait untill someone asked for it and then worry about it. And now someone has..... :) -- Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From mhough@fmrib.ox.ac.uk Thu Dec 9 06:17:06 2004 From: mhough@fmrib.ox.ac.uk (Morgan Hough) Date: Thu Dec 9 06:17:06 2004 Subject: [MINC-users] NifTi <-> MINC ? In-Reply-To: References: <1102586427.3751.14.camel@kafka.pet.auh.dk> Message-ID: <1102590794.2578.8.camel@dhania.fmrib.ox.ac.uk> I have put a NIFTI structural file on http://www.fmrib.ox.ac.uk/~mhough/data.html I will put up a 4D functional dataset in a minute. I am just repackaging the FIL's example datasets from http://www.fil.ion.ucl.ac.uk/spm/data/ I am using their fMRI event-related repetition priming for SPM 99 data if you want the Analyze files (I am almost over quota in my directory:). Cheers, -Morgan -- Morgan Hough DPhil student FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK mhough@fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough tel +44 (0) 1865 222545 fax +44 (0) 1865 222717 On Thu, 2004-12-09 at 10:47, Andrew Janke wrote: > On Thu, 9 Dec 2004, Christopher Bailey wrote: > > > Dear list (not to mention Andrew ;), > > > > Has anyone out there written a NifTi <-> MINC converter? With the new > > analyze replacement, there's some hope of L-R consistency etc. when > > converting to/from MINC. I still vow to lobby inclusion of MINC I/O in > > FSL, but until that happens, I'm stuck with converting. > > > > Just wanted to hear if anyone had already put effort into this > > (re-inventing the wheel, and all that...). > > Guilty as charged. I have begun some initial work on adding another analyze > "type" to ana2mnc but haven't released anyhting yet. If only because I am yet to > see some example NIFTI-1 files. So if you have some and can put them on a > download site somewhere I'll then have something to test what I have with! > > My current approach was to wait untill someone asked for it and then worry about > it. And now someone has..... :) > > > > -- > Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) > Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From cjb@pet.auh.dk Thu Dec 9 06:50:09 2004 From: cjb@pet.auh.dk (Christopher Bailey) Date: Thu Dec 9 06:50:09 2004 Subject: [MINC-users] NifTi <-> MINC ? In-Reply-To: References: <1102586427.3751.14.camel@kafka.pet.auh.dk> Message-ID: <1102592962.3751.130.camel@kafka.pet.auh.dk> Thought so! I see Morgan has already provided some example data. Perhaps the details of the file (dimensions, steps, etc) would be handy when testing a converter. Morgan? As a caveat emptor to what I said previously, the next two paragraphs are by Mark Jenkinson on the FSL mailing list: " The current FSL release is a beta release and we have not yet taken advantage of the full set of possibilities that the nifti file format creates. Part of this is that we do not use qforms in any of our processing at present. We do use sforms for calculating standard space coordinates, as is implemented in the current version of fslview. Therefore, at present all fsl routines work in ijk coordinates in the same way that they always have before. As Dave says, the next version of fsl will be likely to support qforms. " So for some time to come we should be aware that the full NifTi specification is not used by FSL programs (SPM?). -Chris (volunteer beta tester) On Thu, 2004-12-09 at 11:47, Andrew Janke wrote: > On Thu, 9 Dec 2004, Christopher Bailey wrote: > > > Dear list (not to mention Andrew ;), > > > > Has anyone out there written a NifTi <-> MINC converter? With the new > > analyze replacement, there's some hope of L-R consistency etc. when > > converting to/from MINC. I still vow to lobby inclusion of MINC I/O in > > FSL, but until that happens, I'm stuck with converting. > > > > Just wanted to hear if anyone had already put effort into this > > (re-inventing the wheel, and all that...). > > Guilty as charged. I have begun some initial work on adding another analyze > "type" to ana2mnc but haven't released anyhting yet. If only because I am yet to > see some example NIFTI-1 files. So if you have some and can put them on a > download site somewhere I'll then have something to test what I have with! > > My current approach was to wait untill someone asked for it and then worry about > it. And now someone