From lau at bic.mni.mcgill.ca Fri Feb 3 10:38:37 2006 From: lau at bic.mni.mcgill.ca (Jonathan LAU) Date: Fri, 3 Feb 2006 10:38:37 -0500 Subject: [MINC-users] mni_autoreg and bicpl cannot find minc2 during configuration Message-ID: <20060203153837.GB3329926@shadow.bic.mni.mcgill.ca> Hi, Sorry if this issue has already been addressed before. I am trying to compile the basic packages against minc2 (minc2.0.09). So far, I have been able to successfully install the packages in the following order: netcdf-3.6.0-p1 hdf5-1.6.1 EBTKS-1.4 minc-2.0.09 However, for mni_autoreg-0.98u and bicpl-1.4.2, I get the following problem: > ./configure --prefix=foo_dir --with-build-path=foo_dir (where foo_dir is where all the other packages are installed) ... checking for library minc... no configure: error: cannot find required library minc ... This was not a problem when I previously installed against minc1.4. Is there some flag that I need to specify during configuration to get the script to recognize minc2? I tried defining LD_LIBRARY_PATH=foo_dir/lib and LD_RUN_PATH=foo_dir/lib as initial configuration parameters but this didn't see to work for me. Help is appreciated! Cheers, Jonathan From acveilleux at mrs.mni.mcgill.ca Fri Feb 3 11:05:09 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 3 Feb 2006 11:05:09 -0500 Subject: [MINC-users] mni_autoreg and bicpl cannot find minc2 during configuration In-Reply-To: <20060203153837.GB3329926@shadow.bic.mni.mcgill.ca>; from lau@bic.mni.mcgill.ca on Fri, Feb 03, 2006 at 10:38:37AM -0500 References: <20060203153837.GB3329926@shadow.bic.mni.mcgill.ca> Message-ID: <20060203110509.A6245@mrs.mni.mcgill.ca> On Fri, Feb 03, 2006 at 10:38:37AM -0500, Jonathan LAU wrote: > > > ./configure --prefix=foo_dir --with-build-path=foo_dir > (where foo_dir is where all the other packages are installed) Add --with-minc2 to the configure command-line and try it again. Alex From lau at bic.mni.mcgill.ca Fri Feb 3 11:20:19 2006 From: lau at bic.mni.mcgill.ca (Jonathan LAU) Date: Fri, 3 Feb 2006 11:20:19 -0500 Subject: [MINC-users] mni_autoreg and bicpl cannot find minc2 during configuration In-Reply-To: <20060203110509.A6245@mrs.mni.mcgill.ca> References: <20060203153837.GB3329926@shadow.bic.mni.mcgill.ca> <20060203110509.A6245@mrs.mni.mcgill.ca> Message-ID: <20060203162018.GC3329926@shadow.bic.mni.mcgill.ca> Awesome thanks! Jonathan On Fri, Feb 03, 2006 at 11:05:09AM -0500, Alexandre CARMEL-VEILLEUX wrote: > On Fri, Feb 03, 2006 at 10:38:37AM -0500, Jonathan LAU wrote: > > > > > ./configure --prefix=foo_dir --with-build-path=foo_dir > > (where foo_dir is where all the other packages are installed) > > Add --with-minc2 to the configure command-line and try it again. > > Alex > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From steven.robbins at videotron.ca Sun Feb 5 01:54:39 2006 From: steven.robbins at videotron.ca (Steve M. Robbins) Date: Sun, 05 Feb 2006 01:54:39 -0500 Subject: [MINC-users] problems installing mni - N3 In-Reply-To: <43D63022.6060804@upvnet.upv.es> References: <43D63022.6060804@upvnet.upv.es> Message-ID: <20060205065436.GA8062@nyongwa.montreal.qc.ca> On Tue, Jan 24, 2006 at 02:48:18PM +0100, Juanjo Lull (UPV) wrote: > Hi Jason (or whoever is in charge of N3 by now...), > I have been trying to install N3, and after many hours of hard trying I > feel desperate because I always get the same error: No EBTKS libraries > found. I have those libraries installed, but no way. ./configure says it > can't find them and there is no possibility to compile the code. In this case, "configure" is misleading you. The log file you attach shows the following: > configure:4146: checking for library EBTKS > configure:4166: g++ -o conftest -g -O2 -I/home/jualulno/EBTKS-1.4/include -I/usr/local/mni/include -L/usr/local/mni/lib conftest.cc -lEBTKS >&5 > /usr/local/mni/lib/libEBTKS.a(MString.o)(.gnu.linkonce.t._ZNSt13_Format_cacheIcE6_S_getERSt8ios_base+0x69): In function `MString::MString[not-in-charge](char const*)': > /tmp/epm-build/EBTKS-1.3/templates/SimpleArray.h:60: undefined reference to `std::_Format_cache::_Format_cache[in-charge]()' > /usr/local/mni/lib/libEBTKS.a(MString.o)(.gnu.linkonce.t._ZNSt13_Format_cacheIcE11_S_callbackENSt8ios_base5eventERS1_i+0xd6): In function `MString::MString[not-in-charge](MString const&)': > /tmp/epm-build/EBTKS-1.3/templates/SimpleArray.h:60: undefined reference to `std::_Format_cache::_Format_cache[in-charge]()' > collect2: ld returned 1 exit status So we know that libEBTKS was found, in file /usr/local/mni/lib/libEBTKS.a Is that where you expected it? In plain language, the linker is saying that function MString::Mstring() found in libEBTKS requires function std::_Format_cache, which cannot be found. This often indicates that you have upgraded the C++ comiler or system libc since libEBTKS was built. Try rebuilding libEBTKS. -Steve From rbrooks at cyberus.ca Tue Feb 7 13:51:18 2006 From: rbrooks at cyberus.ca (Rupert Brooks) Date: Tue, 7 Feb 2006 13:51:18 -0500 Subject: [MINC-users] possible bug in cygwin minc2 tools Message-ID: Hi, I think i may have found a small bug in the Cygwin minc tools. If this is not the right place to report it please let me know where. It appears to me that minctoraw is bailing out when it encounters a byte of value 26 in a raw data file. If its what i think it is, Ive seen this type of thing before, and its because windows thinks of this byte (CTRL-Z) as an end of file character. There is some sort of option you pass to the in/out stream (in C++ anyway) to get around it. Anyway, to demonstrate the problem, i used the attached binary file, and the following command line. The numbers dont matter, i cut and pasted it from something. Anyway, this works great on the attached binary file, on unix, but fails on WinXP with the following message (the attached binary is just the following bytes 0 26 0 26 0 26 0 26) rawtominc: Premature end of file. I am using the Windows binaries for MINC2 contributed by Leila Baghdadi linked from the following page. http://www.bic.mni.mcgill.ca/software/minc/ I do not know whether this problem afflicts other MINC compilations. Rupert rawtominc -zyx -byte -unsigned -clobber -input 8bytes.raw -xstep 0.30664 -ystep 0.492 -zstep 0.30664 -origin -54.388 -66.8634 -43.9706 -xdircos 0.9965045488 -0.0338332 -0.0763806179 -ydircos 0.0280853 0.996779 -0.0751118973 -zdircos 0.0786759 0.0727041732 0.9942455 8bytes.mnc 2 2 2 -- -------------------------------------------------------------- Rupert Brooks McGill Centre for Intelligent Machines (www.cim.mcgill.ca) Ph.D Program in Intelligent Systems http://www.cyberus.ca/~rbrooks From bert at bic.mni.mcgill.ca Tue Feb 7 13:59:32 2006 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Tue, 7 Feb 2006 13:59:32 -0500 Subject: [MINC-users] possible bug in cygwin minc2 tools In-Reply-To: Message-ID: Hi Rupert, Thanks for the note. I'm sure your analysis is correct. I'll doublecheck our build processes for Windows and make sure this is fixed. -bert On Tue, 7 Feb 2006, Rupert Brooks wrote: > Hi, > > I think i may have found a small bug in the Cygwin minc tools. If > this is not the right place to report it please let me know where. > > It appears to me that minctoraw is bailing out when it encounters a > byte of value 26 in a raw data file. If its what i think it is, Ive > seen this type of thing before, and its because windows thinks of this > byte (CTRL-Z) as an end of file character. There is some sort of > option you pass to the in/out stream (in C++ anyway) to get around it. > > Anyway, to demonstrate the problem, i used the attached binary file, > and the following command line. The numbers dont matter, i cut and > pasted it from something. Anyway, this works great on the attached > binary file, on unix, but fails on WinXP with the following message > (the attached binary is just the following bytes 0 26 0 26 0 26 0 26) > > rawtominc: Premature end of file. > > I am using the Windows binaries for MINC2 contributed by Leila > Baghdadi linked from the following page. > http://www.bic.mni.mcgill.ca/software/minc/ I do not know whether this > problem afflicts other MINC compilations. > > Rupert > > rawtominc -zyx -byte -unsigned -clobber -input 8bytes.raw -xstep 0.30664 -ystep > 0.492 -zstep 0.30664 -origin -54.388 -66.8634 -43.9706 > -xdircos 0.9965045488 -0.0338332 -0.0763806179 > -ydircos 0.0280853 0.996779 -0.0751118973 > -zdircos 0.0786759 0.0727041732 0.9942455 8bytes.mnc 2 2 2 > > > > > > -- > -------------------------------------------------------------- > Rupert Brooks > McGill Centre for Intelligent Machines (www.cim.mcgill.ca) > Ph.D Program in Intelligent Systems > http://www.cyberus.ca/~rbrooks > From lau at bic.mni.mcgill.ca Tue Feb 7 16:22:39 2006 From: lau at bic.mni.mcgill.ca (Jonathan LAU) Date: Tue, 7 Feb 2006 16:22:39 -0500 Subject: [MINC-users] bicpl-1.4.2 default output for raster data Message-ID: <20060207212239.GB3441013@shadow.bic.mni.mcgill.ca> Hi, When building the bicpl library, are any of netpbm, ppm or sgi included by default? The README (dated 2003) says none are installed, but just wanted to doublecheck. Cheers, Jonathan From bert at bic.mni.mcgill.ca Tue Feb 7 17:02:41 2006 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Tue, 7 Feb 2006 17:02:41 -0500 Subject: [MINC-users] bicpl-1.4.2 default output for raster data In-Reply-To: <20060207212239.GB3441013@shadow.bic.mni.mcgill.ca> Message-ID: Hi Jonathan, I believe the default is still for image IO to be disabled unless you specify one of the --with-image- options -bert On Tue, 7 Feb 2006, Jonathan LAU wrote: > Hi, > > When building the bicpl library, are any of netpbm, ppm or sgi included by default? The README (dated 2003) says none are installed, but just wanted to doublecheck. > > Cheers, > Jonathan > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Tue Feb 7 22:21:32 2006 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 7 Feb 2006 22:21:32 -0500 Subject: [MINC-users] bicpl-1.4.2 default output for raster data In-Reply-To: References: <20060207212239.GB3441013@shadow.bic.mni.mcgill.ca> Message-ID: Correct, the default is for no image library. The image library is only needed for a small part of the functionality of the bicpl library. (like saving a window as a png/pbm from register/Display) a On 07/02/06, Robert VINCENT wrote: > Hi Jonathan, > > I believe the default is still for image IO to be disabled unless you > specify one of the --with-image- options > > -bert > > On Tue, 7 Feb 2006, Jonathan LAU wrote: > > > Hi, > > > > When building the bicpl library, are any of netpbm, ppm or sgi included by default? The README (dated 2003) says none are installed, but just wanted to doublecheck. > > > > Cheers, > > Jonathan > > > > _______________________________________________ > > 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 > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From lau at bic.mni.mcgill.ca Fri Feb 10 10:18:23 2006 From: lau at bic.mni.mcgill.ca (Jonathan LAU) Date: Fri, 10 Feb 2006 10:18:23 -0500 Subject: [MINC-users] inormalize and minc2 Message-ID: <20060210151823.GB3697454@shadow.bic.mni.mcgill.ca> Hi, I would like to include inormalize with a minc2-based installation I have created. Inormalize-0.99 (from packages.bic) does not include the --with-minc2 flag as part of its configuration script. What do I need to do to get configure to recognize minc2? Cheers, Jonathan From jason at bic.mni.mcgill.ca Mon Feb 13 09:44:53 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Mon, 13 Feb 2006 09:44:53 -0500 Subject: [MINC-users] inormalize and minc2 In-Reply-To: <20060210151823.GB3697454@shadow.bic.mni.mcgill.ca> References: <20060210151823.GB3697454@shadow.bic.mni.mcgill.ca> Message-ID: <43F09B65.7090800@bic.mni.mcgill.ca> Jonathan LAU wrote: >Hi, > >I would like to include inormalize with a minc2-based installation I have created. Inormalize-0.99 (from packages.bic) does not include the --with-minc2 flag as part of its configuration script. > >What do I need to do to get configure to recognize minc2? > > Get the most recent m4 files from CVS (they can be found at librares/mni-acmacros) and put them into the m4 directory of Inormalize. Then rerun autogen.sh - if it didn't come with the tarball, run 'aclocal -Im4; autoheader; automake --add-missing; autoconf', after which you ought to have the ability to compile against minc2. Cheers, Jason >Cheers, >Jonathan > >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From a.janke at gmail.com Mon Feb 13 10:40:53 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 13 Feb 2006 10:40:53 -0500 Subject: [MINC-users] mni_autoreg-0.98v Message-ID: Hi all, As many of you know there were a few bugs introduced in mni_autoreg0.98u as part of the shift to use mni-perllib properly. (as opposed to it's own internal version). I think most of these are now squashed so I think it high time to release 0.98v, the next in the series of strange numbered incremental releases. Who knows by 2010 we may hit version 1.0, heck it took minc ~10 years to reach version 1.0 So without further ado, you can get it here: Source: http://packages.bic.mni.mcgill.ca/tgz/mni_autoreg-0.98v.tar.gz Debian: http://packages.bic.mni.mcgill.ca/deb/mni-autoreg-0.98v-linux-2.6-intel.deb -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From ed.gronenschild at mi.unimaas.nl Tue Feb 14 02:58:22 2006 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Tue, 14 Feb 2006 08:58:22 +0100 Subject: [MINC-users] mni_autoreg-0.98v In-Reply-To: References: Message-ID: Hi Andrew, As I'm using the Mac version I'm wondering if also a new MAC binary of mni_autoreg_0.98v will become available. Current version is _0.98s Regards, Ed On 13 Feb 2006, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote: > Message: 2 > Date: Mon, 13 Feb 2006 10:40:53 -0500 > From: Andrew Janke > Subject: [MINC-users] mni_autoreg-0.98v > To: MINC users mailing list > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > As many of you know there were a few bugs introduced in > mni_autoreg0.98u as part of the shift to use mni-perllib properly. (as > opposed to it's own internal version). > > I think most of these are now squashed so I think it high time to > release 0.98v, the next in the series of strange numbered incremental > releases. Who knows by 2010 we may hit version 1.0, heck it took minc > ~10 years to reach version 1.0 > > So without further ado, you can get it here: > > Source: > http://packages.bic.mni.mcgill.ca/tgz/mni_autoreg-0.98v.tar.gz > > Debian: > > http://packages.bic.mni.mcgill.ca/deb/mni-autoreg-0.98v-linux-2.6- > intel.deb > > -- > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > Canada->Montreal Cell: +1 (514) 924 > 2012 From teodorst at cancerboard.ab.ca Tue Feb 14 17:39:21 2006 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Tue, 14 Feb 2006 15:39:21 -0700 Subject: [MINC-users] animal References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265D8C@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi, I have 10 3T brain image datasets that I need to segment into several ROI's. I looked through the MINC-users archive and I found the following procedure (June 2004): > The procedure is as followed: > > Step 1: mritotal $arg1'_mri.mnc' $arg1'_mri_stx_lin.xfm' > > Step 2: nu_correct $arg1'_mri.mnc' $arg1'_mri_nuc.mnc' > > Step 3: mritotal -nonlinear $arg1'_mri_nuc.mnc' -transformation > $arg1'_mri_stx_lin.xfm' $arg1'_mri_stx_nonlin.xfm' > > Step 4a: mincresample -like > /avgbrain/brain/images/icbm_template_1.00mm.mnc > $arg1'_mri_nuc.mnc' -transformation $arg1'_mri_stx_lin.xfm' > $arg1'_mri_stx_nuc.mnc' > > Step 4b: classify_clean $arg1'_mri_stx_nuc.mnc' > $arg1'_mri_stx_classes.mnc' > > Step 5: stx_segment $arg1'_mri_stx_nonlin.xfm' $arg1'_mri_stx_lin.xfm' > $arg1'_mri_stx_classes.mnc' $arg1'_mri_stx_labels.mnc' Is this still the standard procedure? Thank you. Best, Teodor Stanescu PhD candidate, Medical Physics Cross Cancer Institute 11560 University Avenue Edmonton, AB, T6G 1Z2 Phone: (780) 432-8622 Fax: (780) 432-8615 This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From a.janke at gmail.com Wed Feb 15 03:09:00 2006 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 15 Feb 2006 03:09:00 -0500 Subject: [MINC-users] mni_autoreg-0.98v In-Reply-To: References: Message-ID: By popular demand: http://packages.bic.mni.mcgill.ca/osx/mni-autoreg-0.98v.pkg.tar.gz This was built on Tiger, so I shall be interested as to whether this works for the 10.3 and 10.2 users out there as well. I see no reason as to why not, but you never know. a On 2/14/06, Ed