From sorench at gmail.com Sun Jan 1 02:25:35 2012 From: sorench at gmail.com (Soren Christensen) Date: Sun, 1 Jan 2012 18:25:35 +1100 Subject: [MINC-users] How to write header information with the MINC2 API Message-ID: Happy New Years first of all! I am trying to write some attributes to a MINC2 file using the C API (using miset_attr_values). The problem is I am not able to get my variable at the correct position in the hierarchy. I would like to write a variable, attribute pair so that it appears as such when I use mincheader. My understanding is that I should put the variables in this path: miset_attr_values( volume , MI_TYPE_STRING, "/minc-2.0/info", "myvar", 1,"L"); but this gives me an error. I can create an arbitrary group and put the variable there, but that wont be listed as a standard variable using mincheader or mincinfo. How do I put in a variable so that it can be queried using the usual mincinfo -attvalue [varname]:[attname] ? Cheers Soren From pierre.bellec at criugm.qc.ca Sun Jan 1 21:09:51 2012 From: pierre.bellec at criugm.qc.ca (Pierre Bellec) Date: Sun, 1 Jan 2012 21:09:51 -0500 Subject: [MINC-users] compiling the minc bundle Message-ID: Dear Minc users, I am using the big Makefile Vladimir Vonof wrote to compile a full minc bundle on a server where I do not have access to sudo. I followed the instructions from the Minc wikibook: http://en.wikibooks.org/wiki/MINC/Tutorials/SourceInstall#Step_5:_Run_your_build.28s.29 After downloading the make file, I ran the following line: make minc-full BUILD_DIR=$HOME/tmp/build_minc INSTALL_DIR=$HOME/progs/minc-2011-12 Everything went well for a while but it crashed when compiling mni_perllib-0.08 mkdir /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/mni_perllib: Permission denied at /usr/lib/perl5/5.8.8/ExtUtils/Install.pm line 207 make[1]: *** [pure_site_install] Error 13 make[1]: Leaving directory `/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08' make: *** [/home/pbellec/progs/minc-2011-12/perl/MNI.pm] Error 2 Any suggestion on how to fix this problem will be very much appreciated. Pierre PS: Here's the whole compilation message just in case: mkdir -p /home/pbellec/tmp/build_minc/src mkdir -p /home/pbellec/progs/minc-2011-12/bin mkdir -p /home/pbellec/progs/minc-2011-12/lib mkdir -p /home/pbellec/progs/minc-2011-12/include mkdir -p /home/pbellec/progs/minc-2011-12/share/mni-models mkdir -p /home/pbellec/progs/minc-2011-12/share/mni_autoreg mkdir -p /home/pbellec/progs/minc-2011-12/share/man/man1 mkdir -p /home/pbellec/progs/minc-2011-12/share/man/man3 ls -l total 512 -rw-r--r-- 1 pbellec gsf-624-02 36 Jan 1 21:08 1 drwxr-xr-x 2 pbellec gsf-624-02 32768 Jan 1 20:59 bin -rw-r--r-- 1 pbellec gsf-624-02 423 Jan 1 21:08 compilation_error.txt drwxr-xr-x 3 pbellec gsf-624-02 32768 Dec 31 00:46 etc drwxr-xr-x 5 pbellec gsf-624-02 32768 Jan 1 20:59 include drwxr-xr-x 3 pbellec gsf-624-02 32768 Jan 1 20:59 lib -rw-r--r-- 1 pbellec gsf-624-02 40111 Dec 31 00:33 Makefile drwxr-xr-x 4 pbellec gsf-624-02 32768 Dec 31 00:40 man drwxr-xr-x 4 pbellec gsf-624-02 32768 Dec 31 00:46 perl drwxr-xr-x 9 pbellec gsf-624-02 32768 Dec 31 00:43 share cd /home/pbellec/tmp/build_minc/src/mni_perllib-0.08 && \ echo -e /home/pbellec/progs/minc-2011-12 \\n\\n\\n > dummy_response_file && \ echo perl ./Makefile.PL SITEPREFIX=/home/pbellec/progs/minc-2011-12 \ INSTALLDIRS=site \ INSTALLSITELIB=/home/pbellec/progs/minc-2011-12/perl \ INSTALLSITEBIN=/home/pbellec/progs/minc-2011-12/bin \ INSTALLSITEMAN1DIR=/home/pbellec/progs/minc-2011-12/share/man/man1 \ INSTALLSITEMAN3DIR=/home/pbellec/progs/minc-2011-12/share/man/man3 < dummy_response_file && \ perl ./Makefile.PL SITEPREFIX=/home/pbellec/progs/minc-2011-12 \ INSTALLDIRS=site \ INSTALLSITELIB=/home/pbellec/progs/minc-2011-12/perl \ INSTALLSITEBIN=/home/pbellec/progs/minc-2011-12/bin \ INSTALLSITEMAN1DIR=/home/pbellec/progs/minc-2011-12/share/man/man1 \ INSTALLSITEMAN3DIR=/home/pbellec/progs/minc-2011-12/share/man/man3 < dummy_response_file && \ make && \ make install && \ touch /home/pbellec/progs/minc-2011-12/perl/MNI.pm perl ./Makefile.PL SITEPREFIX=/home/pbellec/progs/minc-2011-12 INSTALLDIRS=site INSTALLSITELIB=/home/pbellec/progs/minc-2011-12/perl INSTALLSITEBIN=/home/pbellec/progs/minc-2011-12/bin INSTALLSITEMAN1DIR=/home/pbellec/progs/minc-2011-12/share/man/man1 INSTALLSITEMAN3DIR=/home/pbellec/progs/minc-2011-12/share/man/man3 I need to know the default directory for static, per-package data (eg., models). This is used so that packages distributed from the MNI have a consistent, uniform way of searching for such data. Whatever directory you specify, you can change your mind later by redoing the configure/build/install cycle for the MNI Perl Library; or, you can just put symbolic links in the directory you specify here, pointing to the real location of the data for whatever MNI packages you use at your site. And users can always override this default directory using the MNI_DATAPATH environment variable. Default directory for model data [/usr/local/mni/data]? Default directory for model data [/usr/local/mni/data]? Writing Makefile for mni_perllib make[1]: Entering directory `/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08' rm -f MNI/DataDir.pm sed 's|@DEFAULT_DATA_DIR@|/usr/local/mni/data|' MNI/DataDir.pm.in > MNI/DataDir.pm chmod 444 MNI/DataDir.pm Skip blib/lib/MNI/TagPoint.pm (unchanged) Skip blib/lib/MNI/Spawn.pm (unchanged) Skip blib/lib/MNI/Startup.pm (unchanged) Skip blib/lib/MNI.pm (unchanged) Skip blib/lib/mni_perllib.pod (unchanged) Skip blib/lib/MNI/MiscUtilities.pm (unchanged) Skip blib/lib/MNI/FileUtilities.pm (unchanged) Skip blib/lib/MNI/Spawn.pod (unchanged) Skip blib/lib/MNI/PathUtilities.pm (unchanged) Skip blib/lib/MNI/TagSet.pm (unchanged) Skip blib/lib/MNI/NumericUtilities.pm (unchanged) Skip blib/lib/MNI/MincUtilities.pm (unchanged) Skip blib/lib/MNI/DataDir.pm (unchanged) Skip blib/lib/MNI/Batch.pm (unchanged) Manifying blib/man3/MNI::TagPoint.3pm Manifying blib/man3/MNI::Startup.3pm Manifying blib/man3/MNI::MiscUtilities.3pm Manifying blib/man3/mni_perllib.3pm Manifying blib/man3/MNI::FileUtilities.3pm Manifying blib/man3/MNI::Spawn.3pm Manifying blib/man3/MNI::PathUtilities.3pm Manifying blib/man3/MNI::NumericUtilities.3pm Manifying blib/man3/MNI::TagSet.3pm Manifying blib/man3/MNI::DataDir.3pm Manifying blib/man3/MNI::MincUtilities.3pm Manifying blib/man3/MNI::Batch.3pm make[1]: Leaving directory `/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08' make[1]: Entering directory `/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08' Skip blib/lib/MNI/TagPoint.pm (unchanged) Skip blib/lib/MNI/Spawn.pm (unchanged) Skip blib/lib/MNI/Startup.pm (unchanged) Skip blib/lib/MNI.pm (unchanged) Skip blib/lib/mni_perllib.pod (unchanged) Skip blib/lib/MNI/MiscUtilities.pm (unchanged) Skip blib/lib/MNI/FileUtilities.pm (unchanged) Skip blib/lib/MNI/Spawn.pod (unchanged) Skip blib/lib/MNI/PathUtilities.pm (unchanged) Skip blib/lib/MNI/TagSet.pm (unchanged) Skip blib/lib/MNI/NumericUtilities.pm (unchanged) Skip blib/lib/MNI/MincUtilities.pm (unchanged) Skip blib/lib/MNI/DataDir.pm (unchanged) Skip blib/lib/MNI/Batch.pm (unchanged) Manifying blib/man3/MNI::DataDir.3pm Installing /home/pbellec/progs/minc-2011-12/share/man/man3/MNI::DataDir.3pm make[1]: Leaving directory `/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08' From a.janke at gmail.com Mon Jan 2 06:26:01 2012 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 2 Jan 2012 21:26:01 +1000 Subject: [MINC-users] compiling the minc bundle In-Reply-To: References: Message-ID: Hi Pierre, I suspect Vlad will know the real answer but it looks to me as if he is using a different way of specifying the PREFIX for a perl library install than I know. The line that seems pertinent is below: On 2 January 2012 12:09, Pierre Bellec wrote: > perl ./Makefile.PL SITEPREFIX=/home/pbellec/progs/minc-2011-12 I thought this was supposed to look like this: perl ./Makefile.PL PREFIX=/home/pbellec/progs/minc-2011-12 Perhaps the SITEPREFIX and PREFIX is an OSX vs Linux thing. a From pierre.bellec at criugm.qc.ca Tue Jan 3 00:25:50 2012 From: pierre.bellec at criugm.qc.ca (Pierre Bellec) Date: Tue, 3 Jan 2012 00:25:50 -0500 Subject: [MINC-users] compiling the minc bundle In-Reply-To: References: Message-ID: Thanks Andrew for the fast response. Unfortunately that did not solve the issue. I ended up making a local installation of PERL, and I was able to compile mni_perllib-0.08. The rest of the bundle is compiling now, I'll keep my fingers crossed. Best, Pierre 2012/1/2 Andrew Janke > Hi Pierre, > > I suspect Vlad will know the real answer but it looks to me as if he > is using a different way of specifying the PREFIX for a perl library > install than I know. The line that seems pertinent is below: > > On 2 January 2012 12:09, Pierre Bellec wrote: > > perl ./Makefile.PL SITEPREFIX=/home/pbellec/progs/minc-2011-12 > > I thought this was supposed to look like this: > > perl ./Makefile.PL PREFIX=/home/pbellec/progs/minc-2011-12 > > Perhaps the SITEPREFIX and PREFIX is an OSX vs Linux thing. > > > a > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sorench at gmail.com Tue Jan 3 06:44:07 2012 From: sorench at gmail.com (Soren Christensen) Date: Tue, 3 Jan 2012 22:44:07 +1100 Subject: [MINC-users] How to write header information with the MINC2 API In-Reply-To: References: Message-ID: Hi, Just to reiterate, what I am looking for is a way to enter variables+attributes into a MINC2 file so that they will get listed using the usual mincinto -attvalue [VAR:ATT] file.mnc I have not been able to accomplish this using the MINC2 API function miset_attr_values Using minc_modify_header on a MINC2 file I achieve what I want so I looked at the sources and it seems to me that this is achieve through some of the hdf_convenience function in hdf_conveinience.c. So this implementation is activated through the minc_compat.h mechanism originating in a ncvardef call. In contrast, the implementation used by the MINC2 API does make use of the hdf convenience functions and writes the variable "in a different way" that is not read by mincinfo nor mincheader. When I run an h5dump on a variable I added using minc_modify_header the variable is also labelled a "DATASET" - not exactly sure what this means, but when using miset_attr_values that is not the case. Am I missing an obvious way to create a variable using the MINC2 API or should I just do it via the hdf convenience functions? Cheers Soren On Sun, Jan 1, 2012 at 6:25 PM, Soren Christensen wrote: > Happy New Years first of all! > > I am trying to write some attributes to a MINC2 file using the C API (using > miset_attr_values). > The problem is I am not able to get my variable at the correct position in > the hierarchy. > > I would like to write a variable, attribute pair so that it appears as such > when I use mincheader. My understanding is that I should put the variables > in this path: > miset_attr_values( volume , MI_TYPE_STRING, "/minc-2.0/info", "myvar", > 1,"L"); > but this gives me an error. > > I can create an arbitrary group and put the variable there, but that