has..... :) > > > > -- > Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) > Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From mhough@fmrib.ox.ac.uk Thu Dec 9 07:55:05 2004 From: mhough@fmrib.ox.ac.uk (Morgan Hough) Date: Thu Dec 9 07:55:05 2004 Subject: [MINC-users] NifTi <-> MINC ? In-Reply-To: <1102592962.3751.130.camel@kafka.pet.auh.dk> References: <1102586427.3751.14.camel@kafka.pet.auh.dk> <1102592962.3751.130.camel@kafka.pet.auh.dk> Message-ID: <1102596680.2577.32.camel@dhania.fmrib.ox.ac.uk> Sorry. Good point. I have added information about the files to the webpage (http://www.fmrib.ox.ac.uk/~mhough/data.html) as well as a functional dataset. Hope this is useful. Cheers, -Morgan -- Morgan Hough DPhil student FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK mhough@fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough tel +44 (0) 1865 222545 fax +44 (0) 1865 222717 On Thu, 2004-12-09 at 11:49, Christopher Bailey wrote: > Thought so! > > I see Morgan has already provided some example data. Perhaps the details > of the file (dimensions, steps, etc) would be handy when testing a > converter. Morgan? > > As a caveat emptor to what I said previously, the next two paragraphs > are by Mark Jenkinson on the FSL mailing list: > > " > The current FSL release is a beta release and we have > not yet taken advantage of the full set of possibilities that > the nifti file format creates. Part of this is that we do not > use qforms in any of our processing at present. We do > use sforms for calculating standard space coordinates, > as is implemented in the current version of fslview. > > Therefore, at present all fsl routines work in ijk coordinates > in the same way that they always have before. As Dave says, > the next version of fsl will be likely to support qforms. > " > > So for some time to come we should be aware that the full NifTi > specification is not used by FSL programs (SPM?). > > -Chris (volunteer beta tester) > > On Thu, 2004-12-09 at 11:47, Andrew Janke wrote: > > On Thu, 9 Dec 2004, Christopher Bailey wrote: > > > > > Dear list (not to mention Andrew ;), > > > > > > Has anyone out there written a NifTi <-> MINC converter? With the new > > > analyze replacement, there's some hope of L-R consistency etc. when > > > converting to/from MINC. I still vow to lobby inclusion of MINC I/O in > > > FSL, but until that happens, I'm stuck with converting. > > > > > > Just wanted to hear if anyone had already put effort into this > > > (re-inventing the wheel, and all that...). > > > > Guilty as charged. I have begun some initial work on adding another analyze > > "type" to ana2mnc but haven't released anyhting yet. If only because I am yet to > > see some example NIFTI-1 files. So if you have some and can put them on a > > download site somewhere I'll then have something to test what I have with! > > > > My current approach was to wait untill someone asked for it and then worry about > > it. And now someone has..... :) > > > > > > > > -- > > Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) > > Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From bert@bic.mni.mcgill.ca Thu Dec 9 08:46:05 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Dec 9 08:46:05 2004 Subject: [MINC-users] NifTi <-> MINC ? In-Reply-To: <1102596680.2577.32.camel@dhania.fmrib.ox.ac.uk> Message-ID: Hi all, I've already written a prototype of this converter for inclusion in the next revision of MINC. So far it only works in one direction (MINC -> NIfTI-1). I'd appreciate any test data that you can provide, my main delay has been a lack of decent NIfTI-1 examples. -bert On Thu, 9 Dec 2004, Morgan Hough wrote: > Sorry. Good point. I have added information about the files to the > webpage (http://www.fmrib.ox.ac.uk/~mhough/data.html) as well as a > functional dataset. > > Hope this is useful. > > Cheers, > > -Morgan > > -- > Morgan Hough DPhil student > FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > mhough@fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough > tel +44 (0) 1865 222545 fax +44 (0) 1865 222717 > > On Thu, 2004-12-09 at 11:49, Christopher Bailey wrote: > > Thought so! > > > > I see Morgan has already provided some example data. Perhaps the details > > of the file (dimensions, steps, etc) would be handy when testing a > > converter. Morgan? > > > > As