Gronenschild wrote: > Hi Andrew, > > As I'm using the Mac version I'm wondering if also a new MAC binary > of mni_autoreg_0.98v will become available. Current version is _0.98s > > Regards, > > Ed > > On 13 Feb 2006, at 18:00, minc-users-request at bic.mni.mcgill.ca wrote: > > > Message: 2 > > Date: Mon, 13 Feb 2006 10:40:53 -0500 > > From: Andrew Janke > > Subject: [MINC-users] mni_autoreg-0.98v > > To: MINC users mailing list > > Message-ID: > > > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Hi all, > > > > As many of you know there were a few bugs introduced in > > mni_autoreg0.98u as part of the shift to use mni-perllib properly. (as > > opposed to it's own internal version). > > > > I think most of these are now squashed so I think it high time to > > release 0.98v, the next in the series of strange numbered incremental > > releases. Who knows by 2010 we may hit version 1.0, heck it took minc > > ~10 years to reach version 1.0 > > > > So without further ado, you can get it here: > > > > Source: > > http://packages.bic.mni.mcgill.ca/tgz/mni_autoreg-0.98v.tar.gz > > > > Debian: > > > > http://packages.bic.mni.mcgill.ca/deb/mni-autoreg-0.98v-linux-2.6- > > intel.deb > > > > -- > > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) > > Canada->Montreal Cell: +1 (514) 924 > > 2012 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From colliot at bic.mni.mcgill.ca Mon Feb 20 09:40:31 2006 From: colliot at bic.mni.mcgill.ca (Olivier Colliot) Date: Mon, 20 Feb 2006 15:40:31 +0100 Subject: [MINC-users] Compiling classify with gcc 3.4.3 Message-ID: <43F9D4DF.7040904@bic.mni.mcgill.ca> Hi, I am having trouble compiling "classify" (version 1.0, but the problem is the same with 0.99) It seems to me that the problem is coming from gcc 3.4.3 I included the error message at the end of the email. It seems that the error comes from the fact that default arguments are no longer permitted in a typedef (which is done at line 26 of the file 'class_protos.h'). Has anybody encountered the same problem ? Thanks a lot, Olivier g++ -DHAVE_CONFIG_H -I. -I. -I. -I/pclxserver/data/users/colliot/local/bictools/include -g -O2 -c -o classify.o `test -f 'classify.cc' || echo './'`classify.cc In file included from classify.cc:172: ./class_protos.h:26: error: default arguments are only permitted for function parameters ./class_protos.h:26: error: default arguments are only permitted for function parameters In file included from /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c++/3.4.3/backward/iostream.h:31, from ./ann/ann.h:23, from classify.cc:176: /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c++/3.4.3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the header for the header for C++ includes, or instead of the deprecated header . To disable this warning use -Wno-deprecated. classify.cc: In function `void classify_volume()': classify.cc:1708: error: too few arguments to function make[2]: *** [classify.o] Error 1 make[2]: Leaving directory `/pclxserver/data/users/colliot/local/bictools/sources/classify-1.0' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/pclxserver/data/users/colliot/local/bictools/sources/classify-1.0' make: *** [all] Error 2 From U951678 at STUDMED.AU.DK Mon Feb 20 19:41:01 2006 From: U951678 at STUDMED.AU.DK (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Tue, 21 Feb 2006 01:41:01 +0100 Subject: [MINC-users] mnc2ana problem Message-ID: Hi all, I have a problem converting coronal minc files into analyze format. The mincfile (that Displays right in terms of its dimensions) has dimensions: image: signed__ short 0 to 426 image dimensions: yspace zspace xspace dimension name length step start -------------- ------ ---- ----- yspace 120 1.5 -384 zspace 512 0.46875 -28.125 xspace 512 -0.46875 120 mnc2ana says: mnc2ana mtest.mnc mmm Start: 120 - -384 - -28.125 Step: -0.46875 - 1.5 - 0.46875 Length: 512 - 120 - 512 Dims: yspace - zspace - xspace FSLs avwhd says: ... dim0 4 dim1 512 dim2 120 dim3 512 dim4 0 dim5 0 .... When viewed in FSL it seems as as if the dimensions are swapped around, or more specifically, that the data is dumped as x,z,y but should have been put as x,y,z, but maybe i am wrong? Does anyone how any suggestions towards a quick fix? Many thanks, Soren From a.janke at gmail.com Mon Feb 20 21:47:24 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 20 Feb 2006 21:47:24 -0500 Subject: [MINC-users] animal In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265D8C@ACBEXCHANGE.ad.cancerboard.ab.ca> References: <86A652071AFE5548AA1C648AD489A15E01265D8C@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: Hi Teodor, This looks about right to me. Just remember that the std parameters of nu_correct are most suited to 1.5T data. Thus you will be best off to modify the -distance parameter to something more appropriate. About the half the default value would be a good start. Andrew On 2/14/06, Teodor Stanescu wrote: > Hi, > > I have 10 3T brain image datasets that I need to segment into several ROI's. I looked through the MINC-users archive and I found the following procedure (June 2004): > > > The procedure is as followed: > > > > Step 1: mritotal $arg1'_mri.mnc' $arg1'_mri_stx_lin.xfm' > > > > Step 2: nu_correct $arg1'_mri.mnc' $arg1'_mri_nuc.mnc' > > > > Step 3: mritotal -nonlinear $arg1'_mri_nuc.mnc' -transformation > > $arg1'_mri_stx_lin.xfm' $arg1'_mri_stx_nonlin.xfm' > > > > Step 4a: mincresample -like > > /avgbrain/brain/images/icbm_template_1.00mm.mnc > > $arg1'_mri_nuc.mnc' -transformation $arg1'_mri_stx_lin.xfm' > > $arg1'_mri_stx_nuc.mnc' > > > > Step 4b: classify_clean $arg1'_mri_stx_nuc.mnc' > > $arg1'_mri_stx_classes.mnc' > > > > Step 5: stx_segment $arg1'_mri_stx_nonlin.xfm' $arg1'_mri_stx_lin.xfm' > > $arg1'_mri_stx_classes.mnc' $arg1'_mri_stx_labels.mnc' > > Is this still the standard procedure? > > Thank you. > > Best, > > Teodor Stanescu > > PhD candidate, > Medical Physics > Cross Cancer Institute > 11560 University Avenue > Edmonton, AB, T6G 1Z2 > Phone: (780) 432-8622 > Fax: (780) 432-8615 > > > This e-mail and any attachments may contain confidential and > privileged information. If you are not the intended recipient, > please notify the sender immediately by return e-mail, delete this > e-mail and destroy any copies. Any dissemination or use of this > information by a person other than the intended recipient is > unauthorized and may be illegal. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Mon Feb 20 23:17:57 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 20 Feb 2006 23:17:57 -0500 Subject: [MINC-users] Compiling classify with gcc 3.4.3 In-Reply-To: <43F9D4DF.7040904@bic.mni.mcgill.ca> References: <43F9D4DF.7040904@bic.mni.mcgill.ca> Message-ID: Hi Oliver, No sorry I haven't, but then with C++ nothing really surprises me anymore. I can only suggest you try what the error output suggests.. ie: CFLAGS=-Wno-deprecated ./configure then try make again. a On 2/20/06, Olivier Colliot wrote: > Hi, > > I am having trouble compiling "classify" (version 1.0, but the problem > is the same with 0.99) > It seems to me that the problem is coming from gcc 3.4.3 > > I included the error message at the end of the email. > It seems that the error comes from the fact that default arguments are > no longer permitted in a typedef (which is done at line 26 of the file > 'class_protos.h'). > > Has anybody encountered the same problem ? > > Thanks a lot, > Olivier > > g++ -DHAVE_CONFIG_H -I. -I. -I. > -I/pclxserver/data/users/colliot/local/bictools/include -g -O2 -c -o > classify.o `test -f 'classify.cc' || echo './'`classify.cc > In file included from classify.cc:172: > ./class_protos.h:26: error: default arguments are only permitted for > function parameters > ./class_protos.h:26: error: default arguments are only permitted for > function parameters > In file included from > /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c++/3.4.3/backward/iostream.h:31, > from ./ann/ann.h:23, > from classify.cc:176: > /usr/lib/gcc/i386-redhat-linux/3.4.3/../../../../include/c++/3.4.3/backward/backward_warning.h:32:2: > warning: #warning This file includes at least one deprecated or > antiquated header. Please consider using one of the 32 headers found in > section 17.4.1.2 of the C++ standard. Examples include substituting the > header for the header for C++ includes, or instead > of the deprecated header . To disable this warning use > -Wno-deprecated. > classify.cc: In function `void classify_volume()': > classify.cc:1708: error: too few arguments to function > make[2]: *** [classify.o] Error 1 > make[2]: Leaving directory > `/pclxserver/data/users/colliot/local/bictools/sources/classify-1.0' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > `/pclxserver/data/users/colliot/local/bictools/sources/classify-1.0' > make: *** [all] Error 2 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Tue Feb 21 23:44:06 2006 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 21 Feb 2006 23:44:06 -0500 Subject: [MINC-users] mnc2ana problem In-Reply-To: References: Message-ID: Soren, In short not all analyze apps support the "Analyze 7.5" spec as they should (for various reasons). IN short you'd do well to always mincreshape all your files to zyx order before conversion and also use mnc2nii over mnc2ana. (part of minc 1.4). mnc2nii uses Nifti-1 a more portable analyze. a On 2/20/06, S?ren Christensen wrote: > Hi all, > I have a problem converting coronal minc files into analyze format. > The mincfile (that Displays right in terms of its dimensions) has dimensions: > image: signed__ short 0 to 426 > image dimensions: yspace zspace xspace > dimension name length step start > -------------- ------ ---- ----- > yspace 120 1.5 -384 > zspace 512 0.46875 -28.125 > xspace 512 -0.46875 120 > > mnc2ana says: > > mnc2ana mtest.mnc mmm > Start: 120 - -384 - -28.125 > Step: -0.46875 - 1.5 - 0.46875 > Length: 512 - 120 - 512 > Dims: yspace - zspace - xspace > > FSLs avwhd says: > ... > dim0 4 > dim1 512 > dim2 120 > dim3 512 > dim4 0 > dim5 0 > .... > > > When viewed in FSL it seems as as if the dimensions are swapped around, or more specifically, that the data is dumped as x,z,y but should have been put as x,y,z, but maybe i am wrong? > > Does anyone how any suggestions towards a quick fix? > > > Many 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 || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From U951678 at STUDMED.AU.DK Wed Feb 22 00:30:40 2006 From: U951678 at STUDMED.AU.DK (=?iso-8859-1?Q?S=F8ren_Christensen?=) Date: Wed, 22 Feb 2006 06:30:40 +0100 Subject: [MINC-users] mnc2ana problem References: Message-ID: Thanks for that. I managed to get it working for the particular application by changing the script to first getting the dimorder from the mnc file, then writing the dimension lenghts to the analyze file in fastest->slowest varying order and then finally setting the coronal flag in the Analyze header. I had to use Analyze 7.5 as it seemed the better way to go from the actual Analyze program to MINC. Cheers Soren -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Andrew Janke Sent: Wed 22-02-2006 15:44 To: MINC users mailing list Subject: Re: [MINC-users] mnc2ana problem Soren, In short not all analyze apps support the "Analyze 7.5" spec as they should (for various reasons). IN short you'd do well to always mincreshape all your files to zyx order before conversion and also use mnc2nii over mnc2ana. (part of minc 1.4). mnc2nii uses Nifti-1 a more portable analyze. a On 2/20/06, S?ren Christensen wrote: > Hi all, > I have a problem converting coronal minc files into analyze format. > The mincfile (that Displays right in terms of its dimensions) has dimensions: > image: signed__ short 0 to 426 > image dimensions: yspace zspace xspace > dimension name length step start > -------------- ------ ---- ----- > yspace 120 1.5 -384 > zspace 512 0.46875 -28.125 > xspace 512 -0.46875 120 > > mnc2ana says: > > mnc2ana mtest.mnc mmm > Start: 120 - -384 - -28.125 > Step: -0.46875 - 1.5 - 0.46875 > Length: 512 - 120 - 512 > Dims: yspace - zspace - xspace > > FSLs avwhd says: > ... > dim0 4 > dim1 512 > dim2 120 > dim3 512 > dim4 0 > dim5 0 > .... > > > When viewed in FSL it seems as as if the dimensions are swapped around, or more specifically, that the data is dumped as x,z,y but should have been put as x,y,z, but maybe i am wrong? > > Does anyone how any suggestions towards a quick fix? > > > Many 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 || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From steven.robbins at videotron.ca Wed Feb 22 00:38:28 2006 From: steven.robbins at videotron.ca (Steve M. Robbins) Date: Wed, 22 Feb 2006 00:38:28 -0500 Subject: [MINC-users] Compiling classify with gcc 3.4.3 In-Reply-To: <43F9D4DF.7040904@bic.mni.mcgill.ca> References: <43F9D4DF.7040904@bic.mni.mcgill.ca> Message-ID: <20060222053828.GE9229@nyongwa.montreal.qc.ca> On Mon, Feb 20, 2006 at 03:40:31PM +0100, Olivier Colliot wrote: > Hi, > > I am having trouble compiling "classify" (version 1.0, but the problem > is the same with 0.99) > It seems to me that the problem is coming from gcc 3.4.3 > > I included the error message at the end of the email. > It seems that the error comes from the fact that default arguments are > no longer permitted in a typedef (which is done at line 26 of the file > 'class_protos.h'). > > Has anybody encountered the same problem ? It looks like Bert has. I just built the tip of CVS using gcc 4 without trouble. Then I looked in the ChangeLog and found that Bert had fixed it up. Here's the diff: Index: class_protos.h =================================================================== RCS file: /software/source/INSECT/classify/class_protos.h,v retrieving revision 1.1 retrieving revision 1.2 diff -u -b -B -r1.1 -r1.2 --- class_protos.h 20 Mar 2002 22:16:34 -0000 1.1 +++ class_protos.h 11 Feb 2005 20:15:38 -0000 1.2 @@ -23,7 +23,7 @@ typedef void (*Load_Training)(char *filename); typedef void (*Save_Training)(char *filename); typedef void (*Train)(); -typedef void (*Classify)(int *class_num, Real *class_probs = 0, int *class_labels = 0); +typedef void (*Classify)(int *class_num, Real *class_probs, int *class_labels); /* FUNCTION PROTOTYPES */ Regards, -Steve From Michel.Audette at medizin.uni-leipzig.de Wed Feb 22 04:28:42 2006 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Wed, 22 Feb 2006 10:28:42 +0100 Subject: [MINC-users] using minc with ITK Message-ID: <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> Hello everyone, I am now in Leipzig, Germany, after a 5 year stint in Japan, and I would like to convert people here to MINC, in a future presentation that I will be making. I know that there is a MINC reader and writer for VTK that comes with ATAMAI, but I was wondering whether anyone has worked with ITK in a comparable manner. Best regards, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Philipp-Rosenthal-Strasse 55 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 From jason at bic.mni.mcgill.ca Wed Feb 22 07:55:10 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 22 Feb 2006 07:55:10 -0500 Subject: [MINC-users] using minc with ITK In-Reply-To: <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> References: <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> Message-ID: Yup. See here: http://www.insight-journal.org/view_reviews.php?back=publications.php% 3Fjournalid%3D3%26order%3D%26revision_display%3D&pubid=64 It appears to be scheduled for release with ITK 2.8. Note that it only supports MINC2 files. Jason On 22-Feb-06, at 4:28 AM, Audette, Michel wrote: > Hello everyone, > > I am now in Leipzig, Germany, after a 5 year stint in Japan, and I > would > like to convert people here to MINC, in a future presentation that I > will be making. I know that there is a MINC reader and writer for VTK > that comes with ATAMAI, but I was wondering whether anyone has worked > with ITK in a comparable manner. > > Best regards, > > Michel > > Michel Audette, Ph.D. > Innovation Center Computer Assisted Surgery (ICCAS) > Philipp-Rosenthal-Strasse 55 > Leipzig, Germany > Phone: ++49 (0) 341 / 97 - 1 20 13 > Fax: ++49 (0) 341 / 97 - 1 20 09 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From tpb1 at ualberta.ca Tue Feb 21 15:17:16 2006 From: tpb1 at ualberta.ca (tpb1@ualberta.ca) Date: Tue, 21 Feb 2006 13:17:16 -0700 Subject: [MINC-users] Object opacity Message-ID: <20060221131716.fn005od3b40k0kow@webmail.ualberta.ca> I'm trying to change the transparency of an object in the 3D window in order to reveal other objects behind it. That is, I