From mishkind at gmail.com Mon Apr 2 18:50:17 2012 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Mon, 2 Apr 2012 18:50:17 -0400 Subject: [MINC-users] pyminc and hdf5 Message-ID: Hi, I am getting this HDF5 warning/error when I try to run a very simple python program using pyminc: The minimal program that creates the error: #! /usr/bin/python import pyminc.volumes.factory as pyminc inputfilename = "t1.minc2.posdir.mnc" outputfilename = "copy.mnc" infile = pyminc.volumeFromFile(inputfilename) outfile = pyminc.volumeLikeFile(inputfilename, outputfilename) outfile.writeFile() outfile.closeVolume() infile.closeVolume() The error: HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value The error with PYMINCDEBUG set: HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value sizes [192, 256, 192] separations [0.999999999999998, 1.0, 1.0] starts [-103.827645851979, -111.44957556808501, -84.49910974372] dimnames: ['zspace', 'yspace', 'xspace'] sizes [192, 256, 192] separations [0.999999999999998, 1.0, 1.0] starts [-103.827645851979, -111.44957556808501, -84.49910974372] dimnames: ['zspace', 'yspace', 'xspace'] 0 48381856 c_void_p(48388544) zspace 0 48384368 c_void_p(48388752) yspace 0 48384624 c_void_p(48388960) xspace 3 [48388544, 48388752, 48388960] sizes [192, 256, 192] setting data New Shape: (192, 256, 192) TYPE: short float64 TYPE: int float64 TYPE: double float64 before setting of hyperslab after setting of hyperslab Sample input file that gives the error: http://www.bic.mni.mcgill.ca/users/mishkin/files/t1.minc2.posdir.mnc I only get the error for my own acquired data, but using something like the icbm_152 volume I don't get the error. I've looked for anything funny about my sample input file but haven't spotted anything. Perhaps someone who understands the HDF5 error a bit better can help? thanks, mishkin From baghdadi at phenogenomics.ca Tue Apr 3 10:00:28 2012 From: baghdadi at phenogenomics.ca (Leila Baghdadi) Date: Tue, 3 Apr 2012 10:00:28 -0400 Subject: [MINC-users] pyminc and hdf5 In-Reply-To: Message-ID: <7777565.67741333461628404.JavaMail.root@mail2.phenogenomics.ca> Hi Mishkin, I suspect this is a problem with the hdf5 installation on your machine and not pyminc. I just downloaded your file and it runs file on my machine (ubuntu Lucid), libhdf5-serial 1.8.4-5 baghdadi at mouse30:/projects/souris/baghdadi$ python Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) [GCC 4.4.3] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from pyminc.volumes.factory import * >>> infile=volumeFromFile('/micehome/baghdadi/t1.minc2.posdir.mnc') >>> outfile=volumeLikeFile('/micehome/baghdadi/t1.minc2.posdir.mnc','/micehome/baghdadi/copy.mnc') >>> outfile.writeFile() >>> outfile.closeVolume() >>> infile.closeVolume() Leila ----- Original Message ----- From: Mishkin Derakhshan Sent: Mon, 4/2/2012 6:50pm To: MINC users mailing list Subject: [MINC-users] pyminc and hdf5 Hi, I am getting this HDF5 warning/error when I try to run a very simple python program using pyminc: The minimal program that creates the error: #! /usr/bin/python import pyminc.volumes.factory as pyminc inputfilename = "t1.minc2.posdir.mnc" outputfilename = "copy.mnc" infile = pyminc.volumeFromFile(inputfilename) outfile = pyminc.volumeLikeFile(inputfilename, outputfilename) outfile.writeFile() outfile.closeVolume() infile.closeVolume() The error: HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value The error with PYMINCDEBUG set: HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive major: Invalid arguments to routine minor: Bad value sizes [192, 256, 192] separations [0.999999999999998, 1.0, 1.0] starts [-103.827645851979, -111.44957556808501, -84.49910974372] dimnames: ['zspace', 'yspace', 'xspace'] sizes [192, 256, 192] separations [0.999999999999998, 1.0, 1.0] starts [-103.827645851979, -111.44957556808501, -84.49910974372] dimnames: ['zspace', 'yspace', 'xspace'] 0 48381856 c_void_p(48388544) zspace 0 48384368 c_void_p(48388752) yspace 0 48384624 