From yalingy@usc.edu Wed Oct 6 18:51:05 2004 From: yalingy@usc.edu (yaling yang) Date: Wed Oct 6 17:51:05 2004 Subject: [MINC-users] display keep freezing Message-ID: <014301c4abee$704e43c0$6501a8c0@YALINGYANG> This is a multi-part message in MIME format. --Boundary_(ID_TGVo6/gp8G985UEOvyp/IQ) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Dear All, We are using the Power Mac G4 with 23" screen for running the Display. Somehow, it happens quite often that when we stretch the display window (either the 3D or the three views one), it just froze everything and we have to shut down the computer and restart again. Any suggestion would be really appreciated! Best regards, yaling Yaling Yang Brian and Cognitive Science Program Psychology Department University of Southern California phone: 310-663-2088 email: yalingy@usc.edu --Boundary_(ID_TGVo6/gp8G985UEOvyp/IQ) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT

Dear All,

We are using the Power Mac G4 with 23" screen for running the Display. Somehow, it happens quite often that when we stretch the display window (either the 3D or the three views one), it just froze everything and we have to shut down the computer and restart again.

Any suggestion would be really appreciated!

Best regards,

yaling

Yaling Yang

Brian and Cognitive Science Program

Psychology Department

University of Southern California

phone: 310-663-2088

email: yalingy@usc.edu

--Boundary_(ID_TGVo6/gp8G985UEOvyp/IQ)-- From adamt@fmrif.nimh.nih.gov Thu Oct 7 04:58:05 2004 From: adamt@fmrif.nimh.nih.gov (Adam Thomas) Date: Thu Oct 7 03:58:05 2004 Subject: [MINC-users] MINC 1.3 released In-Reply-To: References: Message-ID: I tried to compile MINC 1.3 on Redhat 9 and got the following error: make[2]: Entering directory `/amnt/tungsten1/Apps/minc-build/minc-1.3' if /bin/sh ./libtool --mode=compile /usr/bin/c99 -DHAVE_CONFIG_H -I. -I. -I. -I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib -I /misc/tungsten1/Apps/MNI-1.3/include -g -O2 -MT volume_io/Prog_utils/time.lo -MD -MP -MF "volume_io/Prog_utils/.deps/time.Tpo" \ -c -o volume_io/Prog_utils/time.lo `test -f 'volume_io/Prog_utils/time.c' || echo './'`volume_io/Prog_utils/time.c; \ then mv "volume_io/Prog_utils/.deps/time.Tpo" "volume_io/Prog_utils/.deps/time.Plo"; \ else rm -f "volume_io/Prog_utils/.deps/time.Tpo"; exit 1; \ fi /usr/bin/c99 -DHAVE_CONFIG_H -I. -I. -I. -I./libsrc -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib -I /misc/tungsten1/Apps/MNI-1.3/include -g -O2 -MT volume_io/Prog_utils/time.lo -MD -MP -MF volume_io/Prog_utils/.deps/time.Tpo -c volume_io/Prog_utils/time.c -o volume_io/Prog_utils/time.o volume_io/Prog_utils/time.c: In function `get_clock_ticks_per_second': volume_io/Prog_utils/time.c:58: `CLK_TCK' undeclared (first use in this function) volume_io/Prog_utils/time.c:58: (Each undeclared identifier is reported only once volume_io/Prog_utils/time.c:58: for each function it appears in.) make[2]: *** [volume_io/Prog_utils/time.lo] Error 1 make[2]: Leaving directory `/amnt/tungsten1/Apps/minc-build/minc-1.3' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/amnt/tungsten1/Apps/minc-build/minc-1.3' make: *** [all] Error 2 Seems to not be finding time.h. Has anyone else seen this? Thanks, -a --- Adam Thomas adamt@nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370 On Thu, 12 Aug 2004, Robert VINCENT wrote: > Hello minc-users, > > I've placed a new release of MINC, version 1.3, on our usual software > distribution sites: > > http://www.bic.mni.mcgill.ca/software/distribution/ > > http://www.bic.mni.mcgill.ca/software/minc/ > > MINC 1.3 fixes the recently discovered incompatibility with netCDF > 3.5.1, > and fixes one or two other bugs and minor build issues. One potentially > serious bug with minccalc has been fixed, it would affect you if you > use minccalc with MINC files which contain a vector dimension. > > A -version flag has been added to most of the tools. > > See the NEWS and ChangeLog files for additional details. > > MINC 1.3 has been built successfully on Linux (RedHat) and IRIX. > > -bert > > > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From bert@bic.mni.mcgill.ca Thu Oct 7 12:51:05 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Oct 7 11:51:05 2004 Subject: [MINC-users] MINC 1.3 released In-Reply-To: Message-ID: Hi Adam, Try using gcc instead of c99. c99 turns off the CLK_TCK macro in time.h on RedHat and Fedora systems (possibly other Linux boxes as well). Thanks, I hope this helps. -bert On Wed, 6 Oct 2004, Adam Thomas wrote: > > I tried to compile MINC 1.3 on Redhat 9 and got the following error: > > make[2]: Entering directory `/amnt/tungsten1/Apps/minc-build/minc-1.3' > if /bin/sh ./libtool --mode=compile /usr/bin/c99 -DHAVE_CONFIG_H -I. > -I. -I. -I./libsrc -I./volume_io/Include -I./volume_io/Include > -I./progs/Proglib -I /misc/tungsten1/Apps/MNI-1.3/include -g -O2 -MT > volume_io/Prog_utils/time.lo -MD -MP -MF > "volume_io/Prog_utils/.deps/time.Tpo" \ > -c -o volume_io/Prog_utils/time.lo `test -f > 'volume_io/Prog_utils/time.c' || echo > './'`volume_io/Prog_utils/time.c; \ > then mv "volume_io/Prog_utils/.deps/time.Tpo" > "volume_io/Prog_utils/.deps/time.Plo"; \ > else rm -f "volume_io/Prog_utils/.deps/time.Tpo"; exit 1; \ > fi > /usr/bin/c99 -DHAVE_CONFIG_H -I. -I. -I. -I./libsrc > -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib -I > /misc/tungsten1/Apps/MNI-1.3/include -g -O2 -MT > volume_io/Prog_utils/time.lo -MD -MP -MF > volume_io/Prog_utils/.deps/time.Tpo -c volume_io/Prog_utils/time.c -o > volume_io/Prog_utils/time.o > volume_io/Prog_utils/time.c: In function `get_clock_ticks_per_second': > volume_io/Prog_utils/time.c:58: `CLK_TCK' undeclared (first use in > this function) > volume_io/Prog_utils/time.c:58: (Each undeclared identifier is > reported only once > volume_io/Prog_utils/time.c:58: for each function it appears in.) > make[2]: *** [volume_io/Prog_utils/time.lo] Error 1 > make[2]: Leaving directory `/amnt/tungsten1/Apps/minc-build/minc-1.3' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/amnt/tungsten1/Apps/minc-build/minc-1.3' > make: *** [all] Error 2 > > > Seems to not be finding time.h. Has anyone else seen this? > > Thanks, > -a > > --- > Adam Thomas adamt@nih.gov > Functional MRI Facility, NIMH/NIH/DHHS > 10 Center Dr, Room B1D708A > Bethesda MD. 20892-1148 > Phone:301-402-6351 Fax: 301-402-1370 > > > On Thu, 12 Aug 2004, Robert VINCENT wrote: > > > Hello minc-users, > > > > I've placed a new release of MINC, version 1.3, on our usual software > > distribution sites: > > > > http://www.bic.mni.mcgill.ca/software/distribution/ > > > > http://www.bic.mni.mcgill.ca/software/minc/ > > > > MINC 1.3 fixes the recently discovered incompatibility with netCDF > > 3.5.1, > > and fixes one or two other bugs and minor build issues. One potentially > > serious bug with minccalc has been fixed, it would affect you if you > > use minccalc with MINC files which contain a vector dimension. > > > > A -version flag has been added to most of the tools. > > > > See the NEWS and ChangeLog files for additional details. > > > > MINC 1.3 has been built successfully on Linux (RedHat) and IRIX. > > > > -bert > > > > > > > > > > > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From yves.roy@umontreal.ca Fri Oct 8 17:15:04 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Fri Oct 8 16:15:04 2004 Subject: [MINC-users] mritotal crashes on bullcalf.... Message-ID: Hi: I ran mritotal (see below) and it crashes in minctracc... I was just wondering if it can be due to some sort of corruption in the MINC image resulting from the conversion from DICOM to MINC. On (probably) another note, I notice that the minc header in the converted files contains less information and in a different format (XML) than if the conversion was done using dcm2mnc for example. Do you think it can be related to the problem? Here is the error I got: bullcalf 108% mritotal doyon_ansa_irmf-sonata-21247-20040303-175816-18.mnc subj2.xfm ... ... /usr/local/mni/bin/minctracc /var/tmp/mritotal_1357678/doyon_ansa_irmf-sonata-21247-20040303-175816-18_16_blur.mnc /usr/local/mni/data/mni_autoreg/average_305_16_blur.mnc /var/tmp/mritotal_1357678/doyon_ansa_irmf-sonata-21247-20040303-175816-18_16.xfm -est_translations -lsq7 -xcorr -center No COG can be calculated -step 4 4 4 -tol 0.01 -simplex 20 Usage: /usr/local/mni/bin/minctracc [] /usr/local/mni/bin/minctracc [-help] mritotal: crashed while running minctracc (exit status=256) Many thanks Yves From tosa@nmr.mgh.harvard.edu Tue Oct 12 11:34:05 2004 From: tosa@nmr.mgh.harvard.edu (Yasunari Tosa) Date: Tue Oct 12 10:34:05 2004 Subject: [MINC-users] mni_perllib-0.07 problem for "make test" Message-ID: <416BEB19.9040103@nmr.mgh.harvard.edu> I encountered problems when I ran "make test" for mni_perllib-0.07. I'm perl-handicapped. Please tell me how to fix. Thank you. Tosa 1. RedHat 9. perl version v.5.8.0 built for i386-linux-thread-multi =============================================== I configured PREFIX=/usr/local/mni/1.2 and data dir to /usr/local/mni/1.2/data # make test rm -f t/datadir.t sed 's|@DEFAULT_DATA_DIR@|/usr/local/mni/1.2/data|' t/datadir.t.in > t/datadir.t chmod 444 t/datadir.t rm -f t/toy_ls sed 's|@PERL@|\#!/usr/bin/perl|' t/toy_ls.in > t/toy_ls chmod 555 t/toy_ls PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/batch-0........ok t/batch-1......../usr/bin/getopt: invalid option -- J /usr/bin/getopt: invalid option -- Q /usr/bin/getopt: invalid option -- S /usr/bin/getopt: invalid option -- s /usr/bin/getopt: invalid option -- o /usr/bin/getopt: invalid option -- e batch: error parsing command-line arguments Error closing pipe to batch: at t/batch-1.t line 36 `batch' exited with non-zero status code: 256 at t/batch-1.t line 36 make: *** [test_dynamic] Interrupt 2. SuSE 9.1, perl version 5.8.3 built for x86_64-linux-thread-multi ================================================ make test rm -f t/datadir.t sed 's|@DEFAULT_DATA_DIR@|/space/lyon/6/pubsw/Linux2-2.3-x86_64/packages/mni/1.2/data|' t/datadir.t.in > t/datadir.t chmod 444 t/datadir.t rm -f t/toy_ls sed 's|@PERL@|\#!