From tosa@nmr.mgh.harvard.edu Wed Apr 7 17:25:03 2004 From: tosa@nmr.mgh.harvard.edu (Yasunari Tosa) Date: Wed Apr 7 16:25:03 2004 Subject: [MINC-users] Perl lib path patch to N3-1.07 Message-ID: <40746396.7060300@nmr.mgh.harvard.edu> This is a multi-part message in MIME format. --------------090301010308040004070207 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, MINC people: I finally made the patch file for perl lib path for N3-1.07. After untarring N3-1.07, put the patch file into N3-1.07 directory. When you do cd N3-1.07 patch -p1 < patch-N3-1.07.txt You get > patching file configure > patching file Makefile.in > patching file src/NUcorrect/field2imp.in > patching file src/NUcorrect/imp2field.in > patching file src/NUcorrect/make_template.in > patching file src/NUcorrect/nu_estimate.in > patching file src/NUcorrect/nu_estimate_np_and_em.in > patching file src/NUcorrect/nu_evaluate.in > patching file src/NUcorrect/resample_labels.in > patching file src/NUcorrect/sharpen_volume.in Now configure has an option of perllibdir, i.e. configure --perllibdir=myspecialdir (other options) The perl script made from the patched files will have use lib "myspecialdir"; Tosa -- Yasunari Tosa, Ph.D. R&D Engineer email: tosa@nmr.mgh.harvard.edu Mass. General Hospital NMR Center phone: Building 149 13th Street fax : Charlestown, MA 02129 --------------090301010308040004070207 Content-Type: text/plain; name="patch-N3-1.07.txt" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline; filename="patch-N3-1.07.txt" *** N3-1.07/configure 2003-11-25 18:22:17.000000000 -0500 --- N3-1.07-tosa/configure 2004-04-07 15:14:58.000000000 -0400 *************** *** 272,278 **** PACKAGE_STRING=3D PACKAGE_BUGREPORT=3D =20 ! ac_subst_vars=3D'SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACK= AGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_t= ransform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir= localstatedir libdir includedir oldincludedir infodir mandir build_alias= host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM I= NSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUT= OMAKE AUTOHEADER MAKEINFO AMTAR install_sh STRIP ac_ct_STRIP INSTALL_STRI= P_PROGRAM AWK SET_MAKE am__leading_dot LN_S CC CFLAGS LDFLAGS CPPFLAGS ac= _ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE = AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXX CXXFL= AGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE RANLIB = ac_ct_RANLIB build build_cpu build_vendor build_os host host_cpu host_ven= dor host_os version time date user machine long_version F77 FFLAGS ac_ct_= F77 FLIBS BLAS_LIBS LAPACK_LIBS PERL modeldir LIBOBJS LTLIBOBJS' ac_subst_files=3D'' =20 # Initialize some variables set by options. --- 272,278 ---- PACKAGE_STRING=3D PACKAGE_BUGREPORT=3D =20 ! ac_subst_vars=3D'SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACK= AGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_t= ransform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir= localstatedir libdir includedir oldincludedir infodir mandir build_alias= host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM I= NSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUT= OMAKE AUTOHEADER MAKEINFO AMTAR install_sh STRIP ac_ct_STRIP INSTALL_STRI= P_PROGRAM AWK SET_MAKE am__leading_dot LN_S CC CFLAGS LDFLAGS CPPFLAGS ac= _ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE = AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXX CXXFL= AGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE RANLIB = ac_ct_RANLIB build build_cpu build_vendor build_os host host_cpu host_ven= dor host_os version time date user machine long_version F77 FFLAGS ac_ct_= F77 FLIBS BLAS_LIBS LAPACK_LIBS PERL perllibdir modeldir LIBOBJS LTLIBOBJ= S' ac_subst_files=3D'' =20 # Initialize some variables set by options. *************** *** 461,466 **** --- 461,469 ---- | --oldin=3D* | --oldi=3D* | --old=3D* | --ol=3D* | --o=3D*) oldincludedir=3D$ac_optarg ;; =20 + --perllibdir=3D* ) + perllibdir=3D$ac_optarg;; +=20 -prefix | --prefix | --prefi | --pref | --pre | --pr | --p) ac_prev=3Dprefix ;; -prefix=3D* | --prefix=3D* | --prefi=3D* | --pref=3D* | --pre=3D* | -= -pr=3D* | --p=3D*) *************** *** 7810,7815 **** --- 7813,7819 ---- s,@modeldir@,$modeldir,;t t s,@LIBOBJS@,$LIBOBJS,;t t s,@LTLIBOBJS@,$LTLIBOBJS,;t t + s,@perllibdir@,$perllibdir,;t t CEOF =20 _ACEOF *** N3-1.07/Makefile.in 2003-11-25 18:22:16.000000000 -0500 --- N3-1.07-tosa/Makefile.in 2004-04-07 15:10:57.000000000 -0400 *************** *** 82,87 **** --- 82,88 ---- PACKAGE_VERSION =3D @PACKAGE_VERSION@ PATH_SEPARATOR =3D @PATH_SEPARATOR@ PERL =3D @PERL@ + perllibdir=3D @perllibdir@ RANLIB =3D @RANLIB@ SET_MAKE =3D @SET_MAKE@ SHELL =3D @SHELL@ *** N3-1.07/src/NUcorrect/field2imp.in 2003-04-16 10:29:34.000000000 -040= 0 --- N3-1.07-tosa/src/NUcorrect/field2imp.in 2004-04-07 14:51:44.000000000= -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 diff -r --context N3-1.07/src/NUcorrect/imp2field.in N3-1.07-tosa/src/NUc= orrect/imp2field.in *** N3-1.07/src/NUcorrect/imp2field.in 2003-04-16 10:29:34.000000000 -040= 0 --- N3-1.07-tosa/src/NUcorrect/imp2field.in 2004-04-07 14:52:13.000000000= -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 diff -r --context