c_void_p(48388960) xspace 3 [48388544, 48388752, 48388960] sizes [192, 256, 192] setting data New Shape: (192, 256, 192) TYPE: short float64 TYPE: int float64 TYPE: double float64 before setting of hyperslab after setting of hyperslab Sample input file that gives the error: http://www.bic.mni.mcgill.ca/users/mishkin/files/t1.minc2.posdir.mnc I only get the error for my own acquired data, but using something like the icbm_152 volume I don't get the error. I've looked for anything funny about my sample input file but haven't spotted anything. Perhaps someone who understands the HDF5 error a bit better can help? thanks, mishkin _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From andrew at biospective.com Wed Apr 4 11:15:46 2012 From: andrew at biospective.com (Andrew Wood) Date: Wed, 4 Apr 2012 11:15:46 -0400 Subject: [MINC-users] pyminc and hdf5 In-Reply-To: <7777565.67741333461628404.JavaMail.root@mail2.phenogenomics.ca> References: <7777565.67741333461628404.JavaMail.root@mail2.phenogenomics.ca> Message-ID: Hi Mishkin, I can reproduce your error with my HDF5 build. I've seen similar failures before which I suspected were related to negative dimension lengths. This failure may be related to the negative dimension lengths given to this volume in the past: [02] Wed Jun 23 13:25:44 2010>>> mincreshape -clobber -dimorder \ zspace,yspace,xspace -dimsize xspace=-1 -dimsize yspace=-1 -dimsize \ zspace=-1 -dimrange zspace=0,192 \ CLMS_001-MNI-5_amc_018_m00_t1g_original.mnc.gz \ CLMS_001-MNI-5_amc_018_m00_t1g.mnc It looks like you can workaround the problem by running the volume through mincresample: $ mincresample -xnelements 192 -znelements 192 -ynelements 256 original.mnc resampled_positive.mnc $ mincdiff -body original.mnc resampled_positive.mnc Binary image comparison: Images are identical. $ ./Mishkin_copy.py original.mnc broken_copy.mnc # fails with some HDF5 builds $ ./Mishkin_copy.py resampled_positive.mnc working_copy.mnc # works Note you'll need to change to volumeFromInstance(inputfilename, outputfilename, data=True) to copy the data in addition to the shape and type. Regards, Andrew On Tue, Apr 3, 2012 at 10:00 AM, Leila Baghdadi wrote: > Hi Mishkin, > > I suspect this is a problem with the hdf5 installation on your machine and > not pyminc. > > I just downloaded your file and it runs file on my machine (ubuntu Lucid), > libhdf5-serial 1.8.4-5 > > baghdadi at mouse30:/projects/souris/baghdadi$ python > Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41) > [GCC 4.4.3] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> from pyminc.volumes.factory import * > >>> infile=volumeFromFile('/micehome/baghdadi/t1.minc2.posdir.mnc') > >>> > outfile=volumeLikeFile('/micehome/baghdadi/t1.minc2.posdir.mnc','/micehome/baghdadi/copy.mnc') > >>> outfile.writeFile() > >>> outfile.closeVolume() > >>> infile.closeVolume() > > > Leila > > ----- Original Message ----- > From: Mishkin Derakhshan > Sent: Mon, 4/2/2012 6:50pm > To: MINC users mailing list > Subject: [MINC-users] pyminc and hdf5 > > Hi, > > I am getting this HDF5 warning/error when I try to run a very simple > python program using pyminc: > > The minimal program that creates the error: > #! /usr/bin/python > import pyminc.volumes.factory as pyminc > inputfilename = "t1.minc2.posdir.mnc" > outputfilename = "copy.mnc" > infile = pyminc.volumeFromFile(inputfilename) > outfile = pyminc.volumeLikeFile(inputfilename, outputfilename) > outfile.writeFile() > outfile.closeVolume() > infile.closeVolume() > > The error: > HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: > #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive > major: Invalid arguments to routine > minor: Bad value > HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: > #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive > major: Invalid arguments to routine > minor: Bad value > HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: > #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive > major: Invalid