wont be > listed as a standard variable using mincheader or mincinfo. > > How do I put in a variable so that it can be queried using the usual > mincinfo -attvalue [varname]:[attname] ? > > > Cheers > Soren > From matthijs at phenogenomics.ca Tue Jan 3 09:40:22 2012 From: matthijs at phenogenomics.ca (Matthijs van Eede) Date: Tue, 3 Jan 2012 09:40:22 -0500 Subject: [MINC-users] compiling the minc bundle In-Reply-To: References: Message-ID: <4F031356.2080903@phenogenomics.ca> When I was using Vlad's Makefile I had to add the following variables to the installation of mni_perllib, but that was not for the exact same problem you had... INSTALLSITEARCH=$(INSTALL_DIR)/perl INSTALLSITESCRIPT=$(INSTALL_DIR)/bin Cheers, Matthijs On 12-01-03 12:25 AM, Pierre Bellec wrote: > Thanks Andrew for the fast response. Unfortunately that did not solve the > issue. I ended up making a local installation of PERL, and I was able to > compile mni_perllib-0.08. The rest of the bundle is compiling now, I'll > keep my fingers crossed. > > Best, > > Pierre > > > > 2012/1/2 Andrew Janke > >> Hi Pierre, >> >> I suspect Vlad will know the real answer but it looks to me as if he >> is using a different way of specifying the PREFIX for a perl library >> install than I know. The line that seems pertinent is below: >> >> On 2 January 2012 12:09, Pierre Bellec wrote: >>> perl ./Makefile.PL SITEPREFIX=/home/pbellec/progs/minc-2011-12 >> I thought this was supposed to look like this: >> >> perl ./Makefile.PL PREFIX=/home/pbellec/progs/minc-2011-12 >> >> Perhaps the SITEPREFIX and PREFIX is an OSX vs Linux thing. >> >> >> a >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From zijdenbos at gmail.com Fri Jan 6 09:17:01 2012 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Fri, 6 Jan 2012 09:17:01 -0500 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? Message-ID: Hello, I am a bit puzzled by this MINC header: minc.hdr (http://cl.ly/1D0x0a3x002Y0w2O242U) specifically w/respect to the spacing along the time dimension. Towards the bottom of the header there is info for the time dimension; however, the time:spacing attribute is "regular". Shouldn't the time:spacing attribute be "irregular", given that the spacing is in fact not regular? -- Alex Zijdenbos Sent with Sparrow (http://www.sparrowmailapp.com) From a.janke at gmail.com Sun Jan 8 11:09:06 2012 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 9 Jan 2012 02:09:06 +1000 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: References: Message-ID: Hi Alex, On 7 January 2012 00:17, Alex Zijdenbos wrote: > I am a bit puzzled by this MINC header: > > minc.hdr (http://cl.ly/1D0x0a3x002Y0w2O242U) > > specifically w/respect to the spacing along the time dimension. Towards the bottom of the header there is info for the time dimension; however, the time:spacing attribute is "regular". Shouldn't the time:spacing attribute be "irregular", given that the spacing is in fact not regular? My read of your header has time at a pretty constant 4s? Steps also can be ever so slightly different, currently defined here as 0.005: https://github.com/andrewjanke/minc/blob/master/conversion/dcm2mnc/dicom_to_minc.h#L106 And a dimension will still be called regular. The logic for this is here: https://github.com/andrewjanke/minc/blob/master/conversion/dcm2mnc/minc_file.c#L182 a From zijdenbos at gmail.com Sun Jan 8 11:31:30 2012 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Sun, 8 Jan 2012 11:31:30 -0500 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: References: Message-ID: On Sun, Jan 8, 2012 at 11:09 AM, Andrew Janke wrote: > Hi Alex, > > On 7 January 2012 00:17, Alex Zijdenbos wrote: >> I am a bit puzzled by this MINC header: >> >> minc.hdr (http://cl.ly/1D0x0a3x002Y0w2O242U) >> >> specifically w/respect to the spacing along the time dimension. Towards the bottom of the header there is info for the time dimension; however, the time:spacing attribute is "regular". Shouldn't the time:spacing attribute be "irregular", given that the spacing is in fact not regular? > > My read of your header has time at a pretty constant 4s? For the most part yes; but there is at least one discontinuity in it, with a step of >86000s, no? > Steps also > can be ever so slightly different, currently defined here as 0.005: > > ? https://github.com/andrewjanke/minc/blob/master/conversion/dcm2mnc/dicom_to_minc.h#L106 > > And a dimension will still be called regular. The logic for this is here: > > ? https://github.com/andrewjanke/minc/blob/master/conversion/dcm2mnc/minc_file.c#L182 That all makes sense I guess; however, shouldn't there conceptually be agreement between the presence of the (ir)regular :spacing attribute value, and the presence of a (likely irregular) list of positions in the data section? In other words, if the spacing is judged to be regular, why would there still be an explicit list of positions in the header (the underlying question being, what do/should applications use)? Thanks, -- A From zijdenbos at gmail.com Sun Jan 8 17:58:47 2012 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Sun, 8 Jan 2012 17:58:47 -0500 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: References: Message-ID: Hm the plot thickens on this spacing issue. I went back to the conversion, and found this in the conversion log: WARNING: Coordinate spacing (4) differs from DICOM slice spacing (5) (perhaps you should consider the -usecoordinates option) Using 5 for the slice spacing value. >From what I can gather, the acquisition actually has 4mm slice thickness with 1mm gaps, bringing