want to make the object in front more transparent than the object behind it (the object in front partially blocks the object in the back) so that the outline of the object in the back can be seen through the object in front. I have played around with the Objects/Change Surface Prop function, but have been unsuccessful in changing the opacity in order to get the effect mentioned above. (Opacity is defined from 0 to 1, with 0 being the transparent, 1 being fully opaque). I also don't know the defaults for ambient, diffuse, specular, shininess and opacity. If anyone has any insights, I would appreciate it. Thanks, Thomas From jason at bic.mni.mcgill.ca Wed Feb 22 08:02:30 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 22 Feb 2006 08:02:30 -0500 Subject: [MINC-users] Object opacity In-Reply-To: <20060221131716.fn005od3b40k0kow@webmail.ualberta.ca> References: <20060221131716.fn005od3b40k0kow@webmail.ualberta.ca> Message-ID: <044D3558-1CCA-4B70-A702-0E31D1949F74@bic.mni.mcgill.ca> The set_object_opacity command (found inside the conglomerate package) is a lot more reliable than the equivalent Display functions - give that a try and see if you can get it to work. Jason On 21-Feb-06, at 3:17 PM, tpb1 at ualberta.ca wrote: > I'm trying to change the transparency of an object in the 3D window in > order to reveal other objects behind it. That is, I want to make the > object in front more transparent than the object behind it (the object > in front partially blocks the object in the back) so that the outline > of the object in the back can be seen through the object in front. I > have played around with the Objects/Change Surface Prop function, but > have been unsuccessful in changing the opacity in order to get the > effect mentioned above. (Opacity is defined from 0 to 1, with 0 being > the transparent, 1 being fully opaque). I also don't know the > defaults > for ambient, diffuse, specular, shininess and opacity. > > If anyone has any insights, I would appreciate it. > > Thanks, > Thomas > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From Michel.Audette at medizin.uni-leipzig.de Wed Feb 22 08:05:08 2006 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Wed, 22 Feb 2006 14:05:08 +0100 Subject: [MINC-users] using minc with ITK References: <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E6965874D@MRZS152229.medizin.uni-leipzig.de> Hi Jason, thanks for the kind reply. I have downloaded the latest minc software here, so I will be working with minc2 from now on. While on the subject, can you, or anyone, explain to me the motivation behind MINC going from a netcdf-based to a hdf5-based implementation? I might as well include this issue in my presentation. Cheers, Michel -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Jason Lerch Sent: Wed 2/22/2006 1:55 PM To: MINC users mailing list Subject: Re: [MINC-users] using minc with ITK Yup. See here: http://www.insight-journal.org/view_reviews.php?back=publications.php% 3Fjournalid%3D3%26order%3D%26revision_display%3D&pubid=64 It appears to be scheduled for release with ITK 2.8. Note that it only supports MINC2 files. Jason On 22-Feb-06, at 4:28 AM, Audette, Michel wrote: > Hello everyone, > > I am now in Leipzig, Germany, after a 5 year stint in Japan, and I > would > like to convert people here to MINC, in a future presentation that I > will be making. I know that there is a MINC reader and writer for VTK > that comes with ATAMAI, but I was wondering whether anyone has worked > with ITK in a comparable manner. > > Best regards, > > Michel > > Michel Audette, Ph.D. > Innovation Center Computer Assisted Surgery (ICCAS) > Philipp-Rosenthal-Strasse 55 > Leipzig, Germany > Phone: ++49 (0) 341 / 97 - 1 20 13 > Fax: ++49 (0) 341 / 97 - 1 20 09 > > _______________________________________________ > 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 jason at bic.mni.mcgill.ca Wed Feb 22 08:20:47 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 22 Feb 2006 08:20:47 -0500 Subject: [MINC-users] using minc with ITK In-Reply-To: <160E3DD4FB702C4CB860C65186686E6965874D@MRZS152229.medizin.uni-leipzig.de> References: <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E6965874D@MRZS152229.medizin.uni-leipzig.de> Message-ID: <371D07BA-3CE2-4F4F-B842-B5A0E06E7C6D@bic.mni.mcgill.ca> On 22-Feb-06, at 8:05 AM, Audette, Michel wrote: > While on the subject, can you, or anyone, explain to me the > motivation behind MINC going from a netcdf-based to a hdf5-based > implementation? I might as well include this issue in my presentation. There are others on this listed who can due a better job of addressing this question than I, but the main reasons are the following: * block-structured storage * multi-resolution images * internal compression In short, HDF5 has better support for extremely large files, something MINC2 was designed to support. Cheers, Jason From a.janke at gmail.com Wed Feb 22 08:44:42 2006 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 22 Feb 2006 08:44:42 -0500 Subject: [MINC-users] using minc with ITK In-Reply-To: <371D07BA-3CE2-4F4F-B842-B5A0E06E7C6D@bic.mni.mcgill.ca> References: <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E6965874D@MRZS152229.medizin.uni-leipzig.de> <371D07BA-3CE2-4F4F-B842-B5A0E06E7C6D@bic.mni.mcgill.ca> Message-ID: > There are others on this listed who can due a better job of > addressing this question than I, but the main reasons are the following: > > * block-structured storage > * multi-resolution images > * internal compression > > In short, HDF5 has better support for extremely large files, > something MINC2 was designed to support. And add to this: netcdf is no longer officially supported... (is now rolled into HDF) -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From jason at bic.mni.mcgill.ca Wed Feb 22 09:37:34 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 22 Feb 2006 09:37:34 -0500 Subject: [MINC-users] Introducing RMINC Message-ID: <43FC772E.7090302@bic.mni.mcgill.ca> Greetings all, Here's a new package for those of you doing stats of various sorts as well as anyone who likes R (an open source stats project) - RMINC. It includes functions to read and write MINC2 files, the ability to apply arbitrary R functions at every voxel, and some optimized modelling functions (t-tests, Wilcoxon Rank-sum tests, correlations, and linear models). Read the attached PDF for more details if you are interested. To install, untar the attached tarball, then install like so: R CMD INSTALL --configure-args='--with-build-path=/some/dir/with/minc2' RMINC note that to install this package in a non-default location set the R_LIBS environment variable (and set it to the same directory when starting R to make sure it can read it). Instructions for use are the in the PDF file. Note that it needs MINC2 volumes - it'll probably die with some horrible error if tried with MINC1. Remember that conversion between them is lossless - use mincconvert -2. It can also only deal with three dimensions at this point (if there's enough demand I'll add on 4d stuff). This is definitely a testing release - I've only tried the attached code on both 32 and 64 bit ubuntu linux. No guarantees, in other words; or, to rephrase, and almost certain guarantee of bugs. So all comments are welcome, especially bug reports and, of course, patches. Cheers, Jason From jason at bic.mni.mcgill.ca Wed Feb 22 11:54:17 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Wed, 22 Feb 2006 11:54:17 -0500 Subject: [MINC-users] Introducing RMINC In-Reply-To: <43FC772E.7090302@bic.mni.mcgill.ca> References: <43FC772E.7090302@bic.mni.mcgill.ca> Message-ID: <43FC9739.7070605@bic.mni.mcgill.ca> Erm, the list doesn't appear to like attachments. So here are the files for those who care: http://www.bic.mni.mcgill.ca/users/jason/RMINC/ Jason Jason Lerch wrote: > Greetings all, > > Here's a new package for those of you doing stats of various sorts as > well as anyone who likes R (an open source stats project) - RMINC. It > includes functions to read and write MINC2 files, the ability to apply > arbitrary R functions at every voxel, and some optimized modelling > functions (t-tests, Wilcoxon Rank-sum tests, correlations, and linear > models). Read the attached PDF for more details if you are interested. > > To install, untar the attached tarball, then install like so: > > R CMD INSTALL > --configure-args='--with-build-path=/some/dir/with/minc2' RMINC > > note that to install this package in a non-default location set the > R_LIBS environment variable (and set it to the same directory when > starting R to make sure it can read it). > > Instructions for use are the in the PDF file. Note that it needs MINC2 > volumes - it'll probably die with some horrible error if tried with > MINC1. Remember that conversion between them is lossless - use > mincconvert -2. It can also only deal with three dimensions at this > point (if there's enough demand I'll add on 4d stuff). > > This is definitely a testing release - I've only tried the attached > code on both 32 and 64 bit ubuntu linux. No guarantees, in other > words; or, to rephrase, and almost certain guarantee of bugs. So all > comments are welcome, especially bug reports and, of course, patches. > > Cheers, > > Jason > >------------------------------------------------------------------------ > >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From ed.gronenschild at mi.unimaas.nl Thu Feb 23 06:15:07 2006 From: ed.gronenschild at mi.unimaas.nl (Ed Gronenschild) Date: Thu, 23 Feb 2006 12:15:07 +0100 Subject: [MINC-users] Problem with Display for Mac Message-ID: <7d68616ac43a056444d6a27020b1bb50@mi.unimaas.nl> When I try to launch Display I get the following error: Malformed Mach-o file This is for version 1.4.0 as well as version 1.4.1. With previous versions this problem did not occur. I' m running OSX 10.3.9. Kind regards, Ed From jason at bic.mni.mcgill.ca Thu Feb 23 08:04:47 2006 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Thu, 23 Feb 2006 08:04:47 -0500 Subject: [MINC-users] Problem with Display for Mac In-Reply-To: <7d68616ac43a056444d6a27020b1bb50@mi.unimaas.nl> References: <7d68616ac43a056444d6a27020b1bb50@mi.unimaas.nl> Message-ID: <7DB97944-D194-4349-882A-5179E466D01D@bic.mni.mcgill.ca> On 23-Feb-06, at 6:15 AM, Ed Gronenschild wrote: > When I try to launch Display I get the following error: > > Malformed Mach-o file > > This is for version 1.4.0 as well as version 1.4.1. Are you compiling these yourself? Or getting the binary versions from somewhere? Jason > With previous versions this problem did not occur. > I' m running OSX 10.3.9. > > Kind regards, > > Ed > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From colliot at bic.mni.mcgill.ca Thu Feb 23 08:14:45 2006 From: colliot at bic.mni.mcgill.ca (Olivier Colliot) Date: Thu, 23 Feb 2006 14:14:45 +0100 Subject: [MINC-users] Compiling classify with gcc 3.4.3 In-Reply-To: <20060222053828.GE9229@nyongwa.montreal.qc.ca> References: <43F9D4DF.7040904@bic.mni.mcgill.ca> <20060222053828.GE9229@nyongwa.montreal.qc.ca> Message-ID: <43FDB545.2070600@bic.mni.mcgill.ca> Thanks for you answer. However, I don't have version 1.1 and it seems that there were additional changes from 1.0 to 1.1 Would it be possible to put a package of 1.1 or 1.2 on the packages.bic.mni.mcgill.ca website ? Steve M. Robbins a ?crit : >On Mon, Feb 20, 2006 at 03:40:31PM +0100, Olivier Colliot wrote: > > >>Hi, >> >>I am having trouble compiling "classify" (version 1.0, but the problem >>is the same with 0.99) >>It seems to me that the problem is coming from gcc 3.4.3 >> >>I included the error message at the end of the email. >>It seems that the error comes from the fact that default arguments are >>no longer permitted in a typedef (which is done at line 26 of the file >>'class_protos.h'). >> >>Has anybody encountered the same problem ? >> >> > >It looks like Bert has. > >I just built the tip of CVS using gcc 4 without trouble. Then I >looked in the ChangeLog and found that Bert had fixed it up. Here's >the diff: > >Index: class_protos.h >=================================================================== >RCS file: /software/source/INSECT/classify/class_protos.h,v >retrieving revision 1.1 >retrieving revision 1.2 >diff -u -b -B -r1.1 -r1.2 >--- class_protos.h 20 Mar 2002 22:16:34 -0000 1.1 >+++ class_protos.h 11 Feb 2005 20:15:38 -0000 1.2 >@@ -23,7 +23,7 @@ > typedef void (*Load_Training)(char *filename); > typedef void (*Save_Training)(char *filename); > typedef void (*Train)(); >-typedef void (*Classify)(int *class_num, Real *class_probs = 0, int *class_labels = 0); >+typedef void (*Classify)(int *class_num, Real *class_probs, int *class_labels); > > /* FUNCTION PROTOTYPES */ > > >Regards, >-Steve >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From adalat at bic.mni.mcgill.ca Thu Feb 23 11:09:56 2006 From: adalat at bic.mni.mcgill.ca (Reza ADALAT) Date: Thu, 23 Feb 2006 11:09:56 -0500 Subject: [MINC-users] Problem with Display for Mac In-Reply-To: <7DB97944-D194-4349-882A-5179E466D01D@bic.mni.mcgill.ca> Message-ID: Hi, Make sure your mni directory at /usr/local/mni/ is empty or does not exist (if you've installed other applications in that directory, back it up first) and then try to reinstall the minc tools by downloading Jason's latest binaries from here: http://www.bic.mni.mcgill.ca/software/distribution/packages/osx/MINC-tools-OS10.3-1.1.0.dmg this should do the trick. I think you've compiled these yourself and have either a non complete installation or a bad link. rz >> On Thu, 23 Feb 2006, Jason Lerch wrote: > > On 23-Feb-06, at 6:15 AM, Ed Gronenschild wrote: > > > When I try to launch Display I get the following error: > > > > Malformed Mach-o file > > > > This is for version 1.4.0 as well as version 1.4.1. > > Are you compiling these yourself? Or getting the binary versions from > somewhere? > > Jason > > > With previous versions this problem did not occur. > > I' m running OSX 10.3.9. > > > > Kind regards, > > > > Ed > > > > _______________________________________________ > > 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 Michel.Audette at medizin.uni-leipzig.de Thu Feb 23 11:33:50 2006 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 23 Feb 2006 17:33:50 +0100 Subject: [MINC-users] using minc with ITK Message-ID: <160E3DD4FB702C4CB860C65186686E69757A34@MRZS152229.medizin.uni-leipzig.de> Thanks to you both, Jason and Andrew. One last thing, and I'll stop making a nuisance of myself. Has anyone made available online a justification of MINC, in terms of pros and cons, against competing image formats, including software tools based on them? It would really bug me to champion MINC, in part based on all my image analysis being MINC-based, only to fall short in convincing the other researchers here at ICCAS to adopt MINC as its definitive medical image format... which might entail that any future work that I do will be based on DICOM or something else. In other words, there must be a better justification on which I can draw than my prior experience with it (other than MINC being self-contained in one file, especially if DICOM is significantly more prevalent...) Cheers, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Philipp-Rosenthal-Strasse 55 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 -----Urspr?ngliche Nachricht----- Von: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] Im Auftrag von Jason Lerch Gesendet: February 22, 2006 2:21 PM An: MINC users mailing list Betreff: Re: [MINC-users] using minc with ITK On 22-Feb-06, at 8:05 AM, Audette, Michel wrote: > While on the subject, can you, or anyone, explain to me the > motivation behind MINC going from a netcdf-based to a hdf5-based > implementation? I might as well include this issue in my presentation. There are others on this listed who can due a better job of addressing this question than I, but the main reasons are the following: * block-structured storage * multi-resolution images * internal compression In short, HDF5 has better support for extremely large files, something MINC2 was designed to support. Cheers, Jason _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From dale at bic.mni.mcgill.ca Thu Feb 23 17:38:41 2006 From: dale at bic.mni.mcgill.ca (Dale Einarson) Date: Thu, 23 Feb 2006 17:38:41 -0500 Subject: [MINC-users] Problem with Display for Mac In-Reply-To: References: Message-ID: <265892710184095919916f4b939a7cbd@bic.mni.mcgill.ca> Hello, This is more likely the effect of Andrew being spread too thin and compounded by us ( Andrew ) not having a 10.3 system to play with. The