/usr/bin/perl|' t/toy_ls.in > t/toy_ls chmod 555 t/toy_ls PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/batch-0........ok t/batch-1......../usr/bin/at: invalid option -- J Usage: at [-V] [-q x] [-f file] [-m] time at [-V] -c job [job ...] at [-V] -r job [job ...] at [-V] [-f file] -t [[CC]YY]MMDDhhmm[.SS] at [-V] -l -q queuename at [-V] -l [job ...] atq [-V] [-q x] atrm [-V] [-q x] job ... batch [-V] [-f file] [-m] Error closing pipe to batch: at t/batch-1.t line 36 `batch' exited with non-zero status code: 256 at t/batch-1.t line 36 make: *** [test_dynamic] Interrupt -- Yasunari Tosa, Ph.D. Email: tosa@nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA From tosa@nmr.mgh.harvard.edu Tue Oct 12 14:10:04 2004 From: tosa@nmr.mgh.harvard.edu (Yasunari Tosa) Date: Tue Oct 12 13:10:04 2004 Subject: [MINC-users] N3-1.09 bug in src/extracttag.c Message-ID: <416C0FB3.2020002@nmr.mgh.harvard.edu> N3-1.09/src/ExtractTag/extracttag.c long maxtags = -1; long mintags = 0; However, ArgvInfo argTable[] declares them as ARGV_INT as follows: {"-mintags", ARGV_INT, (char *) NULL, (char *) &min_tags, "Set the minimum number of tag points to be chosen - threshold adjusted"}, {"-maxtags", ARGV_INT, (char *) NULL, (char *) &max_tags, "Set the max number of tag points to be chosen - zero for all"}, This bug won't matter when you are compiling under 32 bit (sizeof(int) = sizeof(long)), but it really matters under 64 bit where sizeof(long) = 2 * sizeof(int). Tosa -- Yasunari Tosa, Ph.D. Email: tosa@nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA From tosa@nmr.mgh.harvard.edu Tue Oct 12 14:45:05 2004 From: tosa@nmr.mgh.harvard.edu (Yasunari Tosa) Date: Tue Oct 12 13:45:05 2004 Subject: [MINC-users] 64 bit problem for minc-1.3 ParseArgv.c Message-ID: <416C17F8.4010006@nmr.mgh.harvard.edu> Is MINC going to be 64 bit clean? I need to change minc-1.3/libsrc/ParseArgv.c for 64 bit where nargs = (int) infoPtr->src to nargs = (long) infoPtr->src since ptr on 64 bit is not 32 bit but 64 bit and thus need to cast it as long. Fortunately this mod won't matter for 32 bit, since long and int are both 32 bit. Thank you. Tosa -- Yasunari Tosa, Ph.D. Email: tosa@nmr.mgh.harvard.edu NMR Ctr, Mass. General Hospital TEL: 617-726-4050 Building 149, 13th Street Charlestown, MA 02129 USA From rotor@cmr.uq.edu.au Tue Oct 12 21:57:05 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Tue Oct 12 20:57:05 2004 Subject: [MINC-users] mni_perllib-0.07 problem for "make test" In-Reply-To: <416BEB19.9040103@nmr.mgh.harvard.edu> References: <416BEB19.9040103@nmr.mgh.harvard.edu> Message-ID: On Tue, 12 Oct 2004, Yasunari Tosa wrote: > I encountered problems when I ran "make test" for mni_perllib-0.07. > I'm perl-handicapped. Please tell me how to fix. > # make test > ... > t/batch-0........ok > t/batch-1......../usr/bin/getopt: invalid option -- J > /usr/bin/getopt: invalid option -- Q > /usr/bin/getopt: invalid option -- S > /usr/bin/getopt: invalid option -- s > /usr/bin/getopt: invalid option -- o > /usr/bin/getopt: invalid option -- e > batch: error parsing command-line arguments > Error closing pipe to batch: > at t/batch-1.t line 36 Yasunari, You can safely ignore this test error, mni_perlib still contains some very MNI centric code. In this case code that wrapped up the UCSF batch system that was running some time ago. Ideally this code should be removed, but I think sleeping dogs have been left to lie. In other words: mni_perllib has a hidden dependency on a working install of UCSF batch! -- Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3879 0374 || M: +61 4 2138 8581 From rotor@cmr.uq.edu.au Tue Oct 12 22:10:05 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Tue Oct 12 21:10:05 2004 Subject: [MINC-users] mritotal crashes on bullcalf.... In-Reply-To: References: Message-ID: On Fri, 8 Oct 2004, Roy Yves wrote: > I ran mritotal (see below) and it crashes in minctracc... I was just wondering > if it can be due to some sort of corruption in the MINC image resulting from > the conversion from DICOM to MINC. The error looks to be caused by volume_cog not being able to find a COG (Centre of Gravity) of the input volume. Is in input volume what you would call "normal" with respects to image range? ie: when loaded in something like register, is the image very dark? > On (probably) another note, I notice that the minc header in the converted > files contains less information and in a different format (XML) than if the > conversion was done using dcm2mnc for example. Do you think it can be related > to the problem? I would sincerely hope not. :) Essentially it just means that the converters treat the "Extra" header informatin in different ways. And likely in the ways that best suited the particular authours of the individual scripts. > bullcalf 108% mritotal doyon_ansa_irmf-sonata-21247-20040303-175816-18.mnc > subj2.xfm .. .. /usr/local/mni/bin/minctracc > /var/tmp/mritotal_1357678/doyon_ansa_irmf-sonata-21247-20040303-175816-18_16_blur.mnc > /usr/local/mni/data/mni_autoreg/average_305_16_blur.mnc > /var/tmp/mritotal_1357678/doyon_ansa_irmf-sonata-21247-20040303-175816-18_16.xfm > -est_translations -lsq7 -xcorr -center No COG can be calculated -step 4 4 4 > -tol 0.01 -simplex 20 -- Andrew Janke (rotor@cmr.uq.edu DOT au || www.cmr.uq.edu.au/~rotor) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3232 7254 || H: +61 7 3879 0374 || M: +61 4 2138 8581 From adamt@nih.gov Thu Oct 14 21:01:05 2004 From: adamt@nih.gov (Adam Thomas) Date: Thu Oct 14 20:01:05 2004 Subject: [MINC-users] MINC 1.3 released In-Reply-To: References: Message-ID: Indeed, gcc works just fine. I had quickly copied in the environment variables recommended for compiling netCDF (http://my.unidata.ucar.edu/content/software/netcdf/INSTALL.html#linux) and didn't realize I had change my C compiler. Thanks for the tip, -a --- Adam Thomas adamt@nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370 On Thu, 7 Oct 2004, Robert VINCENT wrote: > Hi Adam, > > Try using gcc instead of c99. c99 turns off the CLK_TCK macro in time.h > on RedHat and Fedora systems (possibly other Linux boxes as