the (correct) slice spacing to 5mm. However, the coordinate spacing shows 4mm. If I use dcm2mnc -usecoordinates I get a volume with the header I previously posted; i.e., with a zstep of 4mm and a list of positions, also 4mm apart, in the data section of the header. Although that is internally consistent, the brain comes out looking 'squashed'. Without -usecoordinates, the resulting volume has a zstep of 5mm and is visually correct (in register); however, it still has the same list of zspace coordinates that are 4mm apart. Besides the fact that that is internally inconsistent, whenever I resample the volume it immediately comes out 'squashed' again, so I assume that mincresample relies on the explicit list of coordinates. So it seems that dcm2mnc cannot handle these DICOM data properly somehow (or the DICOM itself is bad). Is there a way to remove the list of zspace coordinates from the MINC header (other than by turning the volume into a stack of slices and re-assembling it again)? Thanks, -- A On Sun, Jan 8, 2012 at 11:31 AM, Alex Zijdenbos wrote: > On Sun, Jan 8, 2012 at 11:09 AM, Andrew Janke wrote: >> Hi Alex, >> >> On 7 January 2012 00:17, Alex Zijdenbos wrote: >>> I am a bit puzzled by this MINC header: >>> >>> minc.hdr (http://cl.ly/1D0x0a3x002Y0w2O242U) >>> >>> specifically w/respect to the spacing along the time dimension. Towards the bottom of the header there is info for the time dimension; however, the time:spacing attribute is "regular". Shouldn't the time:spacing attribute be "irregular", given that the spacing is in fact not regular? >> >> My read of your header has time at a pretty constant 4s? > > For the most part yes; but there is at least one discontinuity in it, > with a step of >86000s, no? > >> Steps also >> can be ever so slightly different, currently defined here as 0.005: >> >> ? https://github.com/andrewjanke/minc/blob/master/conversion/dcm2mnc/dicom_to_minc.h#L106 >> >> And a dimension will still be called regular. The logic for this is here: >> >> ? https://github.com/andrewjanke/minc/blob/master/conversion/dcm2mnc/minc_file.c#L182 > > That all makes sense I guess; however, shouldn't there conceptually be > agreement between the presence of the (ir)regular :spacing > attribute value, and the presence of a (likely irregular) list of > positions in the data section? In other words, if the spacing is > judged to be regular, why would there still be an explicit list of > positions in the header (the underlying question being, what do/should > applications use)? > > Thanks, > > -- A From a.janke at gmail.com Sun Jan 8 18:12:29 2012 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 9 Jan 2012 09:12:29 +1000 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: References: Message-ID: >> My read of your header has time at a pretty constant 4s? > > For the most part yes; but there is at least one discontinuity in it, > with a step of >86000s, no? Well there is that... I just figured something was amiss with your input files as this would be a break of 1 day in between time slices. Are your input files from two separate acquisitions? > That all makes sense I guess; however, shouldn't there conceptually be > agreement between the presence of the (ir)regular :spacing > attribute value, and the presence of a (likely irregular) list of > positions in the data section? In other words, if the spacing is > judged to be regular, why would there still be an explicit list of > positions in the header (the underlying question being, what do/should > applications use)? Myself if a file is defined as regular_ I always just use the start and steps. a From a.janke at gmail.com Sun Jan 8 18:16:32 2012 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 9 Jan 2012 09:16:32 +1000 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: References: Message-ID: > WARNING: Coordinate spacing (4) differs from DICOM slice spacing (5) > ?(perhaps you should consider the -usecoordinates option) > ?Using 5 for the slice spacing value. I did note the "irregular" in the zspace in the header you sent. > Without -usecoordinates, the resulting volume has a zstep of 5mm and > is visually correct (in register); however, it still has the same list > of zspace coordinates that are 4mm apart. Besides the fact that that > is internally inconsistent, whenever I resample the volume it > immediately comes out 'squashed' again, so I assume that mincresample > relies on the explicit list of coordinates. > > So it seems that dcm2mnc cannot handle these DICOM data properly > somehow (or the DICOM itself is bad). In 100% of the cases I have seen with this it is DICOM that is inconsistent. By this I mean that the various manufacturers treat these fields differently. Some include the slice gap in the slice width, some don't. Thus the option. > Is there a way to remove the list of zspace coordinates from the MINC > header (other than by turning the volume into a stack of slices and > re-assembling it again)? This is my method: minc_modify_header -sinsert zspace:spacing="regular_" a From zijdenbos at gmail.com Sun Jan 8 18:58:24 2012 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Sun, 8 Jan 2012 18:58:24 -0500 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: References: Message-ID: <51639FAEFECB422F926C3BFFFB6DA77E@gmail.com> On Sun, Jan 8, 2012 at 6:16 PM, Andrew Janke wrote: > > WARNING: Coordinate spacing (4) differs from DICOM slice spacing (5) > > (perhaps you should consider the -usecoordinates option) > > Using 5 for the slice spacing value. > > > > > I did note the "irregular" in the