arguments to routine > minor: Bad value > > The error with PYMINCDEBUG set: > > HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: > #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive > major: Invalid arguments to routine > minor: Bad value > HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: > #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive > major: Invalid arguments to routine > minor: Bad value > HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 0: > #000: ../../../src/H5T.c line 2120 in H5Tset_size(): size must be positive > major: Invalid arguments to routine > minor: Bad value > sizes [192, 256, 192] > separations [0.999999999999998, 1.0, 1.0] > starts [-103.827645851979, -111.44957556808501, -84.49910974372] > dimnames: ['zspace', 'yspace', 'xspace'] > sizes [192, 256, 192] > separations [0.999999999999998, 1.0, 1.0] > starts [-103.827645851979, -111.44957556808501, -84.49910974372] > dimnames: ['zspace', 'yspace', 'xspace'] > 0 48381856 c_void_p(48388544) zspace > 0 48384368 c_void_p(48388752) yspace > 0 48384624 c_void_p(48388960) xspace > 3 [48388544, 48388752, 48388960] > sizes [192, 256, 192] > setting data > New Shape: (192, 256, 192) > TYPE: short float64 > TYPE: int float64 > TYPE: double float64 > before setting of hyperslab > after setting of hyperslab > > Sample input file that gives the error: > http://www.bic.mni.mcgill.ca/users/mishkin/files/t1.minc2.posdir.mnc > > I only get the error for my own acquired data, but using something > like the icbm_152 volume I don't get the error. I've looked for > anything funny about my sample input file but haven't spotted > anything. Perhaps someone who understands the HDF5 error a bit better > can help? > > thanks, > mishkin > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From eskild at gmail.com Wed Apr 11 04:58:46 2012 From: eskild at gmail.com (Simon Eskildsen) Date: Wed, 11 Apr 2012 10:58:46 +0200 Subject: [MINC-users] Compute distance map from BIC .obj file In-Reply-To: References: <46F6D4D7-E443-4EBE-9497-A793217011E4@student.aau.dk> Message-ID: Hi Ulrik, I have found some of my old code that does almost what you want. Let me know if it's still relevant and I can send you a modified version. Simon On Wed, Mar 21, 2012 at 8:11 PM, Ulrik Landberg Stephansen wrote: > Hi Simon, > > What I am looking for is a tool to do this without having to convert the object to a binary image, which should (in theory) result in a more accurate distance map. > > By signed I mean negative inside and positive outside, yes (or vice versa). The object is closed. > > Ulrik > > > Den 21/03/2012 kl. 13.54 skrev Simon Eskildsen: > >> Hi Ulrik, >> >> You can use scan_object_to_volume from conglomerate and mincchamfer to >> get a distance map. Of course the precision will be limited to the >> voxel sizes and you will not get a signed distance. By signed you mean >> inside / outside the object, right? If the object is closed you'll be >> able to generate the sign with surface_mask2, also from conglomerate. >> >> Simon >> >> On Wed, Mar 21, 2012 at 1:43 PM, Ulrik Landberg Stephansen >> wrote: >>> Hi, >>> >>> I would like to compute the (signed) distance map from a BIC .obj file based on the sampling options in a template MINC volume and save it as a new MINC volume. I.e. for each voxel in the template volume, compute the shortest distance to the surface of the object and use that value as the grayscale value of the corresponding voxel in the output volume. >>> >>> Does such a tool exist, or is it possible using a combination of existing tools? >>> >>> Ulrik >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From usteph08 at student.aau.dk Wed Apr 11 06:47:07 2012 From: usteph08 at student.aau.dk (Ulrik Landberg Stephansen) Date: Wed, 11 Apr 2012 10:47:07 +0000 Subject: [MINC-users] Compute distance map from BIC .obj file In-Reply-To: References: <46F6D4D7-E443-4EBE-9497-A793217011E4@student.aau.dk> Message-ID: <17D86228-1E1A-4601-A7B4-827206379FB0@student.aau.dk> Hi