binaries for MacOSX on http://packages.bic.mni.mcgill.ca have been built on 10.4 and in many cases do not work on anything less. I have pointed more then ten people to Jason's link in the last month. If you have 10.3 indeed the link Reza provided is for you. BTW: I will try to upload 10.3 versions to packages in the next couple of days. I am still working on the builder :) For the non geek Q: How do I know what version I am running? A: click on the blue mouse in the top-left corner and select "about this mac" PS: I will get you all a 10.3 build for the new autoreg too :) Cheers! dale On Feb 23, 2006, at 11:09 AM, Reza ADALAT wrote: > Hi, > > Make sure your mni directory at /usr/local/mni/ is empty or does not > exist > (if you've installed other applications in that directory, back it up > first) and then try to reinstall the minc tools by downloading Jason's > latest binaries from here: > http://www.bic.mni.mcgill.ca/software/distribution/packages/osx/MINC- > tools-OS10.3-1.1.0.dmg > this should do the trick. I think you've compiled these yourself and > have > either a non complete installation or a bad link. > > > rz >> > > > On Thu, 23 Feb 2006, Jason Lerch wrote: > >> >> On 23-Feb-06, at 6:15 AM, Ed Gronenschild wrote: >> >>> When I try to launch Display I get the following error: >>> >>> Malformed Mach-o file >>> >>> This is for version 1.4.0 as well as version 1.4.1. >> >> Are you compiling these yourself? Or getting the binary versions from >> somewhere? >> >> Jason >> >>> With previous versions this problem did not occur. >>> I' m running OSX 10.3.9. >>> >>> Kind regards, >>> >>> Ed >>> >>> _______________________________________________ >>> 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 duchesne at ieee.org Thu Feb 23 17:42:53 2006 From: duchesne at ieee.org (Simon Duchesne) Date: Thu, 23 Feb 2006 23:42:53 +0100 Subject: [MINC-users] Problem with Display for Mac In-Reply-To: <265892710184095919916f4b939a7cbd@bic.mni.mcgill.ca> References: <265892710184095919916f4b939a7cbd@bic.mni.mcgill.ca> Message-ID: <51EF252A-5377-4673-BB9D-A8237CA272E7@ieee.org> dale just to be sure - is there a new package (dmg file) including all of the 10.4 binaries, or do we need to proceed in the old way, that is do it piecemeal ? Thanks Simon On Feb 23, 2006, at 11:38 PM, Dale Einarson wrote: > Hello, > This is more likely the effect of Andrew being spread too thin and > compounded by us ( Andrew ) not having a 10.3 system to play with. > > The binaries for MacOSX on http://packages.bic.mni.mcgill.ca have > been built on 10.4 and in many cases do not work on anything less. I > have pointed more then ten people to Jason's link in the last month. > If you have 10.3 indeed the link Reza provided is for you. > > BTW: I will try to upload 10.3 versions to packages in the next > couple of days. I am still working on the builder :) > > > For the non geek > Q: How do I know what version I am running? > A: click on the blue mouse in the top-left corner and select "about > this mac" > > PS: I will get you all a 10.3 build for the new autoreg too :) > > Cheers! > dale > > > On Feb 23, 2006, at 11:09 AM, Reza ADALAT wrote: > >> Hi, >> >> Make sure your mni directory at /usr/local/mni/ is empty or does not >> exist >> (if you've installed other applications in that directory, back it up >> first) and then try to reinstall the minc tools by downloading >> Jason's >> latest binaries from here: >> http://www.bic.mni.mcgill.ca/software/distribution/packages/osx/MINC- >> tools-OS10.3-1.1.0.dmg >> this should do the trick. I think you've compiled these yourself and >> have >> either a non complete installation or a bad link. >> >> >> rz >> >> >> >> On Thu, 23 Feb 2006, Jason Lerch wrote: >> >>> >>> On 23-Feb-06, at 6:15 AM, Ed Gronenschild wrote: >>> >>>> When I try to launch Display I get the following error: >>>> >>>> Malformed Mach-o file >>>> >>>> This is for version 1.4.0 as well as version 1.4.1. >>> >>> Are you compiling these yourself? Or getting the binary versions >>> from >>> somewhere? >>> >>> Jason >>> >>>> With previous versions this problem did not occur. >>>> I' m running OSX 10.3.9. >>>> >>>> Kind regards, >>>> >>>> Ed >>>> >>>> _______________________________________________ >>>> 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 dale at bic.mni.mcgill.ca Thu Feb 23 21:48:01 2006 From: dale at bic.mni.mcgill.ca (Dale Einarson) Date: Thu, 23 Feb 2006 21:48:01 -0500 Subject: [MINC-users] Problem with Display for Mac In-Reply-To: <51EF252A-5377-4673-BB9D-A8237CA272E7@ieee.org> References: <265892710184095919916f4b939a7cbd@bic.mni.mcgill.ca> <51EF252A-5377-4673-BB9D-A8237CA272E7@ieee.org> Message-ID: Hello, AFAIK http://packages.bic.mni.mcgill.ca/osx/ is piecemeal built on 10.4 and Jason's all-in-one for 10.3 was built about 2 years ago :) http://www.bic.mni.mcgill.ca/software/distribution/packages/osx/ I read from your post that you would prefer that we have an all-in-one package for 10.4.. This does make sense. I can build and all-in-one dmg for 10.4 based on what Andrew has already done... But I can't really test it , since I don't have a 10.4 system :) Anyone want to donate an account ( on an 10.4 system ) to help the cause? Cheers! dale On Feb 23, 2006, at 5:42 PM, Simon Duchesne wrote: > dale > just to be sure - is there a new package (dmg file) including all of > the 10.4 binaries, or do we need to proceed in the old way, that is > do it piecemeal ? > Thanks > Simon > > > On Feb 23, 2006, at 11:38 PM, Dale Einarson wrote: > >> Hello, >> This is more likely the effect of Andrew being spread too thin and >> compounded by us ( Andrew ) not having a 10.3 system to play with. >> >> The binaries for MacOSX on http://packages.bic.mni.mcgill.ca have >> been built on 10.4 and in many cases do not work on anything less. I >> have pointed more then ten people to Jason's link in the last month. >> If you have 10.3 indeed the link Reza provided is for you. >> >> BTW: I will try to upload 10.3 versions to packages in the next >> couple of days. I am still working on the builder :) >> >> >> For the non geek >> Q: How do I know what version I am running? >> A: click on the blue mouse in the top-left corner and select "about >> this mac" >> >> PS: I will get you all a 10.3 build for the new autoreg too :) >> >> Cheers! >> dale >> >> >> On Feb 23, 2006, at 11:09 AM, Reza ADALAT wrote: >> >>> Hi, >>> >>> Make sure your mni directory at /usr/local/mni/ is empty or does not >>> exist >>> (if you've installed other applications in that directory, back it up >>> first) and then try to reinstall the minc tools by downloading >>> Jason's >>> latest binaries from here: >>> http://www.bic.mni.mcgill.ca/software/distribution/packages/osx/MINC- >>> tools-OS10.3-1.1.0.dmg >>> this should do the trick. I think you've compiled these yourself and >>> have >>> either a non complete installation or a bad link. >>> >>> >>> rz >> >>> >>> >>> On Thu, 23 Feb 2006, Jason Lerch wrote: >>> >>>> >>>> On 23-Feb-06, at 6:15 AM, Ed Gronenschild wrote: >>>> >>>>> When I try to launch Display I get the following error: >>>>> >>>>> Malformed Mach-o file >>>>> >>>>> This is for version 1.4.0 as well as version 1.4.1. >>>> >>>> Are you compiling these yourself? Or getting the binary versions >>>> from >>>> somewhere? >>>> >>>> Jason >>>> >>>>> With previous versions this problem did not occur. >>>>> I' m running OSX 10.3.9. >>>>> >>>>> Kind regards, >>>>> > From acveilleux at mrs.mni.mcgill.ca Fri Feb 24 10:25:50 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Fri, 24 Feb 2006 10:25:50 -0500 Subject: [MINC-users] Problem with Display for Mac In-Reply-To: ; from dale@bic.mni.mcgill.ca on Thu, Feb 23, 2006 at 09:48:01PM -0500 References: <265892710184095919916f4b939a7cbd@bic.mni.mcgill.ca> <51EF252A-5377-4673-BB9D-A8237CA272E7@ieee.org> Message-ID: <20060224102550.A25934@mrs.mni.mcgill.ca> Get in touch with me. I have a few 10.4 systems and MINC for them in an all-in-one package is desirable. Maybe I can help you there ;-). Alex On Thu, Feb 23, 2006 at 09:48:01PM -0500, Dale Einarson wrote: > Date: Thu, 23 Feb 2006 21:48:01 -0500 > From: Dale Einarson > To: MINC users mailing list > X-Mailer: Apple Mail (2.623) > Subject: Re: [MINC-users] Problem with Display for Mac > > Hello, > AFAIK http://packages.bic.mni.mcgill.ca/osx/ is piecemeal built > on 10.4 and Jason's all-in-one for 10.3 was built about 2 years ago :) > http://www.bic.mni.mcgill.ca/software/distribution/packages/osx/ > > I read from your post that you would prefer that we have an > all-in-one package for 10.4.. This does make sense. I can build and > all-in-one dmg for 10.4 based on what Andrew has already done... But I > can't really test it , since I don't have a 10.4 system :) > > Anyone want to donate an account ( on an 10.4 system ) to help the > cause? > > Cheers! > dale > > > On Feb 23, 2006, at 5:42 PM, Simon Duchesne wrote: > > > dale > > just to be sure - is there a new package (dmg file) including all of > > the 10.4 binaries, or do we need to proceed in the old way, that is > > do it piecemeal ? > > Thanks > > Simon > > > > > > On Feb 23, 2006, at 11:38 PM, Dale Einarson wrote: > > > >> Hello, > >> This is more likely the effect of Andrew being spread too thin and > >> compounded by us ( Andrew ) not having a 10.3 system to play with. > >> > >> The binaries for MacOSX on http://packages.bic.mni.mcgill.ca have > >> been built on 10.4 and in many cases do not work on anything less. I > >> have pointed more then ten people to Jason's link in the last month. > >> If you have 10.3 indeed the link Reza provided is for you. > >> > >> BTW: I will try to upload 10.3 versions to packages in the next > >> couple of days. I am still working on the builder :) > >> > >> > >> For the non geek > >> Q: How do I know what version I am running? > >> A: click on the blue mouse in the top-left corner and select "about > >> this mac" > >> > >> PS: I will get you all a 10.3 build for the new autoreg too :) > >> > >> Cheers! > >> dale > >> > >> > >> On Feb 23, 2006, at 11:09 AM, Reza ADALAT wrote: > >> > >>> Hi, > >>> > >>> Make sure your mni directory at /usr/local/mni/ is empty or does not > >>> exist > >>> (if you've installed other applications in that directory, back it up > >>> first) and then try to reinstall the minc tools by downloading > >>> Jason's > >>> latest binaries from here: > >>> http://www.bic.mni.mcgill.ca/software/distribution/packages/osx/MINC- > >>> tools-OS10.3-1.1.0.dmg > >>> this should do the trick. I think you've compiled these yourself and > >>> have > >>> either a non complete installation or a bad link. > >>> > >>> > >>> rz >> > >>> > >>> > >>> On Thu, 23 Feb 2006, Jason Lerch wrote: > >>> > >>>> > >>>> On 23-Feb-06, at 6:15 AM, Ed Gronenschild wrote: > >>>> > >>>>> When I try to launch Display I get the following error: > >>>>> > >>>>> Malformed Mach-o file > >>>>> > >>>>> This is for version 1.4.0 as well as version 1.4.1. > >>>> > >>>> Are you compiling these yourself? Or getting the binary versions > >>>> from > >>>> somewhere? > >>>> > >>>> Jason > >>>> > >>>>> With previous versions this problem did not occur. > >>>>> I' m running OSX 10.3.9. > >>>>> > >>>>> Kind regards, > >>>>> > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From dale at bic.mni.mcgill.ca Fri Feb 24 21:47:09 2006 From: dale at bic.mni.mcgill.ca (Dale Einarson) Date: Fri, 24 Feb 2006 21:47:09 -0500 Subject: [MINC-users] MacOS packages faulty? Message-ID: <22a4fd01a70bbd35414adbd689b35bee@bic.mni.mcgill.ca> Hello, I am displease to inform you all that I believe the packages listed below to be faulty... Since I do not have a 10.4 system I will need a volunteer. Someone with a MacOS 10.4 system; download and install anyone of them if it fails there are all probably broken. Please be careful to read the error message at the end!!! http://packages.bic.mni.mcgill.ca/osx/classify-1.0.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/display-1.4.0.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/display-1.4.1.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/glim-image-1.1.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/inormalize-0.99.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/mincblob-1.2.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/mni-autoreg-0.98s.pkg.tar.gz http://packages.bic.mni.mcgill.ca/osx/register-1.3.6.pkg.tar.gz NOTE: It looks like they have been broken for a while. Even the ones on my backup from a month-ago are bad. They look to have been corrupted in the transfer. I am sorry for the pain this may have cause. I will try to have it rectified shortly. PS: My last official day is Tuesday :) Cheers! dale From runa at medphys.ucl.ac.uk Sat Feb 25 09:00:00 2006 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Sat, 25 Feb 2006 14:00:00 +0000 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> Message-ID: <5.2.0.9.0.20060225135713.00bb6888@pop3-server> Hi all, I am working on Linux mode of this package. would you please suggest me which command i will use for transfer image analyze format to minc format for the purpose of NU correction. Many thanks, Yours sincerely, Runa ******************************************************************** * Runa Parveen ** * PhD Student ** * Medical Imaging Group ** * Dept. of Medical Physics & Bioengineering ** * University College London ** * 2nd Floor, New Malet Place Engineering Building ** * Gower Street, off Torrington Place ** * London WC1E 6JA ** * UK ** * Tel. +44 (0) 20 7679 0246 (Dept.) +44 (0) 7984 084 959 (mob.) ** * Fax.+44 (0) 20 7679 0255 (Dept.) ** * e-mail: runa at medphys.ucl.ac.uk ** ********************************************************************* From lau at bic.mni.mcgill.ca Sat Feb 25 10:17:17 2006 From: lau at bic.mni.mcgill.ca (Jonathan LAU) Date: Sat, 25 Feb 2006 10:17:17 -0500 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: <5.2.0.9.0.20060225135713.00bb6888@pop3-server> References: <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> <5.2.0.9.0.20060225135713.00bb6888@pop3-server> Message-ID: Hi Runa, Have you tried ana2mnc? http://www.cmr.uq.edu.au/~rotor/software/ Cheers, jonathan On 2/25/06, Runa Parveen wrote: > Hi all, > > I am working on Linux mode of this package. would you please suggest me > which command i will use for transfer image analyze format to minc format > for the purpose of NU correction. > > Many thanks, > > Yours sincerely, > > Runa > > ******************************************************************** > > * Runa Parveen ** > * PhD Student ** > * Medical Imaging Group ** > * Dept. of Medical Physics & Bioengineering ** > * University College London ** > * 2nd Floor, New Malet Place Engineering Building ** > * Gower Street, off Torrington Place ** > * London WC1E 6JA ** > * > UK > ** > * Tel. +44 (0) 20 7679 0246 (Dept.) > +44 (0) 7984 084 959 (mob.) ** > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > * e-mail: runa at medphys.ucl.ac.uk ** > ********************************************************************* > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sylvain at bic.mni.mcgill.ca Sat Feb 25 12:10:51 2006 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Sat, 25 Feb 2006 12:10:51 -0500 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: Message-ID: Hello I believe Andrew no longer supports ana2mnc. You should be using nii2mnc which recognizes Analyze and NIfTI-1 formats. mnc2nii and nii2mnc are part of MINC release 1.4, available here: http://packages.bic.mni.mcgill.ca/tgz/minc-1.4.tar.gz S On Sat, 25 Feb 2006, Jonathan LAU wrote: > Hi Runa, > > Have you tried ana2mnc? > http://www.cmr.uq.edu.au/~rotor/software/ > > Cheers, > jonathan > > On 2/25/06, Runa Parveen wrote: > > Hi all, > > > > I am working on Linux mode of this package. would you please suggest me > > which command i will use for transfer image analyze format to minc format > > for the purpose of NU correction. > > > > Many thanks, > > > > Yours sincerely, > > > > Runa > > > > ******************************************************************** > > > > * Runa Parveen ** > > * PhD Student ** > > * Medical Imaging Group ** > > * Dept. of Medical Physics & Bioengineering ** > > * University College London ** > > * 2nd Floor, New Malet Place Engineering Building ** > > * Gower Street, off Torrington Place ** > > * London WC1E 6JA ** > > * > > UK > > ** > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > +44 (0) 7984 084 959 (mob.) ** > > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > > * e-mail: runa at medphys.ucl.ac.uk ** > > ********************************************************************* > > > > _______________________________________________ > > 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 > --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (trinity at bic.mni.mcgill.ca) Brain Imaging Centre Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 204 Montreal, Qc., H2W 1S4 From runa at medphys.ucl.ac.uk Sat Feb 25 12:23:50 2006 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Sat, 25 Feb 2006 17:23:50 +0000 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: References: <5.2.0.9.0.20060225135713.00bb6888@pop3-server> <160E3DD4FB702C4CB860C65186686E69757A26@MRZS152229.medizin.uni-leipzig.de> <5.2.0.9.0.20060225135713.00bb6888@pop3-server> Message-ID: <5.2.0.9.0.20060225172142.00baad78@pop3-server> Hi Jonathan, Many thanks for your e-mail. I have not installed that converter that's why I could not find it. I will installed it and let you know if I need to know more. Yours sincerely, Runa ******************************************************************** * Runa Parveen ** * PhD Student ** * Medical Imaging Group ** * Dept. of Medical Physics & Bioengineering ** * University College London ** * 2nd Floor, New Malet Place Engineering Building ** * Gower Street, off Torrington Place ** * London WC1E 6JA ** * UK ** * Tel. +44 (0) 20 7679 0246 (Dept.) +44 (0) 7984 084 959 (mob.) ** * Fax.