zspace in the header you sent. > > > Without -usecoordinates, the resulting volume has a zstep of 5mm and > > is visually correct (in register); however, it still has the same list > > of zspace coordinates that are 4mm apart. Besides the fact that that > > is internally inconsistent, whenever I resample the volume it > > immediately comes out 'squashed' again, so I assume that mincresample > > relies on the explicit list of coordinates. > > > > So it seems that dcm2mnc cannot handle these DICOM data properly > > somehow (or the DICOM itself is bad). > > > > > In 100% of the cases I have seen with this it is DICOM that is > inconsistent. By this I mean that the various manufacturers treat > these fields differently. Some include the slice gap in the slice > width, some don't. Thus the option. > > > Is there a way to remove the list of zspace coordinates from the MINC > > header (other than by turning the volume into a stack of slices and > > re-assembling it again)? > > > > > This is my method: > > minc_modify_header -sinsert zspace:spacing="regular_" Well that sets the zspace:spacing attribute; but if the header still contains an explicit list of coordinates, then those wil be used by things like mincresample. Here is the whole MINC volume: test.mnc (http://cl.ly/2h1h1O1i3G0H0S1i0w1k) Try to resample this like like so: mincresample -zstep 5 test.mnc test_z5.mnc and then pull both volumes up in register :) -- A From a.janke at gmail.com Sun Jan 8 20:21:45 2012 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 9 Jan 2012 11:21:45 +1000 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: <51639FAEFECB422F926C3BFFFB6DA77E@gmail.com> References: <51639FAEFECB422F926C3BFFFB6DA77E@gmail.com> Message-ID: >> This is my method: >> >> ? minc_modify_header -sinsert zspace:spacing="regular_" > > Well that sets the zspace:spacing attribute; but if the header still contains an explicit list of coordinates, then those wil be used by things like mincresample. Here is the whole MINC volume: > > test.mnc (http://cl.ly/2h1h1O1i3G0H0S1i0w1k) > > Try to resample this like like so: > > mincresample -zstep 5 test.mnc test_z5.mnc And this is because I am a goose and said "regular_" instead of "regular__". (two underscores needed!). minc_modify_header -sinsert zspace:spacing="regular__" a From zijdenbos at gmail.com Sun Jan 8 20:39:10 2012 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Sun, 8 Jan 2012 20:39:10 -0500 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: References: <51639FAEFECB422F926C3BFFFB6DA77E@gmail.com> Message-ID: On Sun, Jan 8, 2012 at 8:21 PM, Andrew Janke wrote: >>> This is my method: >>> >>> ? minc_modify_header -sinsert zspace:spacing="regular_" >> >> Well that sets the zspace:spacing attribute; but if the header still contains an explicit list of coordinates, then those wil be used by things like mincresample. Here is the whole MINC volume: >> >> test.mnc (http://cl.ly/2h1h1O1i3G0H0S1i0w1k) >> >> Try to resample this like like so: >> >> mincresample -zstep 5 test.mnc test_z5.mnc > > And this is because I am a goose and said "regular_" instead of > "regular__". ?(two underscores needed!). > > ? minc_modify_header -sinsert zspace:spacing="regular__" ! I had missed that too :( and I just wrote a a volume splitter/restacker to fix it, but as hammers go minc_modify_header is a lot smaller... So "regular_" with one underscore is in fact treated as "irregular" :-) -- A From peter.neelin at gmail.com Tue Jan 10 00:07:37 2012 From: peter.neelin at gmail.com (Peter Neelin) Date: Tue, 10 Jan 2012 00:07:37 -0500 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: References: <51639FAEFECB422F926C3BFFFB6DA77E@gmail.com> Message-ID: On Sun, Jan 8, 2012 at 8:39 PM, Alex Zijdenbos wrote: > So "regular_" with one underscore is in fact treated as "irregular" :-) It is treated as missing - i.e. unknown. The zspace variable dimensions are then checked as a fallback. In your case, it guesses irregular since the variable has the zspace dimension. See https://github.com/andrewjanke/minc/blob/master/progs/mincresample/mincresample.c, line 1005. Peter -- Peter Neelin (peter.neelin at gmail.com) From mishkind at gmail.com Tue Jan 10 14:21:41 2012 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Tue, 10 Jan 2012 14:21:41 -0500 Subject: [MINC-users] mincpik error Message-ID: Hi, In the latest version of mincpik (minc-2.1.01), and possibly in older versions I get the following error: Can't use string ("0") as an ARRAY ref while "strict refs" in use at ./mincpik line 435. I can get rid of the error by changing the offending code from: # get range if not defined if(!defined(@{$opt{'image_range'}[0]})){ print STDERR "Getting image range\n" if $opt{'verbose'}; to this: # get range if not defined my @image_range_array = $opt{'image_range'}; if(!defined($image_range_array[0])){ print STDERR "Getting image range\n" if $opt{'verbose'}; I'm afraid the underlying cause as to why strict is complaining about the way the code is referencing the array is beyond my perl-fu. The error could be specific to the odd invocation I am using just to get an anot_bar? mincpik -lookup '-spectral' -anot_bar lbar.png -image_range 0 0 icbm_avg_152_t1_tal_lin.mnc.gz input.png -clobber hth, mishkin From a.janke at gmail.com Tue Jan 10 20:39:50 2012 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 11 Jan 2012 11:39:50 +1000 Subject: [MINC-users] mincpik error In-Reply-To: References: Message-ID: Hi Mishkin, > Can't use string ("0") as an ARRAY ref while "strict refs" in use at > ./mincpik line 435. > > I can get rid of the error by changing the offending code from: > > ? # get range if not defined > ? if(!defined(@{$opt{'image_range'}[0]})){ > ? ? ?print STDERR "Getting image range\n" if $opt{'verbose'}; > > to this: > ? # get range if not defined > ? my @image_range_array = $opt{'image_range'}; > ? if(!defined($image_range_array[0])){ > ? ? ?print STDERR "Getting image range\n" if $opt{'verbose'}; Interesting, I have no idea why I did that originally. The easiest way to fix this is to just drop the @{...