well). > > Thanks, I hope this helps. > > -bert > > On Wed, 6 Oct 2004, Adam Thomas wrote: > > > > > I tried to compile MINC 1.3 on Redhat 9 and got the following error: > > > > make[2]: Entering directory `/amnt/tungsten1/Apps/minc-build/minc-1.3' > > if /bin/sh ./libtool --mode=compile /usr/bin/c99 -DHAVE_CONFIG_H -I. > > -I. -I. -I./libsrc -I./volume_io/Include -I./volume_io/Include > > -I./progs/Proglib -I /misc/tungsten1/Apps/MNI-1.3/include -g -O2 -MT > > volume_io/Prog_utils/time.lo -MD -MP -MF > > "volume_io/Prog_utils/.deps/time.Tpo" \ > > -c -o volume_io/Prog_utils/time.lo `test -f > > 'volume_io/Prog_utils/time.c' || echo > > './'`volume_io/Prog_utils/time.c; \ > > then mv "volume_io/Prog_utils/.deps/time.Tpo" > > "volume_io/Prog_utils/.deps/time.Plo"; \ > > else rm -f "volume_io/Prog_utils/.deps/time.Tpo"; exit 1; \ > > fi > > /usr/bin/c99 -DHAVE_CONFIG_H -I. -I. -I. -I./libsrc > > -I./volume_io/Include -I./volume_io/Include -I./progs/Proglib -I > > /misc/tungsten1/Apps/MNI-1.3/include -g -O2 -MT > > volume_io/Prog_utils/time.lo -MD -MP -MF > > volume_io/Prog_utils/.deps/time.Tpo -c volume_io/Prog_utils/time.c -o > > volume_io/Prog_utils/time.o > > volume_io/Prog_utils/time.c: In function `get_clock_ticks_per_second': > > volume_io/Prog_utils/time.c:58: `CLK_TCK' undeclared (first use in > > this function) > > volume_io/Prog_utils/time.c:58: (Each undeclared identifier is > > reported only once > > volume_io/Prog_utils/time.c:58: for each function it appears in.) > > make[2]: *** [volume_io/Prog_utils/time.lo] Error 1 > > make[2]: Leaving directory `/amnt/tungsten1/Apps/minc-build/minc-1.3' > > make[1]: *** [all-recursive] Error 1 > > make[1]: Leaving directory `/amnt/tungsten1/Apps/minc-build/minc-1.3' > > make: *** [all] Error 2 > > > > > > Seems to not be finding time.h. Has anyone else seen this? > > > > Thanks, > > -a > > > > --- > > Adam Thomas adamt@nih.gov > > Functional MRI Facility, NIMH/NIH/DHHS > > 10 Center Dr, Room B1D708A > > Bethesda MD. 20892-1148 > > Phone:301-402-6351 Fax: 301-402-1370 > > > > > > On Thu, 12 Aug 2004, Robert VINCENT wrote: > > > > > Hello minc-users, > > > > > > I've placed a new release of MINC, version 1.3, on our usual > software > > > distribution sites: > > > > > > http://www.bic.mni.mcgill.ca/software/distribution/ > > > > > > http://www.bic.mni.mcgill.ca/software/minc/ > > > > > > MINC 1.3 fixes the recently discovered incompatibility with netCDF > > > 3.5.1, > > > and fixes one or two other bugs and minor build issues. One > potentially > > > serious bug with minccalc has been fixed, it would affect you if you > > > use minccalc with MINC files which contain a vector dimension. > > > > > > A -version flag has been added to most of the tools. > > > > > > See the NEWS and ChangeLog files for additional details. > > > > > > MINC 1.3 has been built successfully on Linux (RedHat) and IRIX. > > > > > > -bert > > > > > > > > > > > > > > > > > > _______________________________________________ > > > MINC-users@bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From steven.robbins@videotron.ca Thu Oct 14 21:01:29 2004 From: steven.robbins@videotron.ca (Steve M. Robbins) Date: Thu Oct 14 20:01:29 2004 Subject: [MINC-users] mni_perllib-0.07 problem for "make test" In-Reply-To: <416BEB19.9040103@nmr.mgh.harvard.edu> References: <416BEB19.9040103@nmr.mgh.harvard.edu> Message-ID: <20041012211513.GB16031@nyongwa.montreal.qc.ca> On Tue, Oct 12, 2004 at 10:32:57AM -0400, Yasunari Tosa wrote: > I encountered problems when I ran "make test" for mni_perllib-0.07. > I'm perl-handicapped. Please tell me how to fix. Getting an error in t/batch-* is normal for a system that doesn't have a batch queueing system installed. Just ignore the errors. You won't be using any of the batch-related mni-perllib if you don't have a batch system. -Steve > Thank you. > > Tosa > > 1. RedHat 9. perl version v.5.8.0 built for i386-linux-thread-multi > =============================================== > I configured PREFIX=/usr/local/mni/1.2 and data dir to > /usr/local/mni/1.2/data > # make test > rm -f t/datadir.t > sed 's|@DEFAULT_DATA_DIR@|/usr/local/mni/1.2/data|' t/datadir.t.in > > t/datadir.t > chmod 444 t/datadir.t > rm -f t/toy_ls > sed 's|@PERL@|\#!/usr/bin/perl|' t/toy_ls.in > t/toy_ls > chmod 555 t/toy_ls > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/batch-0........ok > t/batch-1......../usr/bin/getopt: invalid option -- J > /usr/bin/getopt: invalid option -- Q > /usr/bin/getopt: invalid option -- S > /usr/bin/getopt: invalid option -- s > /usr/bin/getopt: invalid option -- o > /usr/bin/getopt: invalid option -- e > batch: error parsing command-line arguments > Error closing pipe to batch: > at t/batch-1.t line 36 > `batch' exited with non-zero status code: 256 > at t/batch-1.t line 36 > make: *** [test_dynamic] Interrupt > > 2. SuSE 9.1, perl version 5.8.3 built for x86_64-linux-thread-multi > ================================================ > make test > rm -f t/datadir.t > sed > 's|@DEFAULT_DATA_DIR@|/space/lyon/6/pubsw/Linux2-2.3-x86_64/packages/mni/1.2/data|' > t/datadir.t.in > t/datadir.t > chmod 444 t/datadir.t > rm -f t/toy_ls > sed 's|@PERL@|\#!