N3-1.07/src/NUcorrect/make_template.in N3-1.07-tosa/src= /NUcorrect/make_template.in *** N3-1.07/src/NUcorrect/make_template.in 2003-11-14 12:16:16.000000000 = -0500 --- N3-1.07-tosa/src/NUcorrect/make_template.in 2004-04-07 14:51:13.00000= 0000 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 diff -r --context N3-1.07/src/NUcorrect/nu_estimate.in N3-1.07-tosa/src/N= Ucorrect/nu_estimate.in *** N3-1.07/src/NUcorrect/nu_estimate.in 2003-04-16 10:29:34.000000000 -0= 400 --- N3-1.07-tosa/src/NUcorrect/nu_estimate.in 2004-04-07 14:52:35.0000000= 00 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 diff -r --context N3-1.07/src/NUcorrect/nu_estimate_np_and_em.in N3-1.07-= tosa/src/NUcorrect/nu_estimate_np_and_em.in *** N3-1.07/src/NUcorrect/nu_estimate_np_and_em.in 2003-04-16 10:29:34.00= 0000000 -0400 --- N3-1.07-tosa/src/NUcorrect/nu_estimate_np_and_em.in 2004-04-07 14:53:= 01.000000000 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 diff -r --context N3-1.07/src/NUcorrect/nu_evaluate.in N3-1.07-tosa/src/N= Ucorrect/nu_evaluate.in *** N3-1.07/src/NUcorrect/nu_evaluate.in 2003-05-29 13:14:24.000000000 -0= 400 --- N3-1.07-tosa/src/NUcorrect/nu_evaluate.in 2004-04-07 14:53:22.0000000= 00 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 diff -r --context N3-1.07/src/NUcorrect/resample_labels.in N3-1.07-tosa/s= rc/NUcorrect/resample_labels.in *** N3-1.07/src/NUcorrect/resample_labels.in 2003-04-16 10:29:34.00000000= 0 -0400 --- N3-1.07-tosa/src/NUcorrect/resample_labels.in 2004-04-07 14:53:40.000= 000000 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx + use lib "xINCDIRx"; =20 # ------------------------------ MNI Header ---------------------------= ------- #@NAME : resample_labels diff -r --context N3-1.07/src/NUcorrect/sharpen_volume.in N3-1.07-tosa/sr= c/NUcorrect/sharpen_volume.in *** N3-1.07/src/NUcorrect/sharpen_volume.in 2003-04-16 10:29:34.000000000= -0400 --- N3-1.07-tosa/src/NUcorrect/sharpen_volume.in 2004-04-07 14:53:58.0000= 00000 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 --------------090301010308040004070207-- From jonathan.taylor@stanford.edu Thu Apr 8 03:01:04 2004 From: jonathan.taylor@stanford.edu (Jonathan Taylor) Date: Thu Apr 8 02:01:04 2004 Subject: [MINC-users] cross compiling minc-1.2 libsrc Message-ID: <1081404043.4576.14.camel@jtaylor2.Stanford.EDU> Hi, I've been playing with minc in python, and have cross-compiled the minc-1.2 library on RedHat9 (not volume_io because it has too many POSIX like calls) to a usable DLL. I had to hack some include statements in netcdf_convenience.c. Specifically, I changed the lines: #ifdef unix #include #include /* For S_IREAD, S_IWRITE */ #include #endif TO #include /* For S_IREAD, S_IWRITE */ #include /* For O_CREAT, O_EXCL, O_RDWR */ #ifdef unix #include #include #endif I was just wondering if minc-developers were interested in the DLL, and if changing these lines will break anything later. I can't see how it would. Best, Jonathan -- Jonathan Taylor Tel: 650.723.9230 Dept. of Statistics Fax: 650.725.8977 Sequoia Hall, 137 www-stat.stanford.edu/~jtaylor 390 Serra Mall Stanford, CA 94305 From rotor@cmr.uq.edu.au Thu Apr 8 03:18:05 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Thu Apr 8 02:18:05 2004 Subject: [MINC-users] cross compiling minc-1.2 libsrc In-Reply-To: <1081404043.4576.14.camel@jtaylor2.Stanford.EDU> References: <1081404043.4576.14.camel@jtaylor2.Stanford.EDU> Message-ID: On Thu, 7 Apr 2004, Jonathan Taylor wrote: > I've been playing with minc in python, and have cross-compiled the > minc-1.2 library on RedHat9 (not volume_io because it has too many POSIX > like calls) to a usable DLL. I had to hack some include statements in > netcdf_convenience.c. As you mention DLL, I assume you mean cross-compiled to Winderz? > Specifically, I changed the lines: > > #ifdef unix > #include > #include /* For S_IREAD, S_IWRITE */ > #include > #endif > > TO > > #include /* For S_IREAD, S_IWRITE */ > #include /* For O_CREAT, O_EXCL, O_RDWR */ > #ifdef unix > #include > #include > #endif > > I was just wondering if minc-developers were interested in the DLL, and > if changing these lines will break anything later. You are not the only one, Gibby Koldenhof has also been working on windows binaries: http://sourceforge.net/projects/mni-minc-win32/ He also made a few changes along the lines of what you have. I have been working on cygwin binaries (dpkg'd). Bert Vincent (one of the primary authours of minc2.0 has also dabbled with windows builds of minc.) Suffice to say, YES there is interest! :) Last I knew Bert was working on including some of these type changes (to make windows builds easier) into the core minc CVS. At least for MINC 2.0, I am unsure about 1.2/x -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From G.Koldenhof@azu.nl Fri Apr 9 20:29:03 2004 From: G.Koldenhof@azu.nl (Gibby Koldenhof) Date: Fri Apr 9 19:29:03 2004 Subject: [MINC-users] converting one format to minc Message-ID: <02c801c41e89$b7398710$0affc30a@quark> Hi Guys, I'm writing up some code to convert a number of file formats to minc (I'm using minc 1.2). For some reason I get strange results. When trying to convert 16bit signed raw data I get strange results. I first convert the raw data using minctoraw: rawtominc -short -input raw.raw -scan_range -xstep 1.0 -ystep 1.0 -zstep 1.0 a.mnc 100 100 100 Which outputs "a.mnc" I then load up raw.raw from my raw load routine and save it to minc (b.mnc): (note that all parameters are correctly set, and this is just the important calls with everything else stripped away) /* ---------- write volume */ volume = create_volume(3, dimensions, type, signed_flag, volset_get_min(volset), volset_get_max(volset)); set_volume_sizes(volume, sizes); for(z = 0 ; z < volset_get_zsize(volset) ; z++) { for(y = 0 ; y < volset_get_ysize(volset) ; y++) { for(x = 0 ; x < volset_get_xsize(volset) ; x++) { double v = volset_get_voxel(volset, x, y, z); set_volume_voxel_value(volume, x, y, z, 0, 0, v); } } } output_volume((char *)filename, type, signed_flag, volset_get_min(volset), volset_get_max(volset), volume, history, NULL); /* end of write volume */ Then I load up a.mnc and b.mnc and do a compare. The loading is performed with: /* load volume */ input_volume(filename, 3, dimensions, NC_SHORT, TRUE, SHRT_MIN, SHRT_MAX, TRUE, &volume, NULL) short * voxels = ... ; ... etc for all voxels GET_VALUE_3D(value, volume, x, y, z); *voxels++ = value; /* end of load volume */ mincinfo says both the files are the same, yet mincdiff tells me that the data is different. And indeed when I internally compare all the voxels about 1/6th of the voxels have a difference of 1 (integer, e.g. a voxel from a.mnc is 203 and from b.mnc is 204 for example) - strangly enough when loading both files into register they look exactly the same (also selecting voxels at different locations and checking the value) ...? .... how ... why ... I can't understand what is going wrong. I do not do any floating point conversion anywhere (since it looks like a roundoff error) ... I tried pretty much everything (e.g. changing the parameters to each call) Anybody got a clue what's going wrong? Cheers, Gibby ---- dump from the output of my converter: converting 'gibby.vpx' to 'b.mnc' and comparing the output with existing file 'a.mnc' progress: prima (University Medical Center Utrecht (UMCU) vpx prima format) prima took h00:m00:s00 (0.22 seconds) swapping dataset 'gibby.vpx' on 'xz' axis progress: swap (swap dataset on xz axis) swap took h00:m00:s02 (2.57 seconds) mirroring dataset 'gibby.vpx' on 'z' axis progress: mirror (mirror dataset on z axis) mirror took h00:m00:s02 (2.70 seconds) saving dataset to 'b.mnc' dumping 'b.mnc' dump of outfile: xsize: 85 dump of outfile: ysize: 89 dump of outfile: zsize: 83 dump of outfile: min: 0 dump of outfile: max: 1212 dump of outfile: dtype: 3 dump of outfile: dsize: 2 dump of outfile: tsize: 627895 dump of outfile: sum: 162.870193 minc: file 'b.mnc' minc: sizes: 85x89x83 minc: nc type = NC_SHORT (signed) minc: dimensions 3 minc: dimension(0): yspace minc: dimension(1): zspace minc: dimension(2): xspace minc: voxel min: -32768.000000 minc: voxel max: 32767.000000 minc: real min: 0.000000 minc: real max: 1212.000000 minc: x_world: 1.000000 minc: y_world: 1.000000 minc: z_world: 1.000000 minc: file 'a.mnc' minc: sizes: 85x89x83 minc: nc type = NC_SHORT (signed) minc: dimensions 3 minc: dimension(0): yspace minc: dimension(1): zspace minc: dimension(2): xspace minc: voxel min: -32768.000000 minc: voxel max: 32767.000000 minc: real min: 0.000000 minc: real max: 1212.000000 minc: x_world: 1.000000 minc: y_world: 1.000000 minc: z_world: 1.000000 dumping 'b.mnc' dump of compare file 1 (b.mnc): xsize: 85 dump of compare file 1 (b.mnc): ysize: 89 dump of compare file 1 (b.mnc): zsize: 83 dump of compare file 1 (b.mnc): min: 0 dump of compare file 1 (b.mnc): max: 1212 dump of compare file 1 (b.mnc): dtype: 3 dump of compare file 1 (b.mnc): dsize: 2 dump of compare file 1 (b.mnc): tsize: 627895 dump of compare file 1 (b.mnc): sum: 162.367286 dumping 'a.mnc' dump of compare file 2 (a.mnc): xsize: 85 dump of compare file 2 (a.mnc): ysize: 89 dump of compare file 2 (a.mnc): zsize: 83 dump of compare file 2 (a.mnc): min: 0 dump of compare file 2 (a.mnc): max: 1212 dump of compare file 2 (a.mnc): dtype: 3 dump of compare file 2 (a.mnc): dsize: 2 dump of compare file 2 (a.mnc): tsize: 627895 dump of compare file 2 (a.mnc): sum: 162.369387 compare: field xsize of dataset 'b.mnc' (85) does compare to dataset 'a.mnc' (85) compare: field ysize of dataset 'b.mnc' (89) does compare to dataset 'a.mnc' (89) compare: field zsize of dataset 'b.mnc' (83) does compare to dataset 'a.mnc' (83) compare: field tsize of dataset 'b.mnc' (627895) does compare to dataset 'a.mnc' (627895) compare: field dsize of dataset 'b.mnc' (2) does compare to dataset 'a.mnc' (2) compare: field dtype of dataset 'b.mnc' (3) does compare to dataset 'a.mnc' (3) compare: field min of dataset 'b.mnc' (0) does compare to dataset 'a.mnc' (0) compare: field max of dataset 'b.mnc' (1212) does compare to dataset 'a.mnc' (1212) compare: number of voxels (resolution) of dataset 'b.mnc' (1255790) do compare to dataset 'a.mnc' (1255790) compare: 112807 of 627895 voxels DO NOT compare between dataset 'b.mnc' and dataset 'a.mnc', largest difference was 1 compare result: *WARNING*: output dataset DOES NOT compare to 'a.mnc' computed difference volume for 'a.mnc' and wrote file 'diff.hdr' dumping 'copy of b.mnc' difference file: xsize: 85 difference file: ysize: 89 difference file: zsize: 83 difference file: min: 0 difference file: max: 1 difference file: dtype: 3 difference file: dsize: 2 difference file: tsize: 627895 difference file: sum: 0.179659 --- dump of mincheader of a.mnc netcdf a { dimensions: yspace = 85 ; zspace = 89 ; xspace = 83 ; variables: int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "image\n", "study" ; int study ; study:parent = "rootvariable" ; study:varid = "MINC standard variable" ; study:vartype = "group________" ; study:version = "MINC Version 1.0" ; study:modality = "MRI__" ; double yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = 1. ; yspace:start = 0. ; double zspace ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = 1. ; zspace:start = 0. ; double xspace ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = 1. ; xspace:start = 0. ; short image(yspace, zspace, xspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:complete = "true_" ; image:signtype = "signed__" ; image:image-max = "--->image-max" ; image:image-min = "--->image-min" ; image:valid_range = -32768., 32767. ; double image-min(yspace) ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; double image-max(yspace) ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; // global attributes: :history = "Tue Apr 6 11:52:52 2004>>> rawtominc -short -coronal -clobber -input ./voor_gibby.raw -scan_range -mri ./voor_gibby.mnc.tmp 85 89 83\n", "Tue Apr 6 11:52:54 2004>>> mincreshape -clobber -coronal ./voor_gibby.mnc.tmp ./voor_gibby.mnc\n", "" ; data: rootvariable = _ ; study = _ ; yspace = 0 ; zspace = 0 ; xspace = 0 ; image-min = _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _ ; image-max = 24, 38, 66, 240, 467, 763, 909, 1075, 1145, 1139, 1212, 1172, 1127, 1136, 1145, 1159, 1117, 1089, 1085, 1075, 1045, 1029, 993, 1026, 1033, 1061, 1097, 1152, 1145, 1155, 1153, 1095, 1058, 1041, 1019, 1008, 1040, 999, 993, 956, 980, 984, 1016, 982, 959, 915, 924, 923, 959, 972, 928, 910, 914, 880, 907, 868, 875, 915, 918, 926, 899, 933, 868, 907, 903, 941, 949, 894, 929, 927, 951, 935, 975, 990, 1006, 941, 948, 963, 1001, 1028, 1103, 1026, 1033, 1078, 1064 ; } --- dump of mincheader of b.mnc netcdf b { dimensions: yspace = 85 ; zspace = 89 ; xspace = 83 ; variables: int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "image" ; double yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = 1. ; yspace:start = 0. ; yspace:units = "mm" ; double zspace ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = 1. ; zspace:start = 0. ; zspace:units = "mm" ; double xspace ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = 1. ; xspace:start = 0. ; xspace:units = "mm" ; double image-min ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; double image-max ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; short image(yspace, zspace, xspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:image-max = "--->image-max" ; image:image-min = "--->image-min" ; image:complete = "true_" ; image:signtype = "signed__" ; image:valid_range = 0., 1212. ; // global attributes: :history = "volume created on Sat 10 Apr 2004 01:16:10 by user \'gibby\' (uid=-1) on host \'QUARK\' (win32) by application VoxCon version 1.0.8-Granite[21/03/04]\n", "set name to \'copy of unknown\' on Sat 10 Apr 2004 01:16:10 by user \'gibby\' (uid=-1) on host \'QUARK\' (win32) by application VoxCon version 1.0.8-Granite[21/03/04]\n", "set data on Sat 10 Apr 2004 01:16:10 by user \'gibby\' (uid=-1) on host \'QUARK\' (win32) by application VoxCon version 1.0.8-Granite[21/03/04]\n", "copied history[0] from parent(unknown) by procedure \'duplicate\': \'volume created on Sat 10 Apr 2004 01:16:08 by user \'gibby\' (uid=-1) on host \'QUARK\' (win32) by application VoxCon version 1.0.8-Granite[21/03/04]\'\n", "copied history[1] from parent(unknown) by procedure \'duplicate\': \'swap on \'xz\' axis on Sat 10 Apr 2004 01:16:08 by user \'gibby\' (uid=-1) on host \'QUARK\' (win32) by application VoxCon version 1.0.8-Granite[21/03/04]\'\n", "duplicated from \'unknown\' on Sat 10 Apr 2004 01:16:10 by user \'gibby\' (uid=-1) on host \'QUARK\' (win32) by application VoxCon version 1.0.8-Granite[21/03/04]\n", "mirror on \'z\' axis on Sat 10 Apr 2004 01:16:10 by user \'gibby\' (uid=-1) on host \'QUARK\' (win32) by application VoxCon version 1.0.8-Granite[21/03/04]\n", "generated by VoxCon, version 1.0.8-Granite[21/03/04], command line was: k:\\raychase\\voxcon.exe -i voor_gibby.vpx -o b.mnc -s xz -m z -d -p -f -c a.mnc -C diff.hdr \n", "set name to \'b.mnc\' on Sat 10 Apr 2004 01:16:13 by user \'gibby\' (uid=-1) on host \'QUARK\' (win32) by application VoxCon version 1.0.8-Granite[21/03/04]" ; data: rootvariable = _ ; yspace = 0 ; zspace = 0 ; xspace = 0 ; image-min = _ ; image-max = 1212 ; } ----- From tosa@nmr.mgh.harvard.edu Mon Apr 12 10:53:04 2004 From: tosa@nmr.mgh.harvard.edu (Yasunari Tosa) Date: Mon Apr 12 09:53:04 2004 Subject: [MINC-users] perllib patch try 2 Message-ID: <407A9F0B.1000105@nmr.mgh.harvard.edu> This is a multi-part message in MIME format. --------------040803000103080507060205 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, MNI people: Sorry, I missed one more fix in configure. Attached is the patch for N3-1.08. (The previous