a caveat emptor to what I said previously, the next two paragraphs > > are by Mark Jenkinson on the FSL mailing list: > > > > " > > The current FSL release is a beta release and we have > > not yet taken advantage of the full set of possibilities that > > the nifti file format creates. Part of this is that we do not > > use qforms in any of our processing at present. We do > > use sforms for calculating standard space coordinates, > > as is implemented in the current version of fslview. > > > > Therefore, at present all fsl routines work in ijk coordinates > > in the same way that they always have before. As Dave says, > > the next version of fsl will be likely to support qforms. > > " > > > > So for some time to come we should be aware that the full NifTi > > specification is not used by FSL programs (SPM?). > > > > -Chris (volunteer beta tester) > > > > On Thu, 2004-12-09 at 11:47, Andrew Janke wrote: > > > On Thu, 9 Dec 2004, Christopher Bailey wrote: > > > > > > > Dear list (not to mention Andrew ;), > > > > > > > > Has anyone out there written a NifTi <-> MINC converter? With the new > > > > analyze replacement, there's some hope of L-R consistency etc. when > > > > converting to/from MINC. I still vow to lobby inclusion of MINC I/O in > > > > FSL, but until that happens, I'm stuck with converting. > > > > > > > > Just wanted to hear if anyone had already put effort into this > > > > (re-inventing the wheel, and all that...). > > > > > > Guilty as charged. I have begun some initial work on adding another analyze > > > "type" to ana2mnc but haven't released anyhting yet. If only because I am yet to > > > see some example NIFTI-1 files. So if you have some and can put them on a > > > download site somewhere I'll then have something to test what I have with! > > > > > > My current approach was to wait untill someone asked for it and then worry about > > > it. And now someone has..... :) > > > > > > > > > > > > -- > > > Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) > > > Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 > > > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From cjb@pet.auh.dk Thu Dec 9 09:44:05 2004 From: cjb@pet.auh.dk (Christopher Bailey) Date: Thu Dec 9 09:44:05 2004 Subject: [MINC-users] NifTi <-> MINC ? In-Reply-To: References: Message-ID: <1102603433.3751.243.camel@kafka.pet.auh.dk> Hi, The lack of much "pure" nifti data is probably due to not-that-many dicom2nifti converters out there. A quick Google only produced www.fmrib.ox.ac.uk/~robson/internal/Dicom2Nifti.htm FSL, for example, can read and write both analyze and nifti. By default, anything it's functions/programs write out will be gzipped nifti format. You can be cheaky and do avwmaths input.hdr -mul 1 output.nii.gz to get a nifti "copy" of an analyze file. This will only work in FSL > 3.2 beta. -Chris On Thu, 2004-12-09 at 14:45, Robert VINCENT wrote: > Hi all, > > I've already written a prototype of this converter for inclusion in the > next revision of MINC. So far it only works in one direction (MINC -> > NIfTI-1). I'd appreciate any test data that you can provide, my main > delay has been a lack of decent NIfTI-1 examples. > > -bert > > On Thu, 9 Dec 2004, Morgan Hough wrote: > > > Sorry. Good point. I have added information about the files to the > > webpage (http://www.fmrib.ox.ac.uk/~mhough/data.html) as well as a > > functional dataset. > > > > Hope this is useful. > > > > Cheers, > > > > -Morgan > > > > -- > > Morgan Hough DPhil student > > FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > > mhough@fmrib.ox.ac.uk www.fmrib.ox.ac.uk/~mhough > > tel +44 (0) 1865 222545 fax +44 (0) 1865 222717 > > > > On Thu, 2004-12-09 at 11:49, Christopher Bailey wrote: > > > Thought so! > > > > > > I see Morgan has already provided some example data. Perhaps the details > > > of the file (dimensions, steps, etc) would be handy when testing a > > > converter. Morgan? > > > > > > As a caveat emptor to what I said previously, the next two paragraphs > > > are by Mark Jenkinson on the FSL mailing list: > > > > > > " > > > The current FSL release is a beta release and we have > > > not yet taken advantage of the full set of possibilities that > > > the nifti file format creates. Part of this is that we do not > > > use qforms in any of our processing at present. We