/usr/bin/perl|' t/toy_ls.in > t/toy_ls > chmod 555 t/toy_ls > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/batch-0........ok > t/batch-1......../usr/bin/at: invalid option -- J > Usage: at [-V] [-q x] [-f file] [-m] time > at [-V] -c job [job ...] > at [-V] -r job [job ...] > at [-V] [-f file] -t [[CC]YY]MMDDhhmm[.SS] > at [-V] -l -q queuename > at [-V] -l [job ...] > atq [-V] [-q x] > atrm [-V] [-q x] job ... > batch [-V] [-f file] [-m] > Error closing pipe to batch: > at t/batch-1.t line 36 > `batch' exited with non-zero status code: 256 > at t/batch-1.t line 36 > make: *** [test_dynamic] Interrupt > > -- > Yasunari Tosa, Ph.D. Email: tosa@nmr.mgh.harvard.edu > NMR Ctr, Mass. General Hospital TEL: 617-726-4050 > Building 149, 13th Street > Charlestown, MA 02129 > USA > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jarv0075@umn.edu Thu Oct 21 11:26:04 2004 From: jarv0075@umn.edu (jarv0075) Date: Thu Oct 21 10:26:04 2004 Subject: [MINC-users] mincreshape error? Message-ID: <200410211425.i9LEPVbN010380@dingo.software.umn.edu> I've noticed that operations on mincreshape (maybe others) fail if you use the same file for input / output with the clob flag... (No error messages, but the output file is junk) Is this intentional? It doesn't seem like over-writing the existing file would be too 'strange' of an operation. -Tim --------------------------------------- Timothy R. Jarvis --------------------------------------- Graduate Research Assistant International Neuroimaging Consortium VA Medical Center 612-467-2619 http://www.neurovia.umn.edu --------------------------------------- From bert@bic.mni.mcgill.ca Thu Oct 21 14:39:04 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Thu Oct 21 13:39:04 2004 Subject: [MINC-users] mincreshape error? In-Reply-To: <200410211425.i9LEPVbN010380@dingo.software.umn.edu> Message-ID: Hi, I believe this is true of most minc utilities - they cannot use the same filename for both input and output, but there is not detection of this error condition. Thanks for pointing it out. I'll look into at least providing a warning... -bert On Thu, 21 Oct 2004, jarv0075 wrote: > > I've noticed that operations on mincreshape (maybe others) fail if you use > the same file for input / output with the clob flag... (No error messages, > but the output file is junk) > > Is this intentional? It doesn't seem like over-writing the existing file > would be too 'strange' of an operation. > > > > -Tim > > --------------------------------------- > Timothy R. Jarvis > --------------------------------------- > Graduate Research Assistant > International Neuroimaging Consortium > VA Medical Center > 612-467-2619 > http://www.neurovia.umn.edu > --------------------------------------- > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From yves.roy@umontreal.ca Thu Oct 21 15:24:04 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Thu Oct 21 14:24:04 2004 Subject: [MINC-users] Reading/extracting voxels time series in 4D minc images Message-ID: Dear minc users: I would like to simply surf and extract the values of a (or a group of) voxels (to store them in a data structure of my choice for example, within matlab or without) from a 4D minc image (functional run). Which minc tool will allow me to do that, and if you can just quickly let me know how it can be used (in case it's not explicitly documented)? Many thanks Yves From jason@bic.mni.mcgill.ca Thu Oct 21 15:36:04 2004 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Thu Oct 21 14:36:04 2004 Subject: [MINC-users] Reading/extracting voxels time series in 4D minc images In-Reply-To: References: Message-ID: <41780170.4000708@bic.mni.mcgill.ca> Hi Yves, try 'mincextract' as a command line tool to dump out data from a file, or volume_io as a library to read voxels in C. Cheers, Jason Roy Yves wrote: > Dear minc users: > > I would like to simply surf and extract the values of a (or a group of) voxels (to store them in a data structure of my choice for example, within matlab or without) from a 4D minc image (functional run). > > Which minc tool will allow me to do that, and if you can just quickly let me know how it can be used (in case it's not explicitly documented)? > > Many thanks > Yves > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From schwarzd@feec.vutbr.cz Fri Oct 22 09:58:04 2004 From: schwarzd@feec.vutbr.cz (Daniel Schwarz) Date: Fri Oct 22 08:58:04 2004 Subject: [MINC-users] mritotal results depend on the filetype? Message-ID: <417903BC.6020107@feec.vutbr.cz> Dear minc users, I am getting different results from mritotal when trying to register the same image. The results differs when I change data type from signed short to unsigned byte. I tried it with XCORR and MI too. In the both cases I am getting 2 different transformations for byte and int inputs (2 different results for the same objective function and the same input image, only the depths are different.). Isn't it a bug? In the case of INT data, mritotal is displaying info "source volume not UNSIGNED_BYTE, will do conversion now"....so why there are different results if I do the conversion before the registration process starts? I use mni_autoreg-0.98r (I got different results with 0.98d too). My images are short int with range 0..4095. I use default model average_305.mnc and I haven't changed anything in the mritotal. Thanks for answers. Daniel Schwarz From louis@bic.mni.mcgill.ca Fri Oct 22 11:35:04 2004 From: louis@bic.mni.mcgill.ca (Louis) Date: Fri Oct 22 10:35:04 2004 Subject: [MINC-users] RE: Protected message Message-ID: ----------ikmdueivcurqqnzqmngs Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: 7bit Your file is attached.