}, I have committed a fix for this here: https://github.com/andrewjanke/minc/commit/ba0cea6b141d874feea60238690f548d2f034baa Thanks a From zijdenbos at gmail.com Tue Jan 10 22:41:41 2012 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Tue, 10 Jan 2012 22:41:41 -0500 Subject: [MINC-users] dcm2mnc and (ir)regular spacing? In-Reply-To: References: <51639FAEFECB422F926C3BFFFB6DA77E@gmail.com> Message-ID: Always a nice surprise to see the father of MINC show up again! :) I think now everything fits (well except for the dicom slice spacing confusion, but I guess that is what it is). Thanks both, -- Alex On Tue, Jan 10, 2012 at 12:07 AM, Peter Neelin wrote: > On Sun, Jan 8, 2012 at 8:39 PM, Alex Zijdenbos wrote: > >> So "regular_" with one underscore is in fact treated as "irregular" :-) > > It is treated as missing - i.e. unknown. The zspace variable > dimensions are then checked as a fallback. In your case, it guesses > irregular since the variable has the zspace dimension. See > https://github.com/andrewjanke/minc/blob/master/progs/mincresample/mincresample.c, > line 1005. > > Peter > -- > Peter Neelin > (peter.neelin at gmail.com) > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Thu Jan 12 01:53:24 2012 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 12 Jan 2012 16:53:24 +1000 Subject: [MINC-users] [Job advert] Come work in Oz Message-ID: Hi all, Want to work in the best place in the world? (Clearly, that'd be Brisbane, Australia). http://www.unijobs.com.au/show.php?title=senior_software_developer_56663 Short version: Think a distributed version of OpenStreetMap for Multiscale Neuroimaging/Histology data. Thanks a From thomas.funck at mail.mcgill.ca Mon Jan 16 10:09:57 2012 From: thomas.funck at mail.mcgill.ca (Thomas Funck) Date: Mon, 16 Jan 2012 15:09:57 +0000 Subject: [MINC-users] MINC installation issue Message-ID: <53F3FD0032C9CC4BA836E8F0FC2890650587C4@EXMBX2010-4.campus.MCGILL.CA> Hi, I had minc installed and working but something went wrong with my libraries and so now I am trying to reinstall it (from source). However for the life of me I can't find the correct HDF5 version to install it with. I've tried older versions of HDF5 (1.6.9) and I get the following errors when trying to use the minc2 library: /usr/bin/ld: warning: libhdf5.so.7, needed by /usr/local/neuro/lib//libminc2.so, not found (try using -rpath or -rpath-link) /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Acreate1' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eauto_is_v2' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eget_auto1' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Aiterate1' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Dcreate1' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Gcreate1' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eset_auto2' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Gopen2' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Acreate2' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eget_auto2' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Pget_filter1' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Dopen1' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eset_auto1' /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Gopen1' On the other hand, when I install HDF5(1.8.9) I get the following errors: libsrc/hdf_convenience.c: In function ?hdf_id_add?: libsrc/hdf_convenience.c:83:9: error: too few arguments to function ?H5Gopen2? /usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here libsrc/hdf_convenience.c: In function ?hdf_var_add?: libsrc/hdf_convenience.c:185:9: error: too few arguments to function ?H5Dopen2? /usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here libsrc/hdf_convenience.c: In function ?hdf_put_dimorder?: libsrc/hdf_convenience.c:621:5: error: too few arguments to function ?H5Acreate2? /usr/local/neuro/include/H5Apublic.h:44:16: note: declared here libsrc/hdf_convenience.c: In function ?hdf_set_length?: libsrc/hdf_convenience.c:928:28: error: too few arguments to function ?H5Acreate2? /usr/local/neuro/include/H5Apublic.h:44:16: note: declared here libsrc/hdf_convenience.c: In function ?hdf_attput?: libsrc/hdf_convenience.c:1106:37: error: too few arguments to function ?H5Dcreate2? /usr/local/neuro/include/H5Dpublic.h:104:14: note: declared here libsrc/hdf_convenience.c:1110:13: error: incompatible type for argument 2 of ?H5Aiterate2? /usr/local/neuro/include/H5Apublic.h:74:16: note: expected ?H5_index_t? but argument is of type ?unsigned int *? libsrc/hdf_convenience.c:1110:13: error: incompatible type for argument 3 of ?H5Aiterate2? /usr/local/neuro/include/H5Apublic.h:74:16: note: expected ?H5_iter_order_t? but argument is of type ?herr_t (*)(hid_t, const char *, void *)? libsrc/hdf_convenience.c:1110:13: error: too few arguments to function ?H5Aiterate2? /usr/local/neuro/include/H5Apublic.h:74:16: note: declared here libsrc/hdf_convenience.c:1189:9: error: too few arguments to function ?H5Acreate2? /usr/local/neuro/include/H5Apublic.h:44:16: note: declared here