+44 (0) 20 7679 0255 (Dept.) ** * e-mail: runa at medphys.ucl.ac.uk ** ********************************************************************* At 10:17 25/02/2006 -0500, you wrote: >Hi Runa, > >Have you tried ana2mnc? >http://www.cmr.uq.edu.au/~rotor/software/ > >Cheers, >jonathan > >On 2/25/06, Runa Parveen wrote: > > Hi all, > > > > I am working on Linux mode of this package. would you please suggest me > > which command i will use for transfer image analyze format to minc format > > for the purpose of NU correction. > > > > Many thanks, > > > > Yours sincerely, > > > > Runa > > > > ******************************************************************** > > > > * Runa > Parveen ** > > * PhD > Student ** > > * Medical Imaging Group ** > > * Dept. of Medical Physics & Bioengineering ** > > * University College London ** > > * 2nd Floor, New Malet Place Engineering Building ** > > * Gower Street, off Torrington Place ** > > * London WC1E 6JA ** > > * > > UK > > ** > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > +44 (0) 7984 084 959 (mob.) ** > > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > > * e-mail: runa at medphys.ucl.ac.uk ** > > ********************************************************************* > > > > _______________________________________________ > > 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 runa at medphys.ucl.ac.uk Sat Feb 25 12:43:16 2006 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Sat, 25 Feb 2006 17:43:16 +0000 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: References: Message-ID: <5.2.0.9.0.20060225174145.00ba7728@pop3-server> Hi Sylvain, I have installed this package but when I tried to use nii2mnc, it did not recognize, what would be the problem, please let me know. thanks, runa At 12:10 25/02/2006 -0500, you wrote: >Hello > >I believe Andrew no longer supports ana2mnc. > >You should be using nii2mnc which recognizes Analyze and NIfTI-1 formats. > >mnc2nii and nii2mnc are part of MINC release 1.4, available here: > >http://packages.bic.mni.mcgill.ca/tgz/minc-1.4.tar.gz > >S > >On Sat, 25 Feb 2006, Jonathan LAU wrote: > > > Hi Runa, > > > > Have you tried ana2mnc? > > http://www.cmr.uq.edu.au/~rotor/software/ > > > > Cheers, > > jonathan > > > > On 2/25/06, Runa Parveen wrote: > > > Hi all, > > > > > > I am working on Linux mode of this package. would you please suggest me > > > which command i will use for transfer image analyze format to minc format > > > for the purpose of NU correction. > > > > > > Many thanks, > > > > > > Yours sincerely, > > > > > > Runa > > > > > > ******************************************************************** > > > > > > * Runa > Parveen ** > > > * PhD > Student ** > > > * Medical Imaging Group ** > > > * Dept. of Medical Physics & Bioengineering ** > > > * University College London ** > > > * 2nd Floor, New Malet Place Engineering Building ** > > > * Gower Street, off Torrington Place ** > > > * London WC1E 6JA ** > > > * > > > UK > > > ** > > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > > +44 (0) 7984 084 959 (mob.) ** > > > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > > > * e-mail: runa at medphys.ucl.ac.uk ** > > > ********************************************************************* > > > > > > _______________________________________________ > > > 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 > > > >--- >Sylvain Milot (sylvain at bic.mni.mcgill.ca) > (trinity at bic.mni.mcgill.ca) >Brain Imaging Centre >Montreal Neurological Institute >Webster 2B, Room 208 >Montreal, Qc., Canada, H3A 2B4 >Phone : (514) 398-4965, Fax: 398-8948 >Mobile : (514) 712-1768 >Office : 527 Av Des Pins O., Room 204 > Montreal, Qc., H2W 1S4 > > > >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users Yours sincerely, Runa ******************************************************************** * Runa Parveen ** * PhD Student ** * Medical Imaging Group ** * Dept. of Medical Physics & Bioengineering ** * University College London ** * 2nd Floor, New Malet Place Engineering Building ** * Gower Street, off Torrington Place ** * London WC1E 6JA ** * UK ** * Tel. +44 (0) 20 7679 0246 (Dept.) +44 (0) 7984 084 959 (mob.) ** * Fax.+44 (0) 20 7679 0255 (Dept.) ** * e-mail: runa at medphys.ucl.ac.uk ** ********************************************************************* From bert at bic.mni.mcgill.ca Sat Feb 25 14:36:57 2006 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Sat, 25 Feb 2006 14:36:57 -0500 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: <5.2.0.9.0.20060225174145.00ba7728@pop3-server> Message-ID: Hi Runa, When you say "it did not recognize", do you mean that the command was not found, or that the the command could not recognize the Analyze file you were trying to convert? Can you give me the specific error message? -bert On Sat, 25 Feb 2006, Runa Parveen wrote: > Hi Sylvain, > > I have installed this package but when I tried to use nii2mnc, it did not > recognize, what would be the problem, please let me know. > > thanks, runa > At 12:10 25/02/2006 -0500, you wrote: > > >Hello > > > >I believe Andrew no longer supports ana2mnc. > > > >You should be using nii2mnc which recognizes Analyze and NIfTI-1 formats. > > > >mnc2nii and nii2mnc are part of MINC release 1.4, available here: > > > >http://packages.bic.mni.mcgill.ca/tgz/minc-1.4.tar.gz > > > >S > > > >On Sat, 25 Feb 2006, Jonathan LAU wrote: > > > > > Hi Runa, > > > > > > Have you tried ana2mnc? > > > http://www.cmr.uq.edu.au/~rotor/software/ > > > > > > Cheers, > > > jonathan > > > > > > On 2/25/06, Runa Parveen wrote: > > > > Hi all, > > > > > > > > I am working on Linux mode of this package. would you please suggest me > > > > which command i will use for transfer image analyze format to minc format > > > > for the purpose of NU correction. > > > > > > > > Many thanks, > > > > > > > > Yours sincerely, > > > > > > > > Runa > > > > > > > > ******************************************************************** > > > > > > > > * Runa > > Parveen ** > > > > * PhD > > Student ** > > > > * Medical Imaging Group ** > > > > * Dept. of Medical Physics & Bioengineering ** > > > > * University College London ** > > > > * 2nd Floor, New Malet Place Engineering Building ** > > > > * Gower Street, off Torrington Place ** > > > > * London WC1E 6JA ** > > > > * > > > > UK > > > > ** > > > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > > > +44 (0) 7984 084 959 (mob.) ** > > > > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > > > > * e-mail: runa at medphys.ucl.ac.uk ** > > > > ********************************************************************* > > > > > > > > _______________________________________________ > > > > 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 > > > > > > >--- > >Sylvain Milot (sylvain at bic.mni.mcgill.ca) > > (trinity at bic.mni.mcgill.ca) > >Brain Imaging Centre > >Montreal Neurological Institute > >Webster 2B, Room 208 > >Montreal, Qc., Canada, H3A 2B4 > >Phone : (514) 398-4965, Fax: 398-8948 > >Mobile : (514) 712-1768 > >Office : 527 Av Des Pins O., Room 204 > > Montreal, Qc., H2W 1S4 > > > > > > > >_______________________________________________ > >MINC-users at bic.mni.mcgill.ca > >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > Yours sincerely, > > Runa > > ******************************************************************** > > * Runa Parveen ** > * PhD Student ** > * Medical Imaging Group ** > * Dept. of Medical Physics & Bioengineering ** > * University College London ** > * 2nd Floor, New Malet Place Engineering Building ** > * Gower Street, off Torrington Place ** > * London WC1E 6JA ** > * > UK > ** > * Tel. +44 (0) 20 7679 0246 (Dept.) > +44 (0) 7984 084 959 (mob.) ** > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > * e-mail: runa at medphys.ucl.ac.uk ** > ********************************************************************* > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From runa at medphys.ucl.ac.uk Sat Feb 25 15:14:44 2006 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Sat, 25 Feb 2006 20:14:44 +0000 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: References: <5.2.0.9.0.20060225174145.00ba7728@pop3-server> Message-ID: <5.2.0.9.0.20060225201217.0435ac88@pop3-server> Hi Bert: I used the command nii2mnc t_r.hdr xt_r.mnc but it said command not found. Is there anything I missed when I installed? Thanks, Runa At 14:36 25/02/2006 -0500, you wrote: >Hi Runa, > >When you say "it did not recognize", do you mean that the command was not >found, or that the the command could not recognize the Analyze file you >were trying to convert? Can you give me the specific error message? > > -bert > >On Sat, 25 Feb 2006, Runa Parveen wrote: > > > Hi Sylvain, > > > > I have installed this package but when I tried to use nii2mnc, it did not > > recognize, what would be the problem, please let me know. > > > > thanks, runa > > At 12:10 25/02/2006 -0500, you wrote: > > > > >Hello > > > > > >I believe Andrew no longer supports ana2mnc. > > > > > >You should be using nii2mnc which recognizes Analyze and NIfTI-1 formats. > > > > > >mnc2nii and nii2mnc are part of MINC release 1.4, available here: > > > > > >http://packages.bic.mni.mcgill.ca/tgz/minc-1.4.tar.gz > > > > > >S > > > > > >On Sat, 25 Feb 2006, Jonathan LAU wrote: > > > > > > > Hi Runa, > > > > > > > > Have you tried ana2mnc? > > > > http://www.cmr.uq.edu.au/~rotor/software/ > > > > > > > > Cheers, > > > > jonathan > > > > > > > > On 2/25/06, Runa Parveen wrote: > > > > > Hi all, > > > > > > > > > > I am working on Linux mode of this package. would you please > suggest me > > > > > which command i will use for transfer image analyze format to > minc format > > > > > for the purpose of NU correction. > > > > > > > > > > Many thanks, > > > > > > > > > > Yours sincerely, > > > > > > > > > > Runa > > > > > > > > > > ******************************************************************** > > > > > > > > > > * Runa > > > Parveen ** > > > > > * PhD > > > Student ** > > > > > * Medical Imaging > Group ** > > > > > * Dept. of Medical Physics & Bioengineering ** > > > > > * University College > London ** > > > > > * 2nd Floor, New Malet Place Engineering Building ** > > > > > * Gower Street, off Torrington > Place ** > > > > > * London WC1E 6JA ** > > > > > * > > > > > UK > > > > > ** > > > > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > > > > +44 (0) 7984 084 959 > (mob.) ** > > > > > * Fax.+44 (0) 20 7679 0255 > (Dept.) ** > > > > > * e-mail: runa at medphys.ucl.ac.uk ** > > > > > ********************************************************************* > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > > > > > > >--- > > >Sylvain Milot (sylvain at bic.mni.mcgill.ca) > > > (trinity at bic.mni.mcgill.ca) > > >Brain Imaging Centre > > >Montreal Neurological Institute > > >Webster 2B, Room 208 > > >Montreal, Qc., Canada, H3A 2B4 > > >Phone : (514) 398-4965, Fax: 398-8948 > > >Mobile : (514) 712-1768 > > >Office : 527 Av Des Pins O., Room 204 > > > Montreal, Qc., H2W 1S4 > > > > > > > > > > > >_______________________________________________ > > >MINC-users at bic.mni.mcgill.ca > > >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > Yours sincerely, > > > > Runa > > > > ******************************************************************** > > > > * Runa > Parveen ** > > * PhD > Student ** > > * Medical Imaging Group ** > > * Dept. of Medical Physics & Bioengineering ** > > * University College London ** > > * 2nd Floor, New Malet Place Engineering Building ** > > * Gower Street, off Torrington Place ** > > * London WC1E 6JA ** > > * > > UK > > ** > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > +44 (0) 7984 084 959 (mob.) ** > > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > > * e-mail: runa at medphys.ucl.ac.uk ** > > ********************************************************************* > > > > _______________________________________________ > > 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 Yours sincerely, Runa ******************************************************************** * Runa Parveen ** * PhD Student ** * Medical Imaging Group ** * Dept. of Medical Physics & Bioengineering ** * University College London ** * 2nd Floor, New Malet Place Engineering Building ** * Gower Street, off Torrington Place ** * London WC1E 6JA ** * UK ** * Tel. +44 (0) 20 7679 0246 (Dept.) +44 (0) 7984 084 959 (mob.) ** * Fax.+44 (0) 20 7679 0255 (Dept.) ** * e-mail: runa at medphys.ucl.ac.uk ** ********************************************************************* From a.janke at gmail.com Sat Feb 25 15:36:51 2006 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 26 Feb 2006 06:36:51 +1000 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: <5.2.0.9.0.20060225201217.0435ac88@pop3-server> References: <5.2.0.9.0.20060225174145.00ba7728@pop3-server> <5.2.0.9.0.20060225201217.0435ac88@pop3-server> Message-ID: Hi Runa, nii2mnc is part of minc as of version 1.3 I suggest you install version 1.4 and them you will have all the converters included. (they will be installed int he same place as the mincxxxx binaries). Andrew On 2/26/06, Runa Parveen wrote: > Hi Bert: > > I used the command > nii2mnc t_r.hdr xt_r.mnc > > but it said command not found. > > Is there anything I missed when I installed? > > Thanks, > Runa > > At 14:36 25/02/2006 -0500, you wrote: > >Hi Runa, > > > >When you say "it did not recognize", do you mean that the command was not > >found, or that the the command could not recognize the Analyze file you > >were trying to convert? Can you give me the specific error message? > > > > -bert > > > >On Sat, 25 Feb 2006, Runa Parveen wrote: > > > > > Hi Sylvain, > > > > > > I have installed this package but when I tried to use nii2mnc, it did not > > > recognize, what would be the problem, please let me know. > > > > > > thanks, runa > > > At 12:10 25/02/2006 -0500, you wrote: > > > > > > >Hello > > > > > > > >I believe Andrew no longer supports ana2mnc. > > > > > > > >You should be using nii2mnc which recognizes Analyze and NIfTI-1 formats. > > > > > > > >mnc2nii and nii2mnc are part of MINC release 1.4, available here: > > > > > > > >http://packages.bic.mni.mcgill.ca/tgz/minc-1.4.tar.gz > > > > > > > >S > > > > > > > >On Sat, 25 Feb 2006, Jonathan LAU wrote: > > > > > > > > > Hi Runa, > > > > > > > > > > Have you tried ana2mnc? > > > > > http://www.cmr.uq.edu.au/~rotor/software/ > > > > > > > > > > Cheers, > > > > > jonathan > > > > > > > > > > On 2/25/06, Runa Parveen wrote: > > > > > > Hi all, > > > > > > > > > > > > I am working on Linux mode of this package. would you please > > suggest me > > > > > > which command i will use for transfer image analyze format to > > minc format > > > > > > for the purpose of NU correction. > > > > > > > > > > > > Many thanks, > > > > > > > > > > > > Yours sincerely, > > > > > > > > > > > > Runa > > > > > > > > > > > > ******************************************************************** > > > > > > > > > > > > * Runa > > > > Parveen ** > > > > > > * PhD > > > > Student ** > > > > > > * Medical Imaging > > Group ** > > > > > > * Dept. of Medical Physics & Bioengineering ** > > > > > > * University College > > London ** > > > > > > * 2nd Floor, New Malet Place Engineering Building ** > > > > > > * Gower Street, off Torrington > > Place ** > > > > > > * London WC1E 6JA ** > > > > > > * > > > > > > UK > > > > > > ** > > > > > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > > > > > +44 (0) 7984 084 959 > > (mob.) ** > > > > > > * Fax.