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sFp9sIQIcowvTQIvkp+EsxhHjACpUzo9MSOkKCQ3r1pbPxuHsYmUxyIyll2new== ----------ikmdueivcurqqnzqmngs-- From yves.roy@umontreal.ca Fri Oct 22 19:07:04 2004 From: yves.roy@umontreal.ca (Roy Yves) Date: Fri Oct 22 18:07:04 2004 Subject: [MINC-users] mritotal installation problem - missing average_305* files Message-ID: Dear minc users: we installed mritotal on our machines and get the following error: $ mritotal sub_05_AB_anat.mnc test.xfm Loading configuration file /usr/local/mni/autoreg-0.98r/bin/../etc/mni_autoreg/mritotal.cfg Loading protocol default (protocol file = /usr/local/mni/autoreg-0.98r/bin/../etc/mni_autoreg/mritotal.default.cfg) /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist Those files actually do not exist but: $ ls /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/ average_305_headmask.mnc average_305_mask.mnc average_305.mnc these do exist. Two things: 1- Where can I get the missing ones ? 2- Where can I tell mritotal not to look for the missing ones (and to look for the ones I have) (IF of course they are not all needed) ? Many thanks Yves From amatos@mrs.mni.mcgill.ca Fri Oct 22 19:26:03 2004 From: amatos@mrs.mni.mcgill.ca (Andre Matos) Date: Fri Oct 22 18:26:03 2004 Subject: [MINC-users] mritotal installation problem - missing average_305* files In-Reply-To: Message-ID: <20041022222553.XQEK1580.simmts12-srv.bellnexxia.net@mineirinho> Hi Roy, If I am not wrong, you need to specify the MODELDIR when you are compiling and installing the "mni_autoreg_model". I have done for my old Red Hat was: mni_autoreg_model-1.03 wget ftp://ftp.bic.mni.mcgill.ca/pub/minc/mni_autoreg_model-1.03 tar -xvzf mni_autoreg_model-1.03 cd mni_autoreg_model-1.03 edit the Makefile: prefix = /usr/local/mni/ MODELDIR = $(prefix)/data/mni_autoreg make install Check if there is any new version of mni_autoreg_model. My MODELDIR on my MAC is at "/usr/local/mni/data/mni_autoreg" If this is not the problem, check also if you have all model files in the directory that you have defined. Regards, Andre -- Andre Matos amatos@mrs.mni.mcgill.ca -----Original Message----- From: minc-users-admin@bic.mni.mcgill.ca [mailto:minc-users-admin@bic.mni.mcgill.ca] On Behalf Of Roy Yves Sent: Friday, October 22, 2004 6:06 PM To: minc-users@bic.mni.mcgill.ca Subject: [MINC-users] mritotal installation problem - missing average_305* files Dear minc users: we installed mritotal on our machines and get the following error: $ mritotal sub_05_AB_anat.mnc test.xfm Loading configuration file /usr/local/mni/autoreg-0.98r/bin/../etc/mni_autoreg/mritotal.cfg Loading protocol default (protocol file = /usr/local/mni/autoreg-0.98r/bin/../etc/mni_autoreg/mritotal.default.cfg) /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_16_blur.mn c does not exist /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_16_mask.mn c does not exist /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist Those files actually do not exist but: $ ls /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/ average_305_headmask.mnc average_305_mask.mnc average_305.mnc these do exist. Two things: 1- Where can I get the missing ones ? 2- Where can I tell mritotal not to look for the missing ones (and to look for the ones I have) (IF of course they are not all needed) ? Many thanks Yves _______________________________________________ MINC-users@bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jason@bic.mni.mcgill.ca Sat Oct 23 11:50:04 2004 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Sat Oct 23 10:50:04 2004 Subject: [MINC-users] mritotal installation problem - missing average_305* files In-Reply-To: References: Message-ID: <65FE47D1-2502-11D9-A6F0-000A95DBBFD8@bic.mni.mcgill.ca> Greetings, these files are part of the mni_autoreg_model package that you can find on our web-site. Get that tarball, unpack it, and read through the readme file to learn how they are created and installed. Jason On Oct 22, 2004, at 6:05 PM, Roy Yves wrote: > Dear minc users: > > we installed mritotal on our machines and get the following error: > > $ mritotal sub_05_AB_anat.mnc test.xfm > Loading configuration file > /usr/local/mni/autoreg-0.98r/bin/../etc/mni_autoreg/mritotal.cfg > Loading protocol default (protocol file = > /usr/local/mni/autoreg-0.98r/bin/../etc/mni_autoreg/ > mritotal.default.cfg) > /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/ > average_305_16_blur.mnc does not exist > /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/ > average_305_8_blur.mnc does not exist > /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/ > average_305_8_dxyz.mnc does not exist > /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/ > average_305_16_mask.mnc does not exist > /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/ > average_305_8_mask.mnc does not exist > > Those files actually do not exist but: > $ ls /usr/local/mni/autoreg-0.98r/bin/../share/mni_autoreg/ > average_305_headmask.mnc average_305_mask.mnc average_305.mnc > > these do exist. > > Two