Simon, It is still relevant. So far I've been suggested to use scan_object_to_volume using a super-resolution image as template and mincchamfer or itk_distance to compute the distance map, but this is not an optimal solution. Ulrik Den 11/04/2012 kl. 10.58 skrev Simon Eskildsen: > Hi Ulrik, > > I have found some of my old code that does almost what you want. Let > me know if it's still relevant and I can send you a modified version. > > Simon > > On Wed, Mar 21, 2012 at 8:11 PM, Ulrik Landberg Stephansen > wrote: >> Hi Simon, >> >> What I am looking for is a tool to do this without having to convert the object to a binary image, which should (in theory) result in a more accurate distance map. >> >> By signed I mean negative inside and positive outside, yes (or vice versa). The object is closed. >> >> Ulrik >> >> >> Den 21/03/2012 kl. 13.54 skrev Simon Eskildsen: >> >>> Hi Ulrik, >>> >>> You can use scan_object_to_volume from conglomerate and mincchamfer to >>> get a distance map. Of course the precision will be limited to the >>> voxel sizes and you will not get a signed distance. By signed you mean >>> inside / outside the object, right? If the object is closed you'll be >>> able to generate the sign with surface_mask2, also from conglomerate. >>> >>> Simon >>> >>> On Wed, Mar 21, 2012 at 1:43 PM, Ulrik Landberg Stephansen >>> wrote: >>>> Hi, >>>> >>>> I would like to compute the (signed) distance map from a BIC .obj file based on the sampling options in a template MINC volume and save it as a new MINC volume. I.e. for each voxel in the template volume, compute the shortest distance to the surface of the object and use that value as the grayscale value of the corresponding voxel in the output volume. >>>> >>>> Does such a tool exist, or is it possible using a combination of existing tools? >>>> >>>> Ulrik >>>> _______________________________________________ >>>> MINC-users at bic.mni.mcgill.ca >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From zijdenbos at gmail.com Tue Apr 17 17:10:34 2012 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Tue, 17 Apr 2012 17:10:34 -0400 Subject: [MINC-users] dcm2mnc and (ir)regular spacing (again) Message-ID: Hello all, I am staring at another dimension step/spacing issue (from a 4D PET volume). In a MINC volume produced by dcm2mnc, I have: $ mincheader test.mnc | grep time time = 4 ; double time(time) ; time:varid = "MINC standard variable" ; time:vartype = "dimension____" ; time:version = "MINC Version 1.0" ; time:spacing = "irregular" ; time:alignment = "start_" ; time:units = "s" ; time:step = 225. ; time:start = 197.88 ; double time-width(time) ; time-width:varid = "MINC standard variable" ; time-width:vartype = "dim-width____" ; time-width:version = "MINC Version 1.0" ; time-width:spacing = "irregular" ; time-width:filtertype = "square____" ; short image(time, zspace, yspace, xspace) ; double image-min(time, zspace) ; double image-max(time, zspace) ; study:start_time = "142857" ; acquisition:start_time = "20110114 142857" ; time = 197.88, 497.88, 797.88, 1097.88 ; time-width = 299.88, 299.88, 299.88, 299.88 ; So time:spacing is listed as "irregular"; and looking at the time- and time-width vars the frame times are 300s apart (give or take). However, the time:step attribute is 225, not 300. Is this basically broken MINC? I assume the time:step attribute somehow is generated from some DICOM field, but is basically wrong? Question perhaps is: when there is conflicting step information, which should take precedence? Thanks, -- Alex From peter.neelin at gmail.com Wed Apr 18 09:41:00 2012 From: peter.neelin at gmail.com (Peter Neelin) Date: Wed, 18 Apr 2012 09:41:00 -0400 Subject: [MINC-users] dcm2mnc and (ir)regular spacing (again) In-Reply-To: References: Message-ID: Hi Alex, On Tue, Apr 17, 2012 at 5:10 PM, Alex Zijdenbos wrote: > So time:spacing is listed as "irregular"; and looking at the time- and > time-width vars the frame times are 300s apart (give or take). > However, the time:step