libsrc/hdf_convenience.c: In function ?hdf_vardef?: libsrc/hdf_convenience.c:1384:9: error: too few arguments to function ?H5Dcreate2? /usr/local/neuro/include/H5Dpublic.h:104:14: note: declared here libsrc/hdf_convenience.c: In function ?hdf_copy_attr?: libsrc/hdf_convenience.c:2060:4: error: too few arguments to function ?H5Acreate2? /usr/local/neuro/include/H5Apublic.h:44:16: note: declared here libsrc/hdf_convenience.c: In function ?hdf_open_dsets?: libsrc/hdf_convenience.c:2122:6: error: too few arguments to function ?H5Gopen2? /usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here libsrc/hdf_convenience.c:2133:6: error: too few arguments to function ?H5Dopen2? /usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here libsrc/hdf_convenience.c: In function ?hdf_open?: libsrc/hdf_convenience.c:2209:9: error: too few arguments to function ?H5Dopen2? /usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here libsrc/hdf_convenience.c:2240:9: error: too few arguments to function ?H5Dopen2? /usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here libsrc/hdf_convenience.c:2248:9: error: too few arguments to function ?H5Dopen2? /usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here libsrc/hdf_convenience.c:2259:5: error: too few arguments to function ?H5Gopen2? /usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here libsrc/hdf_convenience.c:2265:5: error: too few arguments to function ?H5Gopen2? /usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here libsrc/hdf_convenience.c: In function ?hdf_create?: libsrc/hdf_convenience.c:2299:5: error: too few arguments to function ?H5Gcreate2? /usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here libsrc/hdf_convenience.c:2303:5: error: too few arguments to function ?H5Gcreate2? /usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here libsrc/hdf_convenience.c:2308:5: error: too few arguments to function ?H5Gcreate2? /usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here libsrc/hdf_convenience.c:2313:5: error: too few arguments to function ?H5Gcreate2? /usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here libsrc/hdf_convenience.c:2318:5: error: too few arguments to function ?H5Gcreate2? /usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here Any suggestion what HDF5 library I should use? Many thanks for the help! Thomas From a.janke at gmail.com Mon Jan 16 18:34:16 2012 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 17 Jan 2012 09:34:16 +1000 Subject: [MINC-users] MINC installation issue In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC2890650587C4@EXMBX2010-4.campus.MCGILL.CA> References: <53F3FD0032C9CC4BA836E8F0FC2890650587C4@EXMBX2010-4.campus.MCGILL.CA> Message-ID: Hi Thomas, On 17 January 2012 01:09, Thomas Funck wrote: > I've tried older versions of HDF5 (1.6.9) and ?I get the following errors when trying to use the minc2 library: > /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Acreate1' > > <...> > > On the other hand, when I install HDF5(1.8.9) I get the following errors: > libsrc/hdf_convenience.c:83:9: error: too few arguments to function ?H5Gopen2? > /usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here The version of HDF5 I am using is 1.8.4 but 1.8.9 should be fine. Are you doing a "make clean" and re-running configure between compilation attempts with the different versions? It's possibly also best to remove config.cache Also make sure you are using the '--with-minc2' configure switch. a From sean at rogue-research.com Wed Jan 18 15:47:04 2012 From: sean at rogue-research.com (Sean McBride) Date: Wed, 18 Jan 2012 15:47:04 -0500 Subject: [MINC-users] MINC tools installation on Mac OS X 10.7 Lion Message-ID: <20120118204704.99694198@mail.rogue-research.com> Hello MINC experts, What should one download to install the MINC tools on Mac OS X 10.7 Lion? Looking here: I see packages for 10.4 and 10.5. Is the latter known to work well on Lion? I'd prefer to install official binaries than build everything from source (which has not been straightforward, at least in the past). Thanks, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From a.janke at gmail.com Sun Jan 22 06:33:33 2012 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 22 Jan 2012 21:33:33 +1000 Subject: [MINC-users] MINC tools installation on Mac OS X 10.7 Lion In-Reply-To: <20120118204704.99694198@mail.rogue-research.com> References: <20120118204704.99694198@mail.rogue-research.com> Message-ID: Hi Sean, For a number of reasons my favoured approach for MINC on OSX as of late is MacPorts. https://github.com/hassemlal/MacPorts This is the work of Haz-Edine Assemlal of the CIM, I have had reports of this working for some users and others get a checksum error.... Jason Lerch also has a OSX bundle somewhere that he points others at from time to time. Myself I'm still Mac Impaired but do SSH in to one at work from time to time to test the MacPorts stuff so can't be of much help. a On 19 January 2012 06:47, Sean McBride wrote: > Hello MINC experts, > > What should one download to install the MINC tools on Mac OS X 10.7 Lion? ?Looking here: > > > > I see packages for 10.4 and 10.5. ?Is the latter known to work well on Lion? ?I'd prefer to install official binaries than build everything from source (which has not been straightforward, at least in the past). > > Thanks, > > -- > ____________________________________________________________ > Sean McBride, B. Eng ? ? ? ? ? ? ? ? sean at rogue-research.com > Rogue Research ? ? ? ? ? ? ? ? ? ? ? ?www.rogue-research.com > Mac Software Developer ? ? ? ? ? ? ?Montr?al, Qu?bec, Canada > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From thomas.funck at mail.mcgill.ca Mon Jan 23 10:48:13 2012 From: thomas.funck at mail.mcgill.ca (Thomas Funck) Date: Mon, 23 Jan 2012 15:48:13 +0000 Subject: [MINC-users] FW: MINC-users Digest, Vol 78, Issue 11 In-Reply-To: References: Message-ID: <53F3FD0032C9CC4BA836E8F0FC2890650649B9@EXMBX2010-2.campus.MCGILL.CA> Hi Andrew, Thanks for the help! I tried your suggestions but minc-2.0.18 but I'm still getting the same errors. When I tried to configure with minc package with '--minc-2' but it said that this option was not recognized. Any other ideas? Cheers, Thomas ________________________________________ From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca] Sent: Tuesday, January 17, 2012 12:00 PM To: minc-users at bic.mni.mcgill.ca Subject: MINC-users Digest, Vol 78, Issue 11 Send MINC-users mailing list submissions to minc-users at bic.mni.mcgill.ca To subscribe or unsubscribe via the World Wide Web, visit http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users or, via email, send a message with subject or body 'help' to minc-users-request at bic.mni.mcgill.ca You can reach the person managing the list at minc-users-owner at bic.mni.mcgill.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of MINC-users digest..." Today's Topics: 1. Re: MINC installation issue (Andrew Janke) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Jan 2012 09:34:16 +1000 From: Andrew Janke Subject: Re: [MINC-users] MINC installation issue To: MINC users mailing list Message-ID: Content-Type: text/plain; charset=windows-1252 Hi Thomas, On 17 January 2012 01:09, Thomas Funck wrote: > I've tried older versions of HDF5 (1.6.9) and ?I get the following errors when trying to use the minc2 library: > /usr/local/neuro/lib//libminc2.so: undefined reference to `H5Acreate1' > > <...> > > On the other hand, when I install HDF5(1.8.9) I get the following errors: > libsrc/hdf_convenience.c:83:9: error: too few arguments to function ?H5Gopen2? > /usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here The version of HDF5 I am using is 1.8.4 but 1.8.9 should be fine. Are you doing a "make clean" and re-running configure between compilation attempts with the different versions? It's possibly also best to remove config.cache Also make sure you are using the '--with-minc2' configure switch. a ------------------------------ _______________________________________________ MINC-users mailing list MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users End of MINC-users Digest, Vol 78, Issue 11 ****************************************** From a.janke at gmail.com Mon Jan 23 21:05:14 2012 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 24 Jan 2012 12:05:14 +1000 Subject: [MINC-users] FW: MINC-users Digest, Vol 78, Issue 11 In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC2890650649B9@EXMBX2010-2.campus.MCGILL.CA> References: <53F3FD0032C9CC4BA836E8F0FC2890650649B9@EXMBX2010-2.campus.MCGILL.CA> Message-ID: Hi Thomas, On 24 January 2012 01:48, Thomas Funck wrote: > Thanks for the help! I tried your suggestions but minc-2.0.18 but I'm still getting the same errors. When I tried to configure with minc package with '--minc-2' but it said that this option was not recognized. Any other ideas? The option should be --enable-minc2. Was this what you used? thanks a From thomas.funck at mail.mcgill.ca Tue Jan 24 12:09:55 2012 From: thomas.funck at mail.mcgill.ca (Thomas Funck) Date: Tue, 24 Jan 2012 17:09:55 +0000 Subject: [MINC-users] MINC-users Digest, Vol 78, Issue 15 In-Reply-To: References: Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065066C51@EXMBX2010-4.campus.MCGILL.CA> Yes, sorry for not being clear, I used the line: "./configure --enable-minc2 --prefix=/usr/local/neuro" to configure, but I get the warning: "configure: WARNING: unrecognized options: --enable-minc2" Thanks again, Thomas ________________________________________ From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca] Sent: Tuesday, January 24, 2012 12:00 PM To: minc-users at bic.mni.mcgill.ca Subject: MINC-users Digest, Vol 78, Issue 15 Send MINC-users mailing list submissions to minc-users at bic.mni.mcgill.ca To subscribe or unsubscribe via the World Wide Web, visit http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users or, via email, send a message with subject or body 'help' to minc-users-request at bic.mni.mcgill.ca You can reach the person managing the list at minc-users-owner at bic.mni.mcgill.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of MINC-users digest..." Today's Topics: 1. Re: FW: MINC-users Digest, Vol 78, Issue 11 (Andrew Janke) ---------------------------------------------------------------------- Message: 1 Date: Tue, 24 Jan 2012 12:05:14 +1000 From: Andrew Janke Subject: Re: [MINC-users] FW: MINC-users Digest, Vol 78, Issue 11 To: MINC users mailing list Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Hi Thomas, On 24 January 2012 01:48, Thomas Funck wrote: > Thanks for the help! I tried your suggestions but minc-2.0.18 but I'm still getting the same errors. When I tried to configure with minc package with '--minc-2' but it said that this option was not recognized. Any other ideas? The option should be --enable-minc2. Was this what you used? thanks a ------------------------------ _______________________________________________ MINC-users mailing list MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users End of MINC-users Digest, Vol 78, Issue 15 ******************************************