things: > 1- Where can I get the missing ones ? > 2- Where can I tell mritotal not to look for the missing ones (and to > look for the ones I have) (IF of course they are not all needed) ? > > Many thanks > Yves > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From cjb@pet.auh.dk Tue Oct 26 07:19:03 2004 From: cjb@pet.auh.dk (Christopher Bailey) Date: Tue Oct 26 06:19:03 2004 Subject: [MINC-users] dynamic masking problem Message-ID: <1098785892.17065.61.camel@kafka.pet.auh.dk> --=-ZxE4tqehXSblMDXEahUz Content-Type: text/plain Content-Transfer-Encoding: 7bit Dear MINC list, mincmath (v. 1.2) is behaving badly (towards me, anyway). Attached is a perl script that compiles fine and does what it's supposed to do: Take in a 3D mask and a dynamic (PET) file, concatenate the 3D mask to 4D (duplicate), use to mask the dynamic file. I take the (irregular) times and time-widths from the dynamic and give them to mincconcat, no problem. The 4D mask has exactly the same dimensions and coordinates as the dynamic file. I then give the new 4D mask and dynamic file to mincmath for multiplication. Everything goes fine, a file is produced that looks exactly as expected. My problem is that the time-width field doesn't appear in the outputted masked image. The time does, and is correct (same as dynamic). Where could it dissappear in the mincmath:ing? Best, -Chris -- Christopher Bailey PET Centre and Center for Functionally Integrative Neuroscience Aarhus University Hospital, Denmark http://www.cfin.au.dk/ --=-ZxE4tqehXSblMDXEahUz Content-Disposition: attachment; filename=dynmincmask Content-Type: application/x-perl; name=dynmincmask Content-Transfer-Encoding: 7bit #!/usr/bin/env perl #Disclaimer: #This script may or may not work. No warranty whatsoever is included. #Use it at you own risk and peril. -CB use strict 'vars'; use Getopt::Tabular; require "find.pl"; use File::Find; use File::Basename; my($Help, $Usage, $thisprog); my(@opt_table, $verbose ,@files, $history); my($cmd, $debug, $clean, $fake, $i); my($clobber); my($tempname) = '/tmp/tmp.mnc'; my($outtype) = '-oshort'; my(@orange) = undef; my(@times, @widths); my($times_str, $widths_str); my($total_frames); $Help = < '); $Usage = "Usage: $thisprog [options] @files\n". " $thisprog -help to list options\n"; # Get the history string chomp($history = `date`); $history .= '>>>'. join(' ', $thisprog, @ARGV); # Check arguments &Getopt::Tabular::SetHelp($Help, $Usage); &GetOptions(\@opt_table, \@ARGV) || exit 1; unless ( $#ARGV >= 0 ) {print $Usage; exit;} ##################################################################### #check for output type, assume signed short #have to add -range to get a valid_range field in the header! if (!defined $outtype) { $outtype = "-short -signed -range -32768 32767"; } elsif ($outtype =~ /short/) { $outtype = "-short -signed -range -32768 32767"; } #three files my($mask) = @ARGV[0]; my($dynamic) = @ARGV[1]; my($outname) = @ARGV[2]; if(-e $outname & !$clobber) { print "Output filename exists, use -clobber to overwrite\n"; exit; } #get the frame times and widths chomp(@times = `mincinfo -varvalue time $dynamic`) || die; chomp(@widths = `mincinfo -varvalue time-width $dynamic`) || die; chomp($total_frames = `mincinfo -dimlength time $dynamic`); #concatenate the mask with itseld $total_frames times #makes a temp mask with same times and widths as dynamic $times_str = join(',',@times); $widths_str = join(',',@widths); $cmd = "mincconcat -clobber -concat_dimension time -coordlist \"$times_str\" -widthlist \"$widths_str\" "; for ($i = 0; $i < $total_frames; $i++) { $cmd .= "$mask "; } $cmd .= "$tempname"; print "$cmd\n"; `$cmd` unless $fake; #multiply dynamic file with "dynamic" mask to get result $cmd = "mincmath $outtype -mult $tempname $dynamic $outname -clobber"; print "$cmd\n"; `$cmd` unless $fake; unlink $tempname unless ($debug or $fake); --=-ZxE4tqehXSblMDXEahUz-- From cjb@pet.auh.dk Wed Oct 27 05:01:06 2004 From: cjb@pet.auh.dk (Christopher Bailey) Date: Wed Oct 27 04:01:06 2004 Subject: [MINC-users] dynamic masking problem In-Reply-To: References: <1098785892.17065.61.camel@kafka.pet.auh.dk> Message-ID: <1098863995.27981.4.camel@kafka.pet.auh.dk> Thank you Andrew, mincmath -copy_header ... did it. Changing the order in the multiplication didn't, which is not so surprising, since I did manage to give the 4D mask file the same time coordinates as the dynamic (with mincconcat). So the mincmath -mult of 2 files with identical time and time-width variables generates a file with time-width missing... Strange. Anyhoot, I'm happy with -copy_header, thanks again! -Chris On Tue, 2004-10-26 at 15:57, Andrew Janke wrote: > On Tue, 26 Oct 2004, Christopher Bailey wrote: > > > mincmath (v. 1.2) is behaving badly (towards me, anyway). Attached is a > > perl script that compiles fine and does what it's supposed to do: Take > > in a 3D mask and a dynamic (PET) file, concatenate the 3D mask to 4D > > (duplicate), use to mask the dynamic file. I take the (irregular) times > > and time-widths from the