attribute is 225, not 300. > > Is this basically broken MINC? Yes, it is broken. The step should be some form of average. > I assume the time:step attribute > somehow is generated from some DICOM field, but is basically wrong? No, it is computed. The broken code is in dcm2mnc/minc_file.c, in function minc_set_spacing(). It appears that the code is going down the "if (regular)" branch and incorrectly computing the step by summing the difference between coordinates for N-1 values, then dividing by N (line 532). It then calls check_regular to see if it is regular and finds that the (wrong) step value does not match the coordinate spacing and marks the spacing as irregular. Peter -- Peter Neelin (peter.neelin at gmail.com) From zijdenbos at gmail.com Wed Apr 18 13:41:19 2012 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Wed, 18 Apr 2012 13:41:19 -0400 Subject: [MINC-users] dcm2mnc and (ir)regular spacing (again) In-Reply-To: References: Message-ID: On Wed, Apr 18, 2012 at 9:41 AM, Peter Neelin wrote: > Hi Alex, > > On Tue, Apr 17, 2012 at 5:10 PM, Alex Zijdenbos wrote: > >> So time:spacing is listed as "irregular"; and looking at the time- and >> time-width vars the frame times are 300s apart (give or take). >> However, the time:step attribute is 225, not 300. >> >> Is this basically broken MINC? > > Yes, it is broken. The step should be some form of average. > >> I assume the time:step attribute >> somehow is generated from some DICOM field, but is basically wrong? > > No, it is computed. The broken code is in dcm2mnc/minc_file.c, in > function minc_set_spacing(). It appears that the code is going down > the "if (regular)" branch and incorrectly computing the step by > summing the difference between coordinates for N-1 values, then > dividing by N (line 532). It then calls check_regular to see if it is > regular and finds that the (wrong) step value does not match the > coordinate spacing and marks the spacing as irregular. OK I see - thanks! So that line 532 should divide by N-1 (I filed an issue on github). Seems like all along this could have resulted in wrong step sizes in many MINC volumes generated by dcm2mnc... -- A From vladimir.fonov at gmail.com Fri Apr 20 19:49:06 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 20 Apr 2012 19:49:06 -0400 Subject: [MINC-users] new minc-toolkit binary package Message-ID: Hello Everybody, I've created a binary destribution of most of commonly used minc tools in a single package: for Ubuntu 11.04 (will work on newer versions as well, Andrew Janke also succesfully installed it on Ubuntu 10.10) http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Ubuntu_11.04-x86_64.deb for Debian 6: http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Debian_6.0-x86_64.deb for MacOS X 10.7: http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Darwin-x86_64.dmg It includes most of the standard minc tools, Display, Register and a basic image processing pipeline based on the one developed for NIHPD project ( standard_pipeline.pl) Everything is currently installed in /opt/minc , to avoid conflict with standard /usr/local/bic location. To use , source evironment in /opt/minc/minc-toolkit-config.sh for bash or /opt/minc/minc-toolkit-config.csh for tcsh Unfortunately, Display and Register show everything in pink on MacOS X - maybe somebody with mac knowledge could take a look at it. The package is based on minc-toolkit superbuild package hosted on github: https://github.com/BIC-MNI/minc-toolkit If you feel like build it, read README.txt at the bottom of github page Also, available collection of anatomical templates ( ICBM 152 Nonlinear atlases version 2009 ): For Debian/Ubuntu: http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.deb For MacOS X: http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.dmg anatomical templates will be installed in /opt/minc/share/icbm152_model_09a and /opt/minc/share/icbm152_model_09c I have also made a package for testing installation, right now it is running