+44 (0) 20 7679 0255 > > (Dept.) ** > > > > > > * e-mail: runa at medphys.ucl.ac.uk ** > > > > > > ********************************************************************* > > > > > > > > > > > > _______________________________________________ > > > > > > 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 > > > > > > > > > > > > >--- > > > >Sylvain Milot (sylvain at bic.mni.mcgill.ca) > > > > (trinity at bic.mni.mcgill.ca) > > > >Brain Imaging Centre > > > >Montreal Neurological Institute > > > >Webster 2B, Room 208 > > > >Montreal, Qc., Canada, H3A 2B4 > > > >Phone : (514) 398-4965, Fax: 398-8948 > > > >Mobile : (514) 712-1768 > > > >Office : 527 Av Des Pins O., Room 204 > > > > Montreal, Qc., H2W 1S4 > > > > > > > > > > > > > > > >_______________________________________________ > > > >MINC-users at bic.mni.mcgill.ca > > > >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > Yours sincerely, > > > > > > Runa > > > > > > ******************************************************************** > > > > > > * Runa > > Parveen ** > > > * PhD > > Student ** > > > * Medical Imaging Group ** > > > * Dept. of Medical Physics & Bioengineering ** > > > * University College London ** > > > * 2nd Floor, New Malet Place Engineering Building ** > > > * Gower Street, off Torrington Place ** > > > * London WC1E 6JA ** > > > * > > > UK > > > ** > > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > > +44 (0) 7984 084 959 (mob.) ** > > > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > > > * e-mail: runa at medphys.ucl.ac.uk ** > > > ********************************************************************* > > > > > > _______________________________________________ > > > 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 > > Yours sincerely, > > Runa > > ******************************************************************** > > * Runa Parveen ** > * PhD Student ** > * Medical Imaging Group ** > * Dept. of Medical Physics & Bioengineering ** > * University College London ** > * 2nd Floor, New Malet Place Engineering Building ** > * Gower Street, off Torrington Place ** > * London WC1E 6JA ** > * > UK > ** > * Tel. +44 (0) 20 7679 0246 (Dept.) > +44 (0) 7984 084 959 (mob.) ** > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > * e-mail: runa at medphys.ucl.ac.uk ** > ********************************************************************* > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From runa at medphys.ucl.ac.uk Sat Feb 25 15:58:23 2006 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Sat, 25 Feb 2006 20:58:23 +0000 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: References: <5.2.0.9.0.20060225201217.0435ac88@pop3-server> <5.2.0.9.0.20060225174145.00ba7728@pop3-server> <5.2.0.9.0.20060225201217.0435ac88@pop3-server> Message-ID: <5.2.0.9.0.20060225205336.04372898@pop3-server> Hi Andrew, I installed minc version 1.4 and I am looking for the command nii2mnc, But not found, other commands in there. don't know what's the problem? Runa At 06:36 26/02/2006 +1000, you wrote: >Hi Runa, > >nii2mnc is part of minc as of version 1.3 I suggest you install >version 1.4 and them you will have all the converters included. (they >will be installed int he same place as the mincxxxx binaries). > > >Andrew > > >On 2/26/06, Runa Parveen wrote: > > Hi Bert: > > > > I used the command > > nii2mnc t_r.hdr xt_r.mnc > > > > but it said command not found. > > > > Is there anything I missed when I installed? > > > > Thanks, > > Runa > > > > At 14:36 25/02/2006 -0500, you wrote: > > >Hi Runa, > > > > > >When you say "it did not recognize", do you mean that the command was not > > >found, or that the the command could not recognize the Analyze file you > > >were trying to convert? Can you give me the specific error message? > > > > > > -bert > > > > > >On Sat, 25 Feb 2006, Runa Parveen wrote: > > > > > > > Hi Sylvain, > > > > > > > > I have installed this package but when I tried to use nii2mnc, it > did not > > > > recognize, what would be the problem, please let me know. > > > > > > > > thanks, runa > > > > At 12:10 25/02/2006 -0500, you wrote: > > > > > > > > >Hello > > > > > > > > > >I believe Andrew no longer supports ana2mnc. > > > > > > > > > >You should be using nii2mnc which recognizes Analyze and NIfTI-1 > formats. > > > > > > > > > >mnc2nii and nii2mnc are part of MINC release 1.4, available here: > > > > > > > > > >http://packages.bic.mni.mcgill.ca/tgz/minc-1.4.tar.gz > > > > > > > > > >S > > > > > > > > > >On Sat, 25 Feb 2006, Jonathan LAU wrote: > > > > > > > > > > > Hi Runa, > > > > > > > > > > > > Have you tried ana2mnc? > > > > > > http://www.cmr.uq.edu.au/~rotor/software/ > > > > > > > > > > > > Cheers, > > > > > > jonathan > > > > > > > > > > > > On 2/25/06, Runa Parveen wrote: > > > > > > > Hi all, > > > > > > > > > > > > > > I am working on Linux mode of this package. would you please > > > suggest me > > > > > > > which command i will use for transfer image analyze format to > > > minc format > > > > > > > for the purpose of NU correction. > > > > > > > > > > > > > > Many thanks, > > > > > > > > > > > > > > Yours sincerely, > > > > > > > > > > > > > > Runa > > > > > > > > > > > > > > > ******************************************************************** > > > > > > > > > > > > > > * Runa > > > > > Parveen ** > > > > > > > * PhD > > > > > > Student ** > > > > > > > * Medical Imaging > > > Group ** > > > > > > > * Dept. of Medical Physics & Bioengineering ** > > > > > > > * University College > > > London ** > > > > > > > * 2nd Floor, New Malet Place Engineering Building ** > > > > > > > * Gower Street, off Torrington > > > Place ** > > > > > > > * London WC1E > 6JA ** > > > > > > > * > > > > > > > UK > > > > > > > ** > > > > > > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > > > > > > +44 (0) 7984 084 959 > > > (mob.) ** > > > > > > > * Fax.+44 (0) 20 7679 0255 > > > (Dept.) ** > > > > > > > * e-mail: > runa at medphys.ucl.ac.uk ** > > > > > > > > ********************************************************************* > > > > > > > > > > > > > > _______________________________________________ > > > > > > > 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 > > > > > > > > > > > > > > > >--- > > > > >Sylvain Milot (sylvain at bic.mni.mcgill.ca) > > > > > (trinity at bic.mni.mcgill.ca) > > > > >Brain Imaging Centre > > > > >Montreal Neurological Institute > > > > >Webster 2B, Room 208 > > > > >Montreal, Qc., Canada, H3A 2B4 > > > > >Phone : (514) 398-4965, Fax: 398-8948 > > > > >Mobile : (514) 712-1768 > > > > >Office : 527 Av Des Pins O., Room 204 > > > > > Montreal, Qc., H2W 1S4 > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > >MINC-users at bic.mni.mcgill.ca > > > > >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > Yours sincerely, > > > > > > > > Runa > > > > > > > > ******************************************************************** > > > > > > > > * Runa > > > Parveen ** > > > > * PhD > > > Student ** > > > > * Medical Imaging > Group ** > > > > * Dept. of Medical Physics & Bioengineering ** > > > > * University College > London ** > > > > * 2nd Floor, New Malet Place Engineering Building ** > > > > * Gower Street, off Torrington Place ** > > > > * London WC1E 6JA ** > > > > * > > > > UK > > > > ** > > > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > > > +44 (0) 7984 084 959 > (mob.) ** > > > > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > > > > * e-mail: runa at medphys.ucl.ac.uk ** > > > > ********************************************************************* > > > > > > > > _______________________________________________ > > > > 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 > > > > Yours sincerely, > > > > Runa > > > > ******************************************************************** > > > > * Runa > Parveen ** > > * PhD > Student ** > > * Medical Imaging Group ** > > * Dept. of Medical Physics & Bioengineering ** > > * University College London ** > > * 2nd Floor, New Malet Place Engineering Building ** > > * Gower Street, off Torrington Place ** > > * London WC1E 6JA ** > > * > > UK > > ** > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > +44 (0) 7984 084 959 (mob.) ** > > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > > * e-mail: runa at medphys.ucl.ac.uk ** > > ********************************************************************* > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > >-- >Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) >Canada->Montreal Cell: +1 (514) 924 2012 > >_______________________________________________ >MINC-users at bic.mni.mcgill.ca >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users Yours sincerely, Runa ******************************************************************** * Runa Parveen ** * PhD Student ** * Medical Imaging Group ** * Dept. of Medical Physics & Bioengineering ** * University College London ** * 2nd Floor, New Malet Place Engineering Building ** * Gower Street, off Torrington Place ** * London WC1E 6JA ** * UK ** * Tel. +44 (0) 20 7679 0246 (Dept.) +44 (0) 7984 084 959 (mob.) ** * Fax.+44 (0) 20 7679 0255 (Dept.) ** * e-mail: runa at medphys.ucl.ac.uk ** ********************************************************************* From teodorst at cancerboard.ab.ca Sun Feb 26 00:51:25 2006 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Sat, 25 Feb 2006 22:51:25 -0700 Subject: [MINC-users] animal and conglomerate References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265DB7@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi, 1. I tried to run 'stx_segment' but I got the following error: Possible unintended interpolation of @VERSION in string at /usr/local/mni/bin/stx_segment.pl line 700. /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_grey.mnc does not exist /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_white.mnc does not exist /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_ven_manual.mnc does not exist /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_level0.5_BG.mnc does not exist /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_grey.tag does not exist /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_ven_manual.tag does not exist /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_level0.5_BG.tag does not exist Missing model files at /usr/local/mni/bin/stx_segment.pl line 838. Could anyone suggest me where I could find 'icbm152-v1.0'? 2. I tried to install 'conglomerate-1.5' package but I found no Makefile/Configure file in the archive. How can I get this set of tools installed? Thank you in advance for any suggestion. Teo PhD Candidate Medical Physics Cross Cancer Institute 11560 University Avenue Edmnton, AB, T6G 1Z2 Phone: (780) 432-8622 Fax: (780) 432-8615 This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From jharlap at bic.mni.mcgill.ca Sun Feb 26 08:49:24 2006 From: jharlap at bic.mni.mcgill.ca (Jonathan Harlap) Date: Sun, 26 Feb 2006 08:49:24 -0500 Subject: [MINC-users] animal and conglomerate In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265DB7@ACBEXCHANGE.ad.cancerboard.ab.ca> References: <86A652071AFE5548AA1C648AD489A15E01265DB7@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: <4401B1E4.9060302@bic.mni.mcgill.ca> Hi Teodor, Thanks for pointing out the problem in conglomerate. I've fixed the conglomerate 1.5 package to include a configure script and checked it on one system to ensure it works, so you can download it again and it should be all good... I really couldn't comment on ANIMAL's atlas... Cheers, J Teodor Stanescu wrote: > Hi, > > 1. I tried to run 'stx_segment' but I got the following error: > > Possible unintended interpolation of @VERSION in string at /usr/local/mni/bin/stx_segment.pl line 700. > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_grey.mnc does not exist > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_white.mnc does not exist > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_ven_manual.mnc does not exist > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_level0.5_BG.mnc does not exist > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_grey.tag does not exist > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_ven_manual.tag does not exist > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_level0.5_BG.tag does not exist > Missing model files at /usr/local/mni/bin/stx_segment.pl line 838. > > Could anyone suggest me where I could find 'icbm152-v1.0'? > > 2. I tried to install 'conglomerate-1.5' package but I found no Makefile/Configure file in the archive. How can I get this set of tools installed? > > Thank you in advance for any suggestion. > > Teo > > > PhD Candidate > Medical Physics > Cross Cancer Institute > 11560 University Avenue > Edmnton, AB, T6G 1Z2 > Phone: (780) 432-8622 > Fax: (780) 432-8615 > > > > This e-mail and any attachments may contain confidential and > privileged information. If you are not the intended recipient, > please notify the sender immediately by return e-mail, delete this > e-mail and destroy any copies. Any dissemination or use of this > information by a person other than the intended recipient is > unauthorized and may be illegal. > > > ------------------------------------------------------------------------ > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From bert at bic.mni.mcgill.ca Sun Feb 26 11:25:56 2006 From: bert at bic.mni.mcgill.ca (Robert VINCENT) Date: Sun, 26 Feb 2006 11:25:56 -0500 Subject: [MINC-users] animal and conglomerate In-Reply-To: <4401B1E4.9060302@bic.mni.mcgill.ca> Message-ID: Hi, The ICBM-152 model is here: http://packages.bic.mni.mcgill.ca/tgz/mni-models_icbm152-lin-1.0.tar.gz -bert On Sun, 26 Feb 2006, Jonathan Harlap wrote: > Hi Teodor, > > Thanks for pointing out the problem in conglomerate. I've fixed the > conglomerate 1.5 package to include a configure script and checked it on > one system to ensure it works, so you can download it again and it > should be all good... > > I really couldn't comment on ANIMAL's atlas... > > Cheers, > J > > Teodor Stanescu wrote: > > Hi, > > > > 1. I tried to run 'stx_segment' but I got the following error: > > > > Possible unintended interpolation of @VERSION in string at /usr/local/mni/bin/stx_segment.pl line 700. > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_grey.mnc does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_white.mnc does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_ven_manual.mnc does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_level0.5_BG.mnc does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_grey.tag does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_ven_manual.tag does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_level0.5_BG.tag does not exist > > Missing model files at /usr/local/mni/bin/stx_segment.pl line 838. > > > > Could anyone suggest me where I could find 'icbm152-v1.0'? > > > > 2. I tried to install 'conglomerate-1.5' package but I found no Makefile/Configure file in the archive. How can I get this set of tools installed? > > > > Thank you in advance for any suggestion. > > > > Teo > > > > > > PhD Candidate > > Medical Physics > > Cross Cancer Institute > > 11560 University Avenue > > Edmnton, AB, T6G 1Z2 > > Phone: (780) 432-8622 > > Fax: (780) 432-8615 > > > > > > > > This e-mail and any attachments may contain confidential and > > privileged information. If you are not the intended recipient, > > please notify the sender immediately by return e-mail, delete this > > e-mail and destroy any copies. Any dissemination or use of this > > information by a person other than the intended recipient is > > unauthorized and may be illegal. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 teodorst at cancerboard.ab.ca Sun Feb 26 17:15:06 2006 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Sun, 26 Feb 2006 15:15:06 -0700 Subject: [MINC-users] animal and conglomerate References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265DB8@ACBEXCHANGE.ad.cancerboard.ab.ca> 1. > Thanks for pointing out the problem in conglomerate. I've fixed the > conglomerate 1.5 package to include a configure script and checked it on > one system to ensure it works, so you can download it again and it > should be all good... It runs fine now. Thank you. 2. > Hi, > > The ICBM-152 model is here: > > http://packages.bic.mni.mcgill.ca/tgz/mni-models_icbm152-lin-1.0.tar.gz > > -bert I have this model installed along with 'mni-models_average305-lin-1.0.tar.gz' and 'mni-models_colin27-lin-1.0.tar.gz'. I think 'stx_segment' looks for different files (please see output below) > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_grey.mnc does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_white.mnc does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_ven_manual.mnc does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/atlas_level0.5_BG.mnc does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_grey.tag does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_ven_manual.tag does not exist > > /usr/local/mni/data/ANIMAL_INSECT/icbm152-v1.0/limits_level0.5_BG.tag does not exist > > Missing model files at /usr/local/mni/bin/stx_segment.pl line 838. that are not included (or different labeled?) in 'mni-models_icbm152-lin-1.0.tar.gz'. After building 'mni-models_icbm152-lin-1.0' the files I got installed are as follows: icbm_avg_152_pd_tal_lin_16_blur.mnc icbm_avg_152_pd_tal_lin_16_mask.mnc icbm_avg_152_pd_tal_lin_2_blur.mnc icbm_avg_152_pd_tal_lin_2_dxyz.mnc icbm_avg_152_pd_tal_lin_2_mask.mnc icbm_avg_152_pd_tal_lin_4_blur.mnc icbm_avg_152_pd_tal_lin_4_dxyz.mnc icbm_avg_152_pd_tal_lin_4_mask.mnc icbm_avg_152_pd_tal_lin_8_blur.mnc icbm_avg_152_pd_tal_lin_8_dxyz.mnc icbm_avg_152_pd_tal_lin_8_mask.mnc icbm_avg_152_pd_tal_lin_headmask.mnc icbm_avg_152_pd_tal_lin_mask.mnc icbm_avg_152_pd_tal_lin.mnc icbm_avg_152_t1_tal_lin_16_blur.mnc icbm_avg_152_t1_tal_lin_16_mask.mnc icbm_avg_152_t1_tal_lin_2_blur.mnc icbm_avg_152_t1_tal_lin_2_dxyz.mnc icbm_avg_152_t1_tal_lin_2_mask.mnc icbm_avg_152_t1_tal_lin_4_blur.mnc icbm_avg_152_t1_tal_lin_4_dxyz.mnc icbm_avg_152_t1_tal_lin_4_mask.mnc icbm_avg_152_t1_tal_lin_8_blur.mnc icbm_avg_152_t1_tal_lin_8_dxyz.mnc icbm_avg_152_t1_tal_lin_8_mask.mnc icbm_avg_152_t1_tal_lin_headmask.mnc icbm_avg_152_t1_tal_lin_mask.mnc icbm_avg_152_t1_tal_lin.mnc icbm_avg_152_t2_tal_lin_16_blur.mnc icbm_avg_152_t2_tal_lin_16_mask.mnc icbm_avg_152_t2_tal_lin_2_blur.mnc icbm_avg_152_t2_tal_lin_2_dxyz.mnc icbm_avg_152_t2_tal_lin_2_mask.mnc icbm_avg_152_t2_tal_lin_4_blur.mnc icbm_avg_152_t2_tal_lin_4_dxyz.mnc icbm_avg_152_t2_tal_lin_4_mask.mnc icbm_avg_152_t2_tal_lin_8_blur.mnc icbm_avg_152_t2_tal_lin_8_dxyz.mnc icbm_avg_152_t2_tal_lin_8_mask.mnc icbm_avg_152_t2_tal_lin_headmask.mnc icbm_avg_152_t2_tal_lin_mask.mnc icbm_avg_152_t2_tal_lin.mnc Is 'icbm152-v1.0' a different version of 'mni-models_icbm152-lin-1.0'? Can I actually use 'stx_segment' with 'mni-models_icbm152-lin-1.0'? Thank you for your feedback. Teo PhD Candidate Medical Physics Cross Cancer Institute 11560 University Avenue Edmnton, AB, T6G 1Z2 Phone: (780) 432-8622 Fax: (780) 432-8615 This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From teodorst at cancerboard.ab.ca Sun Feb 26 20:42:13 2006 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Sun, 26 Feb 2006 18:42:13 -0700 Subject: [MINC-users] ROI generation References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265DBA@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi, Is there a tool that would generate ascii files containing the region of interest (ROI) of a certain structure, e.g. skull? Any help would be much appreciated. Thank you. Teo. PhD Candidate Medical Physics Cross Cancer Institute 11560 University Avenue Edmnton, AB, T6G 1Z2 Phone: (780) 432-8622 Fax: (780) 432-8615 This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From a.janke at gmail.com Mon Feb 27 00:00:40 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 27 Feb 2006 15:00:40 +1000 Subject: [MINC-users] ROI generation In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265DBA@ACBEXCHANGE.ad.cancerboard.ab.ca> References: <86A652071AFE5548AA1C648AD489A15E01265DBA@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: By ROI do you mean the values of the data? If so, mincsample is what you want. (it was originally desigend to randomly sample from a mask but it will return all the values if you like). packages.bic.mni.mcgill.ca/tgz/ a On 2/27/06, Teodor Stanescu wrote: > Hi, > > Is there a tool that would generate ascii files containing the region of interest (ROI) of a certain structure, e.g. skull? > > Any help would be much appreciated. Thank you. > > Teo. > > > PhD Candidate > Medical Physics > Cross Cancer Institute > 11560 University Avenue > Edmnton, AB, T6G 1Z2 > Phone: (780) 432-8622 > Fax: (780) 432-8615 > > > This e-mail and any attachments may contain confidential and > privileged information. If you are not the intended recipient, > please notify the sender immediately by return e-mail, delete this > e-mail and destroy any copies. Any dissemination or use of this > information by a person other than the intended recipient is > unauthorized and may be illegal. > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Mon Feb 27 01:12:31 2006 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 27 Feb 2006 16:12:31 +1000 Subject: [MINC-users] Problem with Display for Mac In-Reply-To: <265892710184095919916f4b939a7cbd@bic.mni.mcgill.ca> References: <265892710184095919916f4b939a7cbd@bic.mni.mcgill.ca> Message-ID: > This is more likely the effect of Andrew being spread too thin and > compounded by us ( Andrew ) not having a 10.3 system to play with. Call me Margarine. > The binaries for MacOSX on http://packages.bic.mni.mcgill.ca have > been built on 10.4 and in many cases do not work on anything less. Correct, they are built on Tiger and they are piecemeal. I know I can make a mpkg but just haven't had the time or inclination to figure out how given that you can use the C/L version in OSX and not have to press agree ten times for each package. However I had tested a few of them against "lower" versions and had some success (but not much!). I just figured that most mac people would upgrade to Tiger eventually. Also a lot of the Register Display stuff changes a bit between 10.4 and 10.3. Mind you a few of the packages tend to spit errors during the install on some machines and not others and yet appear to be fine... weird. I am yet to track down as to why the register package for instance installs fine on some machines and yet spits and error (and still works) on others when both are "vanilla" OSX 10.4 installs -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From najma at bic.mni.mcgill.ca Mon Feb 27 10:33:59 2006 From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.) Date: Mon, 27 Feb 2006 10:33:59 -0500 Subject: [MINC-users] mincdti (bmatrix) In-Reply-To: Message-ID: Hello, I am trying to use mincdti on a 45-dir DTI set. I have constructed the b-matrix according to my specific x-y-z directions and have a B-matrix with 46 rows (1 for b=0 and 45 for b=1000), each row comprised of xx, yy, zz, xy, xz, yz, lnY(0). mincinfo DTI_volume.mnc image: signed__ short 0 to 4095 image dimensions: time zspace yspace xspace dimension name length step start -------------- ------ ---- ----- time 46 6.7 0 zspace 45 2.5 -39.3421 yspace 96 -2.5 174.284 xspace 128 -2.5 164.41 however %mincdti -b_matrix ~/bfile.bmat DTI_volume.mnc out produces: mincdti: The number of infiles != Number of B Values Should the size of B-matrix in bfile.mat be something other than 46x7?? ( b-file.mat attached below) Many thanks, Najma MNI Diffusion B_Matrix File % % Example b-matrix (fairly close to most manufacturers) % expressed in terms of: % xx, yy, zz, xy, xz, yz, lnY(0) B_Matrix_Type = Normal_B_Matrix; B_Matrix= 0 0 0 0 0 0 0 794.6012 64.4368 140.9620 -226.2776 95.3055 -334.6768 1 626.2357 9.6369 364.1274 77.6853 59.2374 477.5244 1 57.0163 8.6512 934.3324 -22.2095 -89.9062 230.8077 1 8.6440 11.7081 979.6479 -10.0600 107.0972 -92.0220 1 63.8785 470.7549 465.3666 173.4102 468.0530 172.4149 1 611.7844 382.9671 5.2484 484.0386 44.8328 56.6649 1 494.4128 0.7983 504.7889 -19.8667 20.0740 -499.5739 1 101.3804 219.2992 679.3203 -149.1062 -385.9720 262.4306 1 219.0764 727.9826 52.9409 -399.3543 -196.3163 107.6945 1 5.4296 92.4459 902.1245 22.4042 -288.7866 -69.9872 1 100.2913 875.9973 23.7114 296.4033 -144.1219 -48.7652 1 576.9541 383.2983 39.7476 -470.2611 -123.4309 151.4349 1 26.7401 721.3342 251.9257 138.8832 -426.2894 -82.0763 1 171.8759 20.5822 807.5419 59.4776 -128.9225 -372.5547 1 327.0628 223.4085 449.5287 270.3120 316.9046 383.4373 1 647.4659 257.6159 94.9181 408.4085 -156.3727 -247.9037 1 160.5975 418.4256 420.9769 -259.2260 419.6993 -260.0151 1 271.3839 523.5554 205.0606 376.9410 -327.6593 -235.9029 1 308.1036 537.3972 154.4992 406.9079 288.1448 218.1783 1 164.9505 727.6313 107.4181 -346.4436 279.5725 -133.1115 1 448.8503 163.0358 388.1139 -270.5156 251.5481 -417.3788 1 928.5211 3.4069 68.0719 56.2443 15.2288 251.4085 1 916.4941 81.2455 2.2603 272.8755 -13.5515 -45.5147 1 4.8435 702.3000 292.8566 -58.3230 453.5120 -37.6622 1 678.2513 83.5285 238.2202 -238.0196 -141.0609 401.9616 1 10.5800 285.2599 704.1601 -54.9367 448.1837 -86.3134 1 66.0182 638.1535 295.8284 -205.2553 -434.4927 139.7500 1 343.0769 349.9121 307.0110 -346.4777 -327.7604 324.5433 1 134.5348 285.3352 580.1300 195.9273 -406.8556 -279.3701 1 773.0228 225.8930 1.0842 -417.8761 15.6496 -28.9500 1 816.2269 16.5053 167.2678 116.0693 -52.5434 -369.4976 1 0.0408 407.5226 592.4366 4.0773 -491.3566 -4.9161 1 988.1923 9.8658 1.9419 -98.7388 4.3770 -43.8060 1 453.0983 129.6143 417.2873 242.3387 -232.5649 -434.8243 1 261.8399 738.0373 0.1227 439.5994 9.5179 5.6692 1 348.4199 48.4850 603.0952 -129.9735 -171.0001 458.3998 1 894.5359 86.9584 18.5058 -278.9039 -40.1153 128.6627 1 689.1407 169.9987 140.8606 342.2762 154.7453 311.5650 1 254.9452 23.1941 721.8608 76.8974 129.3943 428.9929 1 164.7735 72.5963 762.6302 -109.3707 235.2958 -354.4873 1 42.1049 125.0845 832.8106 72.5719 322.7564 187.2577 1 52.6042 842.5461 104.8497 210.5266 297.2216 74.2666 1 6.4149 944.1078 49.4773 -77.8225 -216.1295 17.8155 1 427.6010 568.2432 4.1559 492.9314 -48.5957 -42.1551 1 497.6722 411.2065 91.1212 -452.3782 193.5708 -212.9519; From jharlap at bic.mni.mcgill.ca Mon Feb 27 10:44:55 2006 From: jharlap at bic.mni.mcgill.ca (Jonathan HARLAP) Date: Mon, 27 Feb 2006 10:44:55 -0500 Subject: [MINC-users] mincdti (bmatrix) In-Reply-To: References: Message-ID: <20060227154455.GA342326@bic.mni.mcgill.ca> hi najma, i believe mincdti doesn't expect a 4D file, but rather (in your case) 46 x 3D files as input... cheers, j On Mon, Feb 27, 2006 at 10:33:59AM -0500, Najmeh Khalili M. wrote: > > Hello, > > I am trying to use mincdti on a 45-dir DTI set. I have constructed the > b-matrix according to my specific x-y-z directions and have a B-matrix > with 46 rows (1 for b=0 and 45 for b=1000), each row comprised of xx, yy, > zz, xy, xz, yz, lnY(0). > > mincinfo DTI_volume.mnc > image: signed__ short 0 to 4095 > image dimensions: time zspace yspace xspace > dimension name length step start > -------------- ------ ---- ----- > time 46 6.7 0 > zspace 45 2.5 -39.3421 > yspace 96 -2.5 174.284 > xspace 128 -2.5 164.41 > > however > %mincdti -b_matrix ~/bfile.bmat DTI_volume.mnc out > > produces: > mincdti: The number of infiles != Number of B Values > > Should the size of B-matrix in bfile.mat be something other than 46x7?? > ( b-file.mat attached below) > Many thanks, > Najma > > > > MNI Diffusion B_Matrix File > % > % Example b-matrix (fairly close to most manufacturers) > % expressed in terms of: > % xx, yy, zz, xy, xz, yz, lnY(0) > > > B_Matrix_Type = Normal_B_Matrix; > > B_Matrix= > 0 0 0 0 0 0 0 > 794.6012 64.4368 140.9620 -226.2776 95.3055 -334.6768 1 > 626.2357 9.6369 364.1274 77.6853 59.2374 477.5244 1 > 57.0163 8.6512 934.3324 -22.2095 -89.9062 230.8077 1 > 8.6440 11.7081 979.6479 -10.0600 107.0972 -92.0220 1 > 63.8785 470.7549 465.3666 173.4102 468.0530 172.4149 1 > 611.7844 382.9671 5.2484 484.0386 44.8328 56.6649 1 > 494.4128 0.7983 504.7889 -19.8667 20.0740 -499.5739 1 > 101.3804 219.2992 679.3203 -149.1062 -385.9720 262.4306 1 > 219.0764 727.9826 52.9409 -399.3543 -196.3163 107.6945 1 > 5.4296 92.4459 902.1245 22.4042 -288.7866 -69.9872 1 > 100.2913 875.9973 23.7114 296.4033 -144.1219 -48.7652 1 > 576.9541 383.2983 39.7476 -470.2611 -123.4309 151.4349 1 > 26.7401 721.3342 251.9257 138.8832 -426.2894 -82.0763 1 > 171.8759 20.5822 807.5419 59.4776 -128.9225 -372.5547 1 > 327.0628 223.4085 449.5287 270.3120 316.9046 383.4373 1 > 647.4659 257.6159 94.9181 408.4085 -156.3727 -247.9037 1 > 160.5975 418.4256 420.9769 -259.2260 419.6993 -260.0151 1 > 271.3839 523.5554 205.0606 376.9410 -327.6593 -235.9029 1 > 308.1036 537.3972 154.4992 406.9079 288.1448 218.1783 1 > 164.9505 727.6313 107.4181 -346.4436 279.5725 -133.1115 1 > 448.8503 163.0358 388.1139 -270.5156 251.5481 -417.3788 1 > 928.5211 3.4069 68.0719 56.2443 15.2288 251.4085 1 > 916.4941 81.2455 2.2603 272.8755 -13.5515 -45.5147 1 > 4.8435 702.3000 292.8566 -58.3230 453.5120 -37.6622 1 > 678.2513 83.5285 238.2202 -238.0196 -141.0609 401.9616 1 > 10.5800 285.2599 704.1601 -54.9367 448.1837 -86.3134 1 > 66.0182 638.1535 295.8284 -205.2553 -434.4927 139.7500 1 > 343.0769 349.9121 307.0110 -346.4777 -327.7604 324.5433 1 > 134.5348 285.3352 580.1300 195.9273 -406.8556 -279.3701 1 > 773.0228 225.8930 1.0842 -417.8761 15.6496 -28.9500 1 > 816.2269 16.5053 167.2678 116.0693 -52.5434 -369.4976 1 > 0.0408 407.5226 592.4366 4.0773 -491.3566 -4.9161 1 > 988.1923 9.8658 1.9419 -98.7388 4.3770 -43.8060 1 > 453.0983 129.6143 417.2873 242.3387 -232.5649 -434.8243 1 > 261.8399 738.0373 0.1227 439.5994 9.5179 5.6692 1 > 348.4199 48.4850 603.0952 -129.9735 -171.0001 458.3998 1 > 894.5359 86.9584 18.5058 -278.9039 -40.1153 128.6627 1 > 689.1407 169.9987 140.8606 342.2762 154.7453 311.5650 1 > 254.9452 23.1941 721.8608 76.8974 129.3943 428.9929 1 > 164.7735 72.5963 762.6302 -109.3707 235.2958 -354.4873 1 > 42.1049 125.0845 832.8106 72.5719 322.7564 187.2577 1 > 52.6042 842.5461 104.8497 210.5266 297.2216 74.2666 1 > 6.4149 944.1078 49.4773 -77.8225 -216.1295 17.8155 1 > 427.6010 568.2432 4.1559 492.9314 -48.5957 -42.1551 1 > 497.6722 411.2065 91.1212 -452.3782 193.5708 -212.9519; > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From acveilleux at mrs.mni.mcgill.ca Mon Feb 27 12:49:31 2006 From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX) Date: Mon, 27 Feb 2006 12:49:31 -0500 Subject: [MINC-users] CIVET question Message-ID: <20060227124931.A1460@mrs.mni.mcgill.ca> Hello, I'm not sure if this is the right forum for this question, but is it possible to run CIVET for cortical surface extraction on a single hemisphere as opposed to a full brain? I'm especially worried about the possibilities of failures in any one of the registration steps. If there is no direct support for this, could an already run CIVET pipeline be subverted after fact to substitute the input volume for a half volume transformed to overlap the original volume? Alex From teodorst at cancerboard.ab.ca Mon Feb 27 15:05:31 2006 From: teodorst at cancerboard.ab.ca (Teodor Stanescu) Date: Mon, 27 Feb 2006 13:05:31 -0700 Subject: [MINC-users] minc to dicom converter References: Message-ID: <86A652071AFE5548AA1C648AD489A15E01265DBD@ACBEXCHANGE.ad.cancerboard.ab.ca> Hi, Could anyone suggest me a minc to dicom converter? Thanks. Teo PhD Candidate Medical Physics Cross Cancer Institute 11560 University Avenue Edmnton, AB, T6G 1Z2 Phone: (780) 432-8622 Fax: (780) 432-8615 This e-mail and any attachments may contain confidential and privileged information. If you are not the intended recipient, please notify the sender immediately by return e-mail, delete this e-mail and destroy any copies. Any dissemination or use of this information by a person other than the intended recipient is unauthorized and may be illegal. From a.janke at gmail.com Mon Feb 27 21:03:04 2006 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 28 Feb 2006 12:03:04 +1000 Subject: [MINC-users] mincdti (bmatrix) In-Reply-To: <20060227154455.GA342326@bic.mni.mcgill.ca> References: <20060227154455.GA342326@bic.mni.mcgill.ca> Message-ID: Correct... This is so that we can do the entire computation with a lot less memory than opening the entire 4D file! a On 2/28/06, Jonathan HARLAP wrote: > hi najma, > > i believe mincdti doesn't expect a 4D file, but rather (in your case) > 46 x 3D files as input... > > cheers, > j > > > On Mon, Feb 27, 2006 at 10:33:59AM -0500, Najmeh Khalili M. wrote: > > > > Hello, > > > > I am trying to use mincdti on a 45-dir DTI set. I have constructed the > > b-matrix according to my specific x-y-z directions and have a B-matrix > > with 46 rows (1 for b=0 and 45 for b=1000), each row comprised of