patch did not pass configure on Perl.) Here is the example. Note that the location of the perllibdir is fixed when I installed mni_perllib-0.07 and GetOpt by perl Makefile.PL PREFIX=/usr/pubsw/packages/mni/1.2 on RedHat 9.0. N3-1.08>patch -p1 < ../patch-N3-1.08.txt patching file configure patching file Makefile.in patching file src/NUcorrect/field2imp.in patching file src/NUcorrect/imp2field.in patching file src/NUcorrect/make_template.in patching file src/NUcorrect/nu_estimate.in patching file src/NUcorrect/nu_estimate_np_and_em.in patching file src/NUcorrect/nu_evaluate.in patching file src/NUcorrect/resample_labels.in patching file src/NUcorrect/sharpen_volume.in N3-1.08> configure --prefix=/usr/pubsw/packages/mni/1.2 --perllibdir=/usr/pubsw/packages/mni/1.2/lib/perl5/site_perl/5.8.0 I hope that this is the final version of N3-patch ;-) Tosa -- Yasunari Tosa, Ph.D. R&D Engineer email: tosa@nmr.mgh.harvard.edu Mass. General Hospital NMR Center phone: Building 149 13th Street fax : Charlestown, MA 02129 --------------040803000103080507060205 Content-Type: text/plain; name="patch-N3-1.08.txt" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline; filename="patch-N3-1.08.txt" *** N3-1.08/configure 2004-03-09 10:27:01.000000000 -0500 --- N3-1.08-tosa/configure 2004-04-12 09:03:38.000000000 -0400 *************** *** 271,277 **** PACKAGE_STRING=3D PACKAGE_BUGREPORT=3D =20 ! ac_subst_vars=3D'SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACK= AGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_t= ransform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir= localstatedir libdir includedir oldincludedir infodir mandir build_alias= host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM I= NSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUT= OMAKE AUTOHEADER MAKEINFO AMTAR install_sh STRIP ac_ct_STRIP INSTALL_STRI= P_PROGRAM AWK SET_MAKE am__leading_dot LN_S CC CFLAGS LDFLAGS CPPFLAGS ac= _ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE = AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXX CXXFL= AGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE RANLIB = ac_ct_RANLIB build build_cpu build_vendor build_os host host_cpu host_ven= dor host_os version time date user machine long_version F77 FFLAGS ac_ct_= F77 FLIBS BLAS_LIBS LAPACK_LIBS PERL modeldir LIBOBJS LTLIBOBJS' ac_subst_files=3D'' =20 # Initialize some variables set by options. --- 271,277 ---- PACKAGE_STRING=3D PACKAGE_BUGREPORT=3D =20 ! ac_subst_vars=3D'SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACK= AGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_t= ransform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir= localstatedir libdir includedir oldincludedir infodir mandir build_alias= host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM I= NSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUT= OMAKE AUTOHEADER MAKEINFO AMTAR install_sh STRIP ac_ct_STRIP INSTALL_STRI= P_PROGRAM AWK SET_MAKE am__leading_dot LN_S CC CFLAGS LDFLAGS CPPFLAGS ac= _ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE = AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE CXX CXXFL= AGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE RANLIB = ac_ct_RANLIB build build_cpu build_vendor build_os host host_cpu host_ven= dor host_os version time date user machine long_version F77 FFLAGS ac_ct_= F77 FLIBS BLAS_LIBS LAPACK_LIBS PERL perllibdir modeldir LIBOBJS LTLIBOBJ= S' ac_subst_files=3D'' =20 # Initialize some variables set by options. *************** *** 460,465 **** --- 460,468 ---- | --oldin=3D* | --oldi=3D* | --old=3D* | --ol=3D* | --o=3D*) oldincludedir=3D$ac_optarg ;; =20 + --perllibdir=3D* ) + perllibdir=3D$ac_optarg;; +=20 -prefix | --prefix | --prefi | --pref | --pre | --pr | --p) ac_prev=3Dprefix ;; -prefix=3D* | --prefix=3D* | --prefi=3D* | --pref=3D* | --pre=3D* | -= -pr=3D* | --p=3D*) *************** *** 6451,6457 **** =20 =20 if test -z "$modeldir"; then ! modeldir=3D`$PERL -e 'use MNI::DataDir; print MNI::DataDir::install_dir= ("N3");'` fi if test -z "$modeldir"; then { { echo "$as_me:$LINENO: error: \"Cannot determine model installation = directory\"" >&5 --- 6454,6460 ---- =20 =20 if test -z "$modeldir"; then ! modeldir=3D`$PERL -e "use lib '$perllibdir'; use MNI::DataDir; print MN= I::DataDir::install_dir('N3');"` fi if test -z "$modeldir"; then { { echo "$as_me:$LINENO: error: \"Cannot determine model installation = directory\"" >&5 *************** *** 7176,7181 **** --- 7179,7185 ---- s,@modeldir@,$modeldir,;t t s,@LIBOBJS@,$LIBOBJS,;t t s,@LTLIBOBJS@,$LTLIBOBJS,;t t + s,@perllibdir@,$perllibdir,;t t CEOF =20 _ACEOF *** N3-1.08/Makefile.in 2004-03-09 10:27:00.000000000 -0500 --- N3-1.08-tosa/Makefile.in 2004-04-12 08:53:38.000000000 -0400 *************** *** 82,87 **** --- 82,88 ---- PACKAGE_VERSION =3D @PACKAGE_VERSION@ PATH_SEPARATOR =3D @PATH_SEPARATOR@ PERL =3D @PERL@ + perllibdir=3D @perllibdir@ RANLIB =3D @RANLIB@ SET_MAKE =3D @SET_MAKE@ SHELL =3D @SHELL@ *** N3-1.08/src/NUcorrect/field2imp.in 2003-04-16 10:29:34.000000000 -040= 0 --- N3-1.08-tosa/src/NUcorrect/field2imp.in 2004-04-12 08:53:38.000000000= -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 *** N3-1.08/src/NUcorrect/imp2field.in 2003-04-16 10:29:34.000000000 -040= 0 --- N3-1.08-tosa/src/NUcorrect/imp2field.in 2004-04-12 08:53:38.000000000= -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 *** N3-1.08/src/NUcorrect/make_template.in 2004-02-05 11:01:12.000000000 = -0500 --- N3-1.08-tosa/src/NUcorrect/make_template.in 2004-04-12 08:53:38.00000= 0000 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 *** N3-1.08/src/NUcorrect/nu_estimate.in 2003-04-16 10:29:34.000000000 -0= 400 --- N3-1.08-tosa/src/NUcorrect/nu_estimate.in 2004-04-12 08:53:38.0000000= 00 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 *** N3-1.08/src/NUcorrect/nu_estimate_np_and_em.in 2003-04-16 10:29:34.00= 0000000 -0400 --- N3-1.08-tosa/src/NUcorrect/nu_estimate_np_and_em.in 2004-04-12 08:53:= 38.000000000 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 *** N3-1.08/src/NUcorrect/nu_evaluate.in 2003-05-29 13:14:24.000000000 -0= 400 --- N3-1.08-tosa/src/NUcorrect/nu_evaluate.in 2004-04-12 08:53:38.0000000= 00 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 *** N3-1.08/src/NUcorrect/resample_labels.in 2003-04-16 10:29:34.00000000= 0 -0400 --- N3-1.08-tosa/src/NUcorrect/resample_labels.in 2004-04-12 08:53:38.000= 000000 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx + use lib "xINCDIRx"; =20 # ------------------------------ MNI Header ---------------------------= ------- #@NAME : resample_labels *** N3-1.08/src/NUcorrect/sharpen_volume.in 2003-04-16 10:29:34.000000000= -0400 --- N3-1.08-tosa/src/NUcorrect/sharpen_volume.in 2004-04-12 08:53:38.0000= 00000 -0400 *************** *** 1,4 **** --- 1,5 ---- #!xPERLx -w + use lib "xINCDIRx"; #----------------------------------------------------------------------= ----- #@COPYRIGHT : # Copyright 1996, John G. Sled,=20 --------------040803000103080507060205-- From bert@bic.mni.mcgill.ca Tue Apr 13 14:47:05 2004 From: bert@bic.mni.mcgill.ca (Robert VINCENT) Date: Tue Apr 13 13:47:05 2004 Subject: [MINC-users] N3 1.09 and EBTKS 1.3 Message-ID: To all users of N3, Vivek Singh and I have found and corrected a couple of problems in N3. If you are currently using N3 1.07 or 1.08, we recommend you install the latest versions from CVS, or get the most recent version from the BIC website. The IRIX systems at the BIC will be updated within a day or so. -bert From rotor@cmr.uq.edu.au Wed Apr 14 23:34:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Wed Apr 14 22:34:04 2004 Subject: [MINC-users] mincdti - Diffusion Tensor calculation in MINC. Message-ID: I have placed a MINC DTI package here: http://www.cmr.uq.edu.au/~rotor/distro/src/mincdti-1.0.tar.gz There is also a Debian Linux package here: http://www.cmr.uq.edu.au/~rotor/distro/deb/mincdti-1.0-linux-2.4-intel.deb As per usuall there is not much documentation for it (yet) beyond 'mincdti -help'. There are however a few example B-matrix files in the source distribution in the examples/ sub-directory. The basic idea is to: 1) create a bmatrix for your experiment that describes the directions and diffusion encoding strengths of the sequence. 2) run mincdti to resolve the tensor mincdti -b_matrix foo.bmat file1.mnc file2.mnc .... You must have the same number of input files as you have lines in your bmatrix file. 3) run mincdti_maps (a perl script that uses minccalc) to calculate the tensor metrics you would like: mincdti_maps -FA -ADC -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From rotor@cmr.uq.edu.au Thu Apr 15 02:02:04 2004 From: rotor@cmr.uq.edu.au (Andrew Janke) Date: Thu Apr 15 01:02:04 2004 Subject: [MINC-users] mincsample - Generate samplings from MINC files Message-ID: I have placed a package for generating samplings from MINC files here: http://www.cmr.uq.edu.au/~rotor/distro/src/mincsample-1.0.tar.gz There is also a Debian Linux package here: http://www.cmr.uq.edu.au/~rotor/distro/deb/mincsample-1.0-linux-2.4-intel.deb Who would use this? I use it to generate a random sampling from a series of minc files within a supplied mask. If you wish a random sub-set of data from a MINC file, then mincsample is likely for you. -- Andrew Janke ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From ccurrie@paradox.psych.columbia.edu Fri Apr 16 20:08:04 2004 From: ccurrie@paradox.psych.columbia.edu (Christopher Currie) Date: Fri Apr 16 19:08:04 2004 Subject: [MINC-users] normalizing to scalpedt1.img volume Message-ID: Dear MINC-users I'm trying to use mincresample to write normalized volumes based on one of the spm2 provided template brains (i.e., scalpedt1.img, scalpedt1.hdr), but there doesn't seem to be any direct way to do this. It seems somehow I'd need to get a transformational matrix based on scalpedt1.img, but I'm not sure how to do that, so I these are my two questions: 1. Is there any MINC function that can non linearly normalize a volume based on another arbitrary anatomical volume? 