a standard pipeline on two (supplied ) ICBM subjects: For Debian/Ubuntu: http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.deb For MacOS X: http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.dmg Test data is installed in /opt/minc/share/testsuit/ , to run the test execute /opt/minc/run_tests.sh , it will take around 30minutes on modern computer , the output will be in /00200 and /00201 and the log file will be saved in /minc-toolkit-test-.log It would be great if somebody with a Mac could install the package and execute the test suite , to make sure it works as expected (I didn't have a chance). -- Best regards, ?Vladimir S. Fonov ~ vladimir fonov gmail com From vladimir.fonov at gmail.com Sat Apr 21 13:02:04 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Sat, 21 Apr 2012 13:02:04 -0400 Subject: [MINC-users] new minc-toolkit binary package In-Reply-To: References: Message-ID: Hello Everybody, it turns out that test suit /opt/minc/run_tests.sh is incompatible with dash (Ubuntu replacement for bash), so to run it on ubuntu you might have to execute it using bash explicitly i.e: bash /opt/minc/run_tests.sh On Fri, Apr 20, 2012 at 7:49 PM, Vladimir S. FONOV wrote: > Hello Everybody, > > I've created a binary destribution of most of commonly used minc tools > in a single package: > > for Ubuntu 11.04 (will work on newer versions as well, Andrew Janke > also succesfully installed it on Ubuntu 10.10) > http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Ubuntu_11.04-x86_64.deb > > for Debian 6: > http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Debian_6.0-x86_64.deb > > for MacOS X 10.7: > http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Darwin-x86_64.dmg > > It includes most of the standard minc tools, Display, Register and a > basic image processing pipeline based on the one developed for NIHPD > project ( standard_pipeline.pl) Everything is currently installed in > /opt/minc , to avoid conflict with standard /usr/local/bic location. > To use , source evironment in /opt/minc/minc-toolkit-config.sh for > bash or /opt/minc/minc-toolkit-config.csh for tcsh > > Unfortunately, Display and Register ?show everything in pink on MacOS X - maybe > somebody with mac knowledge could take a look at it. > > The package is based on minc-toolkit superbuild package hosted on github: > > https://github.com/BIC-MNI/minc-toolkit > > If you feel like build it, read ?README.txt at the bottom of github page > > > Also, available collection of anatomical templates ( ICBM 152 > Nonlinear atlases version 2009 ): > > For Debian/Ubuntu: > http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.deb > > For MacOS X: > http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.dmg > > anatomical templates will be installed in > /opt/minc/share/icbm152_model_09a and > /opt/minc/share/icbm152_model_09c > > I have also made a package for testing installation, right now it is > running a standard pipeline on two (supplied ) ICBM subjects: > > For Debian/Ubuntu: > http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.deb > > For MacOS X: > http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.dmg > > Test data is installed in /opt/minc/share/testsuit/ , to run the test > execute /opt/minc/run_tests.sh , it will take around > 30minutes on modern computer , the output will be in > /00200 ?and /00201 and the log file will be saved in > /minc-toolkit-test-.log > > It would be great if somebody with a Mac could install the package and > execute the test suite , to make sure it works as expected (I didn't > have a chance). -- Best regards, ?Vladimir S. Fonov ~ vladimir fonov gmail com From zijdenbos at gmail.com Sat Apr 21 13:19:04 2012 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Sat, 21 Apr 2012 13:19:04 -0400 Subject: [MINC-users] new minc-toolkit binary package In-Reply-To: References: Message-ID: Hi Vlad, Very nice work building these packages! I installed and ran the test on OSX Lion, and it looks like the classification