xx, yy, > > zz, xy, xz, yz, lnY(0). > > > > mincinfo DTI_volume.mnc > > image: signed__ short 0 to 4095 > > image dimensions: time zspace yspace xspace > > dimension name length step start > > -------------- ------ ---- ----- > > time 46 6.7 0 > > zspace 45 2.5 -39.3421 > > yspace 96 -2.5 174.284 > > xspace 128 -2.5 164.41 > > > > however > > %mincdti -b_matrix ~/bfile.bmat DTI_volume.mnc out > > > > produces: > > mincdti: The number of infiles != Number of B Values > > > > Should the size of B-matrix in bfile.mat be something other than 46x7?? > > ( b-file.mat attached below) > > Many thanks, > > Najma > > > > > > > > MNI Diffusion B_Matrix File > > % > > % Example b-matrix (fairly close to most manufacturers) > > % expressed in terms of: > > % xx, yy, zz, xy, xz, yz, lnY(0) > > > > > > B_Matrix_Type = Normal_B_Matrix; > > > > B_Matrix= > > 0 0 0 0 0 0 0 > > 794.6012 64.4368 140.9620 -226.2776 95.3055 -334.6768 1 > > 626.2357 9.6369 364.1274 77.6853 59.2374 477.5244 1 > > 57.0163 8.6512 934.3324 -22.2095 -89.9062 230.8077 1 > > 8.6440 11.7081 979.6479 -10.0600 107.0972 -92.0220 1 > > 63.8785 470.7549 465.3666 173.4102 468.0530 172.4149 1 > > 611.7844 382.9671 5.2484 484.0386 44.8328 56.6649 1 > > 494.4128 0.7983 504.7889 -19.8667 20.0740 -499.5739 1 > > 101.3804 219.2992 679.3203 -149.1062 -385.9720 262.4306 1 > > 219.0764 727.9826 52.9409 -399.3543 -196.3163 107.6945 1 > > 5.4296 92.4459 902.1245 22.4042 -288.7866 -69.9872 1 > > 100.2913 875.9973 23.7114 296.4033 -144.1219 -48.7652 1 > > 576.9541 383.2983 39.7476 -470.2611 -123.4309 151.4349 1 > > 26.7401 721.3342 251.9257 138.8832 -426.2894 -82.0763 1 > > 171.8759 20.5822 807.5419 59.4776 -128.9225 -372.5547 1 > > 327.0628 223.4085 449.5287 270.3120 316.9046 383.4373 1 > > 647.4659 257.6159 94.9181 408.4085 -156.3727 -247.9037 1 > > 160.5975 418.4256 420.9769 -259.2260 419.6993 -260.0151 1 > > 271.3839 523.5554 205.0606 376.9410 -327.6593 -235.9029 1 > > 308.1036 537.3972 154.4992 406.9079 288.1448 218.1783 1 > > 164.9505 727.6313 107.4181 -346.4436 279.5725 -133.1115 1 > > 448.8503 163.0358 388.1139 -270.5156 251.5481 -417.3788 1 > > 928.5211 3.4069 68.0719 56.2443 15.2288 251.4085 1 > > 916.4941 81.2455 2.2603 272.8755 -13.5515 -45.5147 1 > > 4.8435 702.3000 292.8566 -58.3230 453.5120 -37.6622 1 > > 678.2513 83.5285 238.2202 -238.0196 -141.0609 401.9616 1 > > 10.5800 285.2599 704.1601 -54.9367 448.1837 -86.3134 1 > > 66.0182 638.1535 295.8284 -205.2553 -434.4927 139.7500 1 > > 343.0769 349.9121 307.0110 -346.4777 -327.7604 324.5433 1 > > 134.5348 285.3352 580.1300 195.9273 -406.8556 -279.3701 1 > > 773.0228 225.8930 1.0842 -417.8761 15.6496 -28.9500 1 > > 816.2269 16.5053 167.2678 116.0693 -52.5434 -369.4976 1 > > 0.0408 407.5226 592.4366 4.0773 -491.3566 -4.9161 1 > > 988.1923 9.8658 1.9419 -98.7388 4.3770 -43.8060 1 > > 453.0983 129.6143 417.2873 242.3387 -232.5649 -434.8243 1 > > 261.8399 738.0373 0.1227 439.5994 9.5179 5.6692 1 > > 348.4199 48.4850 603.0952 -129.9735 -171.0001 458.3998 1 > > 894.5359 86.9584 18.5058 -278.9039 -40.1153 128.6627 1 > > 689.1407 169.9987 140.8606 342.2762 154.7453 311.5650 1 > > 254.9452 23.1941 721.8608 76.8974 129.3943 428.9929 1 > > 164.7735 72.5963 762.6302 -109.3707 235.2958 -354.4873 1 > > 42.1049 125.0845 832.8106 72.5719 322.7564 187.2577 1 > > 52.6042 842.5461 104.8497 210.5266 297.2216 74.2666 1 > > 6.4149 944.1078 49.4773 -77.8225 -216.1295 17.8155 1 > > 427.6010 568.2432 4.1559 492.9314 -48.5957 -42.1551 1 > > 497.6722 411.2065 91.1212 -452.3782 193.5708 -212.9519; > > > > > > _______________________________________________ > > 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 > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From a.janke at gmail.com Mon Feb 27 21:05:54 2006 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 28 Feb 2006 12:05:54 +1000 Subject: [MINC-users] minc to dicom converter In-Reply-To: <86A652071AFE5548AA1C648AD489A15E01265DBD@ACBEXCHANGE.ad.cancerboard.ab.ca> References: <86A652071AFE5548AA1C648AD489A15E01265DBD@ACBEXCHANGE.ad.cancerboard.ab.ca> Message-ID: Teodor, There is none that i know of. (or would want to write for that matter). The reason mainly is due to DICOM's poor support for anything beyond 2D. There are a number of options though: 1) Convert to NifTi-1 mnc2nii At which stage there are some converters out there. 2) Convert to Raw and then use imagemagicks convert on each of the individual slices. 3) Use something like the Debabler Note that none of the above are officially supported to condoned.. :) In short the conversion you are requesting is fraught with both problems and danger meaning that there can be no general converter. a On 2/28/06, Teodor Stanescu wrote: > Hi, > > Could anyone suggest me a minc to dicom converter? Thanks. > > Teo > > PhD Candidate > Medical Physics > Cross Cancer Institute > 11560 University Avenue > Edmnton, AB, T6G 1Z2 > Phone: (780) 432-8622 > Fax: (780) 432-8615 > > > > This e-mail and any attachments may contain confidential and > privileged information. If you are not the intended recipient, > please notify the sender immediately by return e-mail, delete this > e-mail and destroy any copies. Any dissemination or use of this > information by a person other than the intended recipient is > unauthorized and may be illegal. > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > -- Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor) Canada->Montreal Cell: +1 (514) 924 2012 From runa at medphys.ucl.ac.uk Mon Feb 27 23:04:11 2006 From: runa at medphys.ucl.ac.uk (Runa Parveen) Date: Tue, 28 Feb 2006 04:04:11 +0000 Subject: [MINC-users] image transfer from analyze to minc In-Reply-To: References: <5.2.0.9.0.20060225174145.00ba7728@pop3-server> Message-ID: <5.2.0.9.0.20060228035052.00b53df0@pop3-server> Hi All, Many thanks who has helped me to use analyze file format. actually, minc 1.4 was not installed unluckily, But I don't understand other commands were working, like as, minctoraw, mincstats, rawtominc, etc. Anyway, I need to have another suggestion: After transfer the into minc and apply NU correction, then return back to analyze format, the images tranfer in 32 bit real which I don't want. I like to return back after nu correction in the previous values before correction. The suggestion is very much welcome to sort this out. Many thanks Runa At 14:36 25/02/2006 -0500, you wrote: >Hi Runa, > >When you say "it did not recognize", do you mean that the command was not >found, or that the the command could not recognize the Analyze file you >were trying to convert? Can you give me the specific error message? > > -bert > >On Sat, 25 Feb 2006, Runa Parveen wrote: > > > Hi Sylvain, > > > > I have installed this package but when I tried to use nii2mnc, it did not > > recognize, what would be the problem, please let me know. > > > > thanks, runa > > At 12:10 25/02/2006 -0500, you wrote: > > > > >Hello > > > > > >I believe Andrew no longer supports ana2mnc. > > > > > >You should be using nii2mnc which recognizes Analyze and NIfTI-1 formats. > > > > > >mnc2nii and nii2mnc are part of MINC release 1.4, available here: > > > > > >http://packages.bic.mni.mcgill.ca/tgz/minc-1.4.tar.gz > > > > > >S > > > > > >On Sat, 25 Feb 2006, Jonathan LAU wrote: > > > > > > > Hi Runa, > > > > > > > > Have you tried ana2mnc? > > > > http://www.cmr.uq.edu.au/~rotor/software/ > > > > > > > > Cheers, > > > > jonathan > > > > > > > > On 2/25/06, Runa Parveen wrote: > > > > > Hi all, > > > > > > > > > > I am working on Linux mode of this package. would you please > suggest me > > > > > which command i will use for transfer image analyze format to > minc format > > > > > for the purpose of NU correction. > > > > > > > > > > Many thanks, > > > > > > > > > > Yours sincerely, > > > > > > > > > > Runa > > > > > > > > > > ******************************************************************** > > > > > > > > > > * Runa > > > Parveen ** > > > > > * PhD > > > Student ** > > > > > * Medical Imaging > Group ** > > > > > * Dept. of Medical Physics & Bioengineering ** > > > > > * University College > London ** > > > > > * 2nd Floor, New Malet Place Engineering Building ** > > > > > * Gower Street, off Torrington > Place ** > > > > > * London WC1E 6JA ** > > > > > * > > > > > UK > > > > > ** > > > > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > > > > +44 (0) 7984 084 959 > (mob.) ** > > > > > * Fax.+44 (0) 20 7679 0255 > (Dept.) ** > > > > > * e-mail: runa at medphys.ucl.ac.uk ** > > > > > ********************************************************************* > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > > > > > > >--- > > >Sylvain Milot (sylvain at bic.mni.mcgill.ca) > > > (trinity at bic.mni.mcgill.ca) > > >Brain Imaging Centre > > >Montreal Neurological Institute > > >Webster 2B, Room 208 > > >Montreal, Qc., Canada, H3A 2B4 > > >Phone : (514) 398-4965, Fax: 398-8948 > > >Mobile : (514) 712-1768 > > >Office : 527 Av Des Pins O., Room 204 > > > Montreal, Qc., H2W 1S4 > > > > > > > > > > > >_______________________________________________ > > >MINC-users at bic.mni.mcgill.ca > > >http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > Yours sincerely, > > > > Runa > > > > ******************************************************************** > > > > * Runa > Parveen ** > > * PhD > Student ** > > * Medical Imaging Group ** > > * Dept. of Medical Physics & Bioengineering ** > > * University College London ** > > * 2nd Floor, New Malet Place Engineering Building ** > > * Gower Street, off Torrington Place ** > > * London WC1E 6JA ** > > * > > UK > > ** > > * Tel. +44 (0) 20 7679 0246 (Dept.) > > +44 (0) 7984 084 959 (mob.) ** > > * Fax.+44 (0) 20 7679 0255 (Dept.) ** > > * e-mail: runa at medphys.ucl.ac.uk ** > > ********************************************************************* > > > > _______________________________________________ > > 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 Yours sincerely, Runa ******************************************************************** * Runa Parveen ** * PhD Student ** * Medical Imaging Group ** * Dept. of Medical Physics & Bioengineering ** * University College London ** * 2nd Floor, New Malet Place Engineering Building ** * Gower Street, off Torrington Place ** * London WC1E 6JA ** * UK ** * Tel. +44 (0) 20 7679 0246 (Dept.) +44 (0) 7984 084 959 (mob.) ** * Fax.+44 (0) 20 7679 0255 (Dept.) ** * e-mail: runa at medphys.ucl.ac.uk ** ********************************************************************* From najma at bic.mni.mcgill.ca Tue Feb 28 19:18:25 2006 From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.) Date: Tue, 28 Feb 2006 19:18:25 -0500 Subject: [MINC-users] Failure of nu-estimate on older t1-weighted brain data. Message-ID: Greetings, I am trying to perform N3 on t1-data of healthy older brains and I encounter two error messages. (nu_estimate, version 1.10) First, I got the following error for N=50 data sets: Assertion failed at line 742 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) Next, I used an ICBM mask; succeeded in non-uniformity correction of N=45 data sets, but failed in 5 with : Direction cosines of mask.mnc and /tmp/native_t1.mnc do not match Failed to shrink mask volume. nu_estimate: crashed while running nu_estimate_np_and_em (termination status=65280) The data dimension in the failed cases is identical to those that have succeeded. The data quality and the brain structure in failing cases is not visually different. I have not seen this problem in younger brains. Has someone else experienced such errors and can any one give an explanation of what the cause of this might be, please? Best, Najma From alex at bic.mni.mcgill.ca Tue Feb 28 22:54:56 2006 From: alex at bic.mni.mcgill.ca (Alex ZIJDENBOS) Date: Tue, 28 Feb 2006 22:54:56 -0500 Subject: [MINC-users] Failure of nu-estimate on older t1-weighted brain data. In-Reply-To: References: Message-ID: <20060301035456.GA4022@bic.mni.mcgill.ca> I'm not sure what could be going on here; Najma sent me some of the data she used and I ran it through nu_correct v1.10 just fine. I'm not sure why essentially the same version of n3 would behave differently on these data. Are you using a standard install, or a quarantined version? The CachedArray error seems to indicate a failure in creating a temporary file - that could be a machine resource problem (out of /tmp space?). As for the masking, it seems you are trying to mask a native file with a stereotaxic mask, which is likely to produce unexpected results ;) I thought N3 checked at least that the sampling lattice of the source file and mask are the same - it *should* exit gracefully on something like this. -- A On Tue, Feb 28, 2006 at 07:18:25PM -0500, Najmeh Khalili M. wrote: > > Greetings, > > I am trying to perform N3 on t1-data of healthy older brains and I > encounter two error messages. (nu_estimate, version 1.10) > > First, I got the following error for N=50 data sets: > > Assertion failed at line 742 in file templates/CachedArray.cc > nu_estimate_np_and_em: crashed while running volume_stats (termination > status=256) > > Next, I used an ICBM mask; succeeded in non-uniformity correction of N=45 > data sets, but failed in 5 with : > > Direction cosines of mask.mnc and /tmp/native_t1.mnc do not match > Failed to shrink mask volume. > nu_estimate: crashed while running nu_estimate_np_and_em (termination > status=65280) > > The data dimension in the failed cases is identical to those that have > succeeded. The data quality and the brain structure in failing cases is > not visually different. I have not seen this problem in younger brains. > > Has someone else experienced such errors and can any one give an > explanation of what the cause of this might be, please? > > Best, > Najma > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From najma at bic.mni.mcgill.ca Tue Feb 28 23:12:28 2006 From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.) Date: Tue, 28 Feb 2006 23:12:28 -0500 Subject: [MINC-users] Failure of nu-estimate on older t1-weighted brain data. In-Reply-To: <20060301035456.GA4022@bic.mni.mcgill.ca> Message-ID: I agree that using an ICBM mask on a native data is not reasonable, but it worked for most of the cases. However, what is more important is that you can nu_correct this same data without any mask! No, I am not using the standard install! Perhaps Yasser can comment on the quarantine that Dale built for new version of CIVET. I ran PMP on ACES cluster. More informed comments about machines and the installation of tools? Perhaps from Andrew, Jason, Yasser, Dale??? N. On Tue, 28 Feb 2006, Alex ZIJDENBOS wrote: > I'm not sure what could be going on here; Najma sent me some of the > data she used and I ran it through nu_correct v1.10 just fine. I'm not > sure why essentially the same version of n3 would behave differently > on these data. Are you using a standard install, or a quarantined > version? The CachedArray error seems to indicate a failure in creating > a temporary file - that could be a machine resource problem (out of > /tmp space?). > > As for the masking, it seems you are trying to mask a native file with > a stereotaxic mask, which is likely to produce unexpected results ;) I > thought N3 checked at least that the sampling lattice of the source > file and mask are the same - it *should* exit gracefully on something > like this. > > -- A > > On Tue, Feb 28, 2006 at 07:18:25PM -0500, Najmeh Khalili M. wrote: > > > > Greetings, > > > > I am trying to perform N3 on t1-data of healthy older brains and I > > encounter two error messages. (nu_estimate, version 1.10) > > > > First, I got the following error for N=50 data sets: > > > > Assertion failed at line 742 in file templates/CachedArray.cc > > nu_estimate_np_and_em: crashed while running volume_stats (termination > > status=256) > > > > Next, I used an ICBM mask; succeeded in non-uniformity correction of N=45 > > data sets, but failed in 5 with : > > > > Direction cosines of mask.mnc and /tmp/native_t1.mnc do not match > > Failed to shrink mask volume. > > nu_estimate: crashed while running nu_estimate_np_and_em (termination > > status=65280) > > > > The data dimension in the failed cases is identical to those that have > > succeeded. The data quality and the brain structure in failing cases is > > not visually different. I have not seen this problem in younger brains. > > > > Has someone else experienced such errors and can any one give an > > explanation of what the cause of this might be, please? > > > > Best, > > Najma > > > > > > _______________________________________________ > > 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 >