2. Is there any way to extract/derive/build a transformation matrix from a template anatomical, like scalpedt1.img, and put the parameters into an .xfm file? Thanks. - Cheers, Christopher ____________________________________ Christopher Currie Research Assistant/Programmer Department of Psychology, Neuroimaging fMRI lab Columbia University 1190 Amsterdam Ave. New York, NY 10027 Lab phone (temp): 212-854-1860 Email: ccurrie@paradox.psych.columbia.edu From cc2388@columbia.edu Mon Apr 19 16:48:04 2004 From: cc2388@columbia.edu (Christopher) Date: Mon Apr 19 15:48:04 2004 Subject: [MINC-users] spm2mnc & .mat file question/confusion Message-ID: <40842CBD.9020908@columbia.edu> Dear MINC-users, I've been trying to use an MINC script, "mincresample," to normalize volumes using an spm2 template brain, but the input volumes need to be in MINC format. MINC comes with ANALYZE to MINC converters that should work to get everything in the corrrect format, but I'm bit confused about the SPM-based input required -- perhaps this will make more sense to you: "spm2mnc" will convert a SPM ANALYZE .hdr .img .mat tuple to a MINC file. I was thinking smp2mnc could be used to convert an arbitrary ANALYZED-format template anatomical (e.g., spm2/template/scalpedt1.img) into a MINC format (this would be the first step to using this toolbox to normalize volumes to arbitrary template brains), but spm2mnc requires a mat file (?), but it's not clear to me why you need a .mat file or how to get one for scalpedt1.img (you normally get one when you realign a volume or coregister it). I'm still digging into this, but could someone break it down for me? Thanks. - Cheers, Christopher -- ____________________________________ Christopher Currie Research Assistant/Programmer Department of Psychology, Neuroimaging fMRI lab Columbia University 1190 Amsterdam Ave. New York, NY 10027 Lab phone (temp): 212-854-1860 Email: ccurrie@paradox.psych.columbia.edu From k.h.kho@azu.nl Wed Apr 21 14:06:04 2004 From: k.h.kho@azu.nl (Kuan H. Kho) Date: Wed Apr 21 13:06:04 2004 Subject: [MINC-users] spatial location of voxels Message-ID: <6.0.3.0.0.20040421172613.01fc2068@imap.med.uu.nl> Dear MINC users, I was wondering what to what spatial location the MINC coordinates (both voxel and world) refer to. Is that a vertex (which of the 8), the middle of an edge, or the center of a voxel? Furthermore, I was wondering whether there's a command or tool to extract the exact voxel (and world) coordinates for certain conditional voxel values (i.e. thresholds) in a volume. Of course the exact voxel coordinates suffice, for world coordinate = voxel coordinate*step + start, but if there's such a tool existing, it would come in handy. (The reason is that I would like to compare some voxel coordinates from volumes that have been registered, but have different voxel sizes.) Thanks in advance, Kuan Kho Kuan H. Kho Rudolf Magnus Institute of Neuroscience Dept. of Neurosurgery and Psychiatry section: Functional Neuroimaging University Medical Center Utrecht P.O.Box 85500 3508 GA Utrecht The Netherlands Phone: +31-30-2507969/2507977 Fax : +31-30-2542100 email: k.h.kho@azu.nl From rotor@bic.mni.mcgill.ca Wed Apr 21 15:15:04 2004 From: rotor@bic.mni.mcgill.ca (Andrew Janke) Date: Wed Apr 21 14:15:04 2004 Subject: [MINC-users] spatial location of voxels In-Reply-To: <6.0.3.0.0.20040421172613.01fc2068@imap.med.uu.nl> Message-ID: On Wed, 21 Apr 2004, Kuan H. Kho wrote: > I was wondering what to what spatial location the MINC coordinates (both > voxel and world) refer to. Is that a vertex (which of the 8), the middle of > an edge, or the center of a voxel? Centre. > Furthermore, I was wondering whether there's a command or tool to extract > the exact voxel (and world) coordinates for certain conditional voxel > values (i.e. thresholds) in a volume. Of course the exact voxel coordinates > suffice, for world coordinate = voxel coordinate*step + start, but if > there's such a tool existing, it would come in handy. To a threshold? not that I know of. otherwise just voxeltoworld and worldtovoxel will be able to help you. Also remember that the conversion includes the direction cosines. a From jason@bic.mni.mcgill.ca Wed Apr 21 15:24:04 2004 From: jason@bic.mni.mcgill.ca (Jason Lerch) Date: Wed Apr 21 14:24:04 2004 Subject: [MINC-users] spatial location of voxels In-Reply-To: References: Message-ID: On Apr 21, 2004, at 2:14 PM, Andrew Janke wrote: > On Wed, 21 Apr 2004, Kuan H. Kho wrote: > >> I was wondering what to what spatial location the MINC coordinates >> (both >> voxel and world) refer to. Is that a vertex (which of the 8), the >> middle of >> an edge, or the center of a voxel? > > Centre. > >> Furthermore, I was wondering whether there's a command or tool to >> extract >> the exact voxel (and world) coordinates for certain conditional voxel >> values (i.e. thresholds) in a volume. Of course the exact voxel >> coordinates >> suffice, for world coordinate = voxel coordinate*step + start, but if >> there's such a tool existing, it would come in handy. > > To a threshold? not that I know of. otherwise just > > voxeltoworld and worldtovoxel > > will be able to help you. find_peak offers some of that functionality. Jason > > Also remember that the conversion includes the direction cosines. > > > a > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From sylvain@bic.mni.mcgill.ca Wed Apr 21 15:47:05 2004 From: sylvain@bic.mni.mcgill.ca (Sylvain MILOT) Date: Wed Apr 21 14:47:05 2004 Subject: [MINC-users] spatial location of voxels In-Reply-To: <6.0.3.0.0.20040421172613.01fc2068@imap.med.uu.nl> Message-ID: 1 - centre as said previously 2 - minctotag comes to mind On Wed, 21 Apr 2004, Kuan H. Kho wrote: > Dear MINC users, > > I was wondering what to what spatial location the MINC coordinates (both > voxel and world) refer to. Is that a vertex (which of the 8), the middle of > an edge, or the center of a voxel? > > Furthermore, I was wondering whether there's a command or tool to extract > the exact voxel (and world) coordinates for certain conditional voxel > values (i.e. thresholds) in a volume. Of course the exact voxel coordinates > suffice, for world coordinate = voxel coordinate*step + start, but if > there's such a tool existing, it would come in handy. (The reason is that I > would like to compare some voxel coordinates from volumes that have been > registered, but have different voxel sizes.) > > Thanks in advance, > > Kuan Kho > > Kuan H. Kho > Rudolf Magnus Institute of Neuroscience > Dept. of Neurosurgery and Psychiatry > section: Functional Neuroimaging > University Medical Center Utrecht > P.O.Box 85500 > 3508 GA Utrecht > The Netherlands > Phone: +31-30-2507969/2507977 > Fax : +31-30-2542100 > email: k.h.kho@azu.nl > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > --- Sylvain Milot (sylvain@bic.mni.mcgill.ca) Positron Imaging Laboratories Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone: (514)-398-4965, 1996 Fax: 8948 From neelin@bic.mni.mcgill.ca Fri Apr 23 01:42:05 2004 From: neelin@bic.mni.mcgill.ca (Peter NEELIN) Date: Fri Apr 23 00:42:05 2004 Subject: [MINC-users] spatial location of voxels In-Reply-To: Message-ID: On Wed, 21 Apr 2004, Andrew Janke wrote: > On Wed, 21 Apr 2004, Kuan H. Kho wrote: > > > I was wondering what to what spatial location the MINC coordinates (both > > voxel and world) refer to. Is that a vertex (which of the 8), the middle of > > an edge, or the center of a voxel? > > Centre. 'Just a small clarification: The alignment attribute allows one to specify something other than "centre", like start and end. But to my knowledge this is never used for spatial coordinates (only time), and I don't think that any applications handle anything other than centre for spatial coordinates. Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) From cc2388@columbia.edu Fri Apr 23 13:18:04 2004 From: cc2388@columbia.edu (Christopher) Date: Fri Apr 23 12:18:04 2004 Subject: [MINC-users] average_305_headmask.mnc -- what is this? Message-ID: <40894168.8040201@columbia.edu> Dear MINC-users mritotal uses an image, "average_305_headmask.mnc" to normalize scans to a (pseudo-) Talairach space -- could anyone tell me what that is? The other images, the blurred, the masked, those are clear, but what is a "headmask" image? Thanks. - cheers, Christopher -- ____________________________________ Christopher Currie Research Assistant/Programmer Department of Psychology, Neuroimaging fMRI lab Columbia University 1190 Amsterdam Ave. New York, NY 10027 Lab phone (temp): 212-854-1860 Email: ccurrie@paradox.psych.columbia.edu From louis@bic.mni.mcgill.ca Mon Apr 26 09:28:04 2004 From: louis@bic.mni.mcgill.ca (D. Louis Collins) Date: Mon Apr 26 08:28:04 2004 Subject: [MINC-users] average_305_headmask.mnc -- what is this? In-Reply-To: <40894168.8040201@columbia.edu> References: <40894168.8040201@columbia.edu> Message-ID: <122985F2-977D-11D8-86D9-000A959EF478@bic.mni.mcgill.ca> Christopher, the headmask image is simply a mask of the target head skin surface. It is use in one of the intermediate steps of the non-linear fitting to define the tightest bounding box possible for the non-linear deformation. The goal was to save computational time (and space) by not having an unneeded huge deformation field. you can either 1- use the standard headmask in the mni_autoreg model 2- segment the head/skin of your target brain, resample it like your target image and that should do. -Louis On Apr 23, 2004, at 12:16 PM, Christopher wrote: > Dear MINC-users > > mritotal uses an image, "average_305_headmask.mnc" to normalize > scans to a (pseudo-) Talairach space -- could anyone tell me what that > is? The other images, the blurred, the masked, those are clear, but > what is a "headmask" image? Thanks. > > - cheers, > Christopher > > -- > ____________________________________ Christopher Currie > Research Assistant/Programmer Department of Psychology, Neuroimaging > fMRI lab Columbia University 1190 Amsterdam Ave. New York, NY 10027 > Lab phone (temp): 212-854-1860 Email: > ccurrie@paradox.psych.columbia.edu > > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From masa@austin.unimelb.edu.au Thu Apr 29 18:08:07 2004 From: masa@austin.unimelb.edu.au (Masatoshi Koga) Date: Thu Apr 29 17:08:07 2004 Subject: [MINC-users] emma on Mac OS X Message-ID: <000801c42d8d$f4c66d60$1144fa80@austin.unimelb.edu.au> This is a multi-part message in MIME format. --Boundary_(ID_cEIVA4a9Sp97lx15DAsvmA) Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: quoted-printable Hi Jeff, I found the same problem in installing emma on Mac OS X and Matlab6.5. Have you got any solution? Thanks Masatoshi Koga --Boundary_(ID_cEIVA4a9Sp97lx15DAsvmA) Content-type: text/html; charset="iso-8859-1" Content-transfer-encoding: quoted-printable
Hi Jeff,
 
 
I found the same problem in installing = emma on Mac=20 OS X and Matlab6.5.
Have you got any solution?
 
Thanks
 
Masatoshi Koga
 
--Boundary_(ID_cEIVA4a9Sp97lx15DAsvmA)--