do > > > use sforms for calculating standard space coordinates, > > > as is implemented in the current version of fslview. > > > > > > Therefore, at present all fsl routines work in ijk coordinates > > > in the same way that they always have before. As Dave says, > > > the next version of fsl will be likely to support qforms. > > > " > > > > > > So for some time to come we should be aware that the full NifTi > > > specification is not used by FSL programs (SPM?). > > > > > > -Chris (volunteer beta tester) > > > > > > On Thu, 2004-12-09 at 11:47, Andrew Janke wrote: > > > > On Thu, 9 Dec 2004, Christopher Bailey wrote: > > > > > > > > > Dear list (not to mention Andrew ;), > > > > > > > > > > Has anyone out there written a NifTi <-> MINC converter? With the new > > > > > analyze replacement, there's some hope of L-R consistency etc. when > > > > > converting to/from MINC. I still vow to lobby inclusion of MINC I/O in > > > > > FSL, but until that happens, I'm stuck with converting. > > > > > > > > > > Just wanted to hear if anyone had already put effort into this > > > > > (re-inventing the wheel, and all that...). > > > > > > > > Guilty as charged. I have begun some initial work on adding another analyze > > > > "type" to ana2mnc but haven't released anyhting yet. If only because I am yet to > > > > see some example NIFTI-1 files. So if you have some and can put them on a > > > > download site somewhere I'll then have something to test what I have with! > > > > > > > > My current approach was to wait untill someone asked for it and then worry about > > > > it. And now someone has..... :) > > > > > > > > > > > > > > > > -- > > > > Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) > > > > Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 > > > > > > _______________________________________________ > > > MINC-users@bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From m.audette@aist.go.jp Fri Dec 10 01:51:05 2004 From: m.audette@aist.go.jp (Michel Audette) Date: Fri Dec 10 01:51:05 2004 Subject: [MINC-users] reading/writing MINC volumes in ITK Message-ID: <00fa01c4de87$16be2d90$3a751d96@surgsim2> Hello everyone, I have to give a talk and a workshop in mid-January http://www.socmedsim.org/meet2005/meet2005.html , and during my workshop, I plan to discuss publicly available image processing tools that can be used towards building anatomical models for medical simulation. I plan to bring up VTK and the MNI software toolbox, but before I bring up ITK as well, with which I am not very familiar, I was wondering if anyone has written ITK drivers for reading and writing MINC volumes. Please let me know. Michel Michel Audette, Ph.D., Research Fellow, Surgical Simulation, Surgical Assist Technology Group, AIST, Namiki 1-2, Tsukuba, Japan, 305-8564. -------------------------------------------------------- "If you think you can do it, you're right. If you think you can't do it, you're still right." - Henry Ford From cogilvie@ualberta.ca Mon Dec 13 11:51:06 2004 From: cogilvie@ualberta.ca (Catherine Ogilvie) Date: Mon Dec 13 11:51:06 2004 Subject: [MINC-users] reformating minc files for different resolution Message-ID: <41BE8FC8@webmail.ualberta.ca> I am wondering if it is possible to reformat minc 3D images in order to change the resolution/dimensions of the image. I.e., change the best resolution from axial to sagittal. I've heard in analyze you can do this by cubing the voxel size then reformatting, but I'm wondering if this can be done in display or another script/program. thanks for your help catherine ogilvie From jason@bic.mni.mcgill.ca Tue Dec 14 10:21:05 2004 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Tue Dec 14 10:21:05 2004 Subject: [MINC-users] reformating minc files for different resolution In-Reply-To: <41BE8FC8@webmail.ualberta.ca> References: <41BE8FC8@webmail.ualberta.ca> Message-ID: Greetings Catherine, the command 'mincreshape' is what you are looking for - it can reorder dimensions, etc. If you want to change resolution, then 'mincresample' will do what you need. Cheers, Jason On Dec 13, 2004, at 12:01 PM, Catherine Ogilvie wrote: > I am wondering if it is possible to reformat minc 3D images in order > to change > the resolution/dimensions of the image. I.e., change the best > resolution from > axial to sagittal. I've heard in