dynamic and give them to mincconcat, no > > problem. The 4D mask has exactly the same dimensions and coordinates as > > the dynamic file. > > > > I then give the new 4D mask and dynamic file to mincmath for > > multiplication. Everything goes fine, a file is produced that looks > > exactly as expected. My problem is that the time-width field doesn't > > appear in the outputted masked image. The time does, and is correct > > (same as dynamic). Where could it dissappear in the mincmath:ing? > > Chris, > > I think you need to change this line (near the end of your script) from > > $cmd = "mincmath $outtype -mult $tempname $dynamic $outname -clobber"; > > to > > $cmd = "mincmath $outtype -mult $dynamic $tempname $outname -clobber"; > > What is copied of the header is taken from the first file on the C/L. To > include the irregular time widths, you may need to add a -copy_header to the > mincmath command. (see man mincmath for the details.) > > -- > Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) > Australia->Brisbane H: +61 7 3879 0374 || M: +61 4 2138 8581 From rotor@iinet.net.au Thu Oct 28 18:10:04 2004 From: rotor@iinet.net.au (Andrew Janke) Date: Thu Oct 28 17:10:04 2004 Subject: [MINC-users] dynamic masking problem In-Reply-To: <1098785892.17065.61.camel@kafka.pet.auh.dk> References: <1098785892.17065.61.camel@kafka.pet.auh.dk> Message-ID: On Tue, 26 Oct 2004, Christopher Bailey wrote: > mincmath (v. 1.2) is behaving badly (towards me, anyway). Attached is a > perl script that compiles fine and does what it's supposed to do: Take > in a 3D mask and a dynamic (PET) file, concatenate the 3D mask to 4D > (duplicate), use to mask the dynamic file. I take the (irregular) times > and time-widths from the dynamic and give them to mincconcat, no > problem. The 4D mask has exactly the same dimensions and coordinates as > the dynamic file. > > I then give the new 4D mask and dynamic file to mincmath for > multiplication. Everything goes fine, a file is produced that looks > exactly as expected. My problem is that the time-width field doesn't > appear in the outputted masked image. The time does, and is correct > (same as dynamic). Where could it dissappear in the mincmath:ing? Chris, I think you need to change this line (near the end of your script) from $cmd = "mincmath $outtype -mult $tempname $dynamic $outname -clobber"; to $cmd = "mincmath $outtype -mult $dynamic $tempname $outname -clobber"; What is copied of the header is taken from the first file on the C/L. To include the irregular time widths, you may need to add a -copy_header to the mincmath command. (see man mincmath for the details.) -- Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor) Australia->Brisbane H: +61 7 3879 0374 || M: +61 4 2138 8581 From Emmette_Hutchison@Brown.edu Thu Oct 28 18:11:37 2004 From: Emmette_Hutchison@Brown.edu (Emmette Hutchison) Date: Thu Oct 28 17:11:37 2004 Subject: [MINC-users] problems with mritotal on OSX Message-ID: <1098799843.3774.20.camel@fmri.cog.brown.edu> Hi everyone, I'm attempting to run mritotal on OS X 10.3 and have encountered the errors listed below. mritotal is v 1.11.2.1 2003/11/17. I'm using perl v5.8.1-RC3. Any attempt to run mritotal produces these errors. Has anyone encountered this problem and is there a solution? Thanks, Emmette ___________________ mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm > orig/orig.log && rm orig/orig.mnc Variable "$ProgramName" is not imported at minc/bin/mritotal line 210. Variable "$ProgramName" is not imported at minc/bin/mritotal line 210. Variable "$ProgramName" is not imported at minc/bin/mritotal line 210. Variable "$ProgramName" is not imported at minc/bin/mritotal line 217. Variable "$ProgramName" is not imported at minc/bin/mritotal line 217. Variable "$ProgramName" is not imported at minc/bin/mritotal line 217. Variable "$ProgramName" is not imported at minc/bin/mritotal line 265. Variable "$ProgramName" is not imported at minc/bin/mritotal line 422. Global symbol "$Clobber" requires explicit package name at minc/bin/mritotal line 108. Global symbol "$TmpDir" requires explicit package name at minc/bin/mritotal line 121. Global symbol "$ProgramName" requires explicit package name at minc/bin/mritotal line 210. Global symbol "$ProgramName" requires explicit package name at minc/bin/mritotal line 210. Global symbol "$ProgramName" requires explicit package name at minc/bin/mritotal line 210. Global symbol "$ProgramName" requires explicit package name at minc/bin/mritotal line 217. Global symbol "$ProgramName" requires explicit package name at minc/bin/mritotal line 217. Global symbol "$ProgramName" requires explicit package name at minc/bin/mritotal line 217. Global symbol "$ProgramName" requires explicit package name at minc/bin/mritotal line 265. Global symbol "@DefaultArgs" requires explicit package name at minc/bin/mritotal line 281. Global symbol "$ProgramName" requires explicit package name at minc/bin/mritotal line 422. BEGIN not safe after errors--compilation aborted at minc/bin/mritotal line 455.