tag files are missing/misnamed/mislocated in your test pipeline: /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_ntags_1000_bg.tag does not exist /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_ntags_1000_prob_90_nobg.tag does not exist However these two: /opt/minc/share/classify/ntags_1000_bg.tag /opt/minc/share/classify/ntags_1000_prob_90_nobg.tag do exist -- A On Sat, Apr 21, 2012 at 1:02 PM, Vladimir S. FONOV wrote: > Hello Everybody, > > it turns out that test suit /opt/minc/run_tests.sh is incompatible > with dash (Ubuntu replacement for bash), so to run it on ubuntu you > might have to execute it using bash explicitly i.e: > > bash /opt/minc/run_tests.sh > > On Fri, Apr 20, 2012 at 7:49 PM, Vladimir S. FONOV > wrote: >> Hello Everybody, >> >> I've created a binary destribution of most of commonly used minc tools >> in a single package: >> >> for Ubuntu 11.04 (will work on newer versions as well, Andrew Janke >> also succesfully installed it on Ubuntu 10.10) >> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Ubuntu_11.04-x86_64.deb >> >> for Debian 6: >> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Debian_6.0-x86_64.deb >> >> for MacOS X 10.7: >> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Darwin-x86_64.dmg >> >> It includes most of the standard minc tools, Display, Register and a >> basic image processing pipeline based on the one developed for NIHPD >> project ( standard_pipeline.pl) Everything is currently installed in >> /opt/minc , to avoid conflict with standard /usr/local/bic location. >> To use , source evironment in /opt/minc/minc-toolkit-config.sh for >> bash or /opt/minc/minc-toolkit-config.csh for tcsh >> >> Unfortunately, Display and Register ?show everything in pink on MacOS X - maybe >> somebody with mac knowledge could take a look at it. >> >> The package is based on minc-toolkit superbuild package hosted on github: >> >> https://github.com/BIC-MNI/minc-toolkit >> >> If you feel like build it, read ?README.txt at the bottom of github page >> >> >> Also, available collection of anatomical templates ( ICBM 152 >> Nonlinear atlases version 2009 ): >> >> For Debian/Ubuntu: >> http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.deb >> >> For MacOS X: >> http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.dmg >> >> anatomical templates will be installed in >> /opt/minc/share/icbm152_model_09a and >> /opt/minc/share/icbm152_model_09c >> >> I have also made a package for testing installation, right now it is >> running a standard pipeline on two (supplied ) ICBM subjects: >> >> For Debian/Ubuntu: >> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.deb >> >> For MacOS X: >> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.dmg >> >> Test data is installed in /opt/minc/share/testsuit/ , to run the test >> execute /opt/minc/run_tests.sh , it will take around >> 30minutes on modern computer , the output will be in >> /00200 ?and /00201 and the log file will be saved in >> /minc-toolkit-test-.log >> >> It would be great if somebody with a Mac could install the package and >> execute the test suite , to make sure it works as expected (I didn't >> have a chance). > > > > -- > Best regards, > > ?Vladimir S. Fonov ~ vladimir fonov gmail com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Sun Apr 22 00:04:18 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Sun, 22 Apr 2012 00:04:18 -0400 Subject: [MINC-users] new minc-toolkit binary package In-Reply-To: References: Message-ID: Hello Everybody, thank you for testing, I've updated my test package and models package, here are the new versions for Debian/Ubuntu: http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.1-20120421.deb http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.1-20120421.deb And for Mac OS X: http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.1-20120421.dmg http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.1-20120421.dmg On Sat, Apr 21, 2012 at 1:19 PM, Alex Zijdenbos wrote: > Hi Vlad