analyze you can do this by cubing the > voxel > size then reformatting, but I'm wondering if this can be done in > display or > another script/program. > > thanks for your help > > catherine ogilvie > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From rbrook@cim.mcgill.ca Wed Dec 15 05:25:05 2004 From: rbrook@cim.mcgill.ca (Rupert Brooks) Date: Wed Dec 15 05:25:05 2004 Subject: [MINC-users] Re: reading/writing MINC volumes in ITK (Michel Audette) In-Reply-To: <200412101701.iBAH16fs6617496@shadow.bic.mni.mcgill.ca> References: <200412101701.iBAH16fs6617496@shadow.bic.mni.mcgill.ca> Message-ID: <1102952521.1403.7.camel@spender> As far as i know, there is no way to directly read MINC files in itk. I've been working with minc volumes in ITK for a while tho, but i use a kludgey way of getting the data in and out. Hi Michel, I convert into VTK format, using a simple python script based on the ATAMAI www.atamai.com minc reader. I have a corresponding script to go the other way too. ITK reads vtk format fine, but there is a defect in the conversion process which messes up the spacing. So I wrote a small itk program to patch that. Then i am good to go. I have a very clumsy viewer for volumes in the vtk format that lets me sanity check how stuff works out. If you want more details or to try it, let me know. Rupert B. On Fri, 2004-12-10 at 12:01, minc-users-request@bic.mni.mcgill.ca wrote: > Send MINC-users mailing list submissions to > minc-users@bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > or, via email, send a message with subject or body 'help' to > minc-users-request@bic.mni.mcgill.ca > > You can reach the person managing the list at > minc-users-admin@bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MINC-users digest..." > > > Today's Topics: > > 1. reading/writing MINC volumes in ITK (Michel Audette) > > --__--__-- > > Message: 1 > From: "Michel Audette" > To: > Date: Fri, 10 Dec 2004 16:08:44 +0900 > Subject: [MINC-users] reading/writing MINC volumes in ITK > > Hello everyone, > > I have to give a talk and a workshop in mid-January > http://www.socmedsim.org/meet2005/meet2005.html , and during my workshop, I > plan to discuss publicly available image processing tools that can be used > towards building anatomical models for medical simulation. I plan to bring > up VTK and the MNI software toolbox, but before I bring up ITK as well, with > which I am not very familiar, I was wondering if anyone has written ITK > drivers for reading and writing MINC volumes. > > Please let me know. > > Michel > > Michel Audette, Ph.D., > Research Fellow, Surgical Simulation, > Surgical Assist Technology Group, > AIST, > Namiki 1-2, > Tsukuba, Japan, > 305-8564. > -------------------------------------------------------- > "If you think you can do it, you're right. > If you think you can't do it, you're still right." > - Henry Ford > > > > --__--__-- > > _______________________________________________ > MINC-users mailing list > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > End of MINC-users Digest > -- -------------------------------------------------------------- Rupert Brooks McGill Centre for Intelligent Machines (www.cim.mcgill.ca) Ph.D Program in Intelligent Systems http://www.cyberus.ca/~rbrooks rbrook@cim.mcgill.ca From acaroli@oh-fbf.it Fri Dec 17 05:17:06 2004 From: acaroli@oh-fbf.it (Anna Caroli) Date: Fri Dec 17 05:17:06 2004 Subject: [MINC-users] Convert file.tag into Analyze format Message-ID: <000801c4e421$7738ee90$8a005b0a@fbfplv.it> Dear MINC users, Does anybody know how to convert a .tag file into an Analyze one? To better explain the problem: I manually draw ROIs on MRIs using Display software and I got files .tag; now I'd like to study MRIs (with ROIs drawn) with SPM... How can I do that? Thanks a lot for your help and best regards! 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 www.centroAlzheimer.it From bert@bic.mni.mcgill.ca Fri Dec 17 08:33:04 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Fri Dec 17 08:33:04 2004 Subject: [MINC-users] Convert file.tag into Analyze format In-Reply-To: <000801c4e421$7738ee90$8a005b0a@fbfplv.it> Message-ID: Hi Anna, I think it would be possible using a multistep process starting with "tagtominc" to go back to a MINC format file, then using mnc2ana to convert to Analyze. I've never done this so this is may not be the best method. Perhaps others will have a more authoritative suggestion... "tagtominc" is part of the "conglomerate" tools, available here: http://www.bic.mni.mcgill.ca/software/distribution/ "mnc2ana" and "ana2mnc" are available here: http://www.cmr.uq.edu.au/~rotor/software/ I hope this helps. -bert On Fri, 17 Dec 2004, Anna Caroli wrote: > Dear MINC users, > Does anybody know how to convert a .tag file into an Analyze one? > To better explain the problem: I manually draw ROIs on MRIs using Display > software and I got files .tag; now I'd like to study MRIs (with ROIs drawn) > with SPM... How can I do that? Thanks a lot for your help and best regards! > > 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 www.centroAlzheimer.it > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From andrew_janke@iinet.net.au Sat Dec 18 04:18:05 2004 From: andrew_janke@iinet.net.au (Andrew Janke) Date: Sat Dec 18 04:18:05 2004 Subject: [MINC-users] Convert file.tag into Analyze format In-Reply-To: <000801c4e421$7738ee90$8a005b0a@fbfplv.it> References: <000801c4e421$7738ee90$8a005b0a@fbfplv.it> Message-ID: On Fri, 17 Dec 2004, Anna Caroli wrote: > Does anybody know how to convert a .tag file into an Analyze one? > To better explain the problem: I manually draw ROIs on MRIs using Display > software and I got files .tag; now I'd like to study MRIs (with ROIs drawn) > with SPM... How can I do that? Thanks a lot for your help and best regards! THe most straightforward approach may be to save your traced labels as .mnc files within Display. When you are in the save 'menu' you will note that you can either save your labels as a .tag or a .mnc. I believe it is possible to reload your .tag files and then same them as .mnc ie: Display -label labels.tag >From here, I suspect you want your labels with the same sampling as your input file for alater analyze analysis. (Display saves the label in the smallest possible minc volume it cna whilst maintaing the original resolution. So use mincresample: mincresample -like infile.mnc label.mnc label_res.mnc Then convert both to analyze: mnc2ana file.mnc file.hdr mnc2ana label.mnc label.hdr -- Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3390 6332 || M: +61 4 2138 8581 From louis.collins@mcgill.ca Sun Dec 19 03:41:05 2004 From: louis.collins@mcgill.ca (D. Louis Collins) Date: Sun Dec 19 03:41:05 2004 Subject: [MINC-users] Convert file.tag into Analyze format In-Reply-To: <000801c4e421$7738ee90$8a005b0a@fbfplv.it> References: <000801c4e421$7738ee90$8a005b0a@fbfplv.it> Message-ID: <568CDBA2-5038-11D9-BB10-000D93520AA0@mcgill.ca> Anna, When using Display, painted voxels can be saved as labels in a minc volume. The minc volume will be byte valued, and will be in register with the volume used for painting. You can save painted labels: from the top menu -> T(file) -> W(save labels mnc) -> and then type in a filename at the command line. this will save a minc volume of the labels (but the volume will be cropped to the smallest extent that covers the labels). If you want the label volume to have voxel-to-voxel correspondance (for SPM analysis, for example), then do: from the top menu -> T(file) -> 1(crop save labels) -> W(save labels mnc) -> and then type in a filename at the command line. this way, your label volume will be as big as your original (same voxel extents) but might not be in the same order. I believe that by default, the label volumes are in x,y,z order. If you want the label volume to be exactly like the MRI volume (same voxel extents, same ordering) try: mincresample -nearest labels.mnc -like mri.mnc labels_reordered.mnc This command will resample the original labels.mnc file to be exactly like the mri volume in mri.mnc and put the result in labels_reordered.mnc. hope this helps, -Louis On Dec 17, 2004, at 5:16 AM, Anna Caroli wrote: > Dear MINC users, > Does anybody know how to convert a .tag file into an Analyze one? > To better explain the problem: I manually draw ROIs on MRIs using > Display > software and I got files .tag; now I'd like to study MRIs (with ROIs > drawn) > with SPM... How can I do that? Thanks a lot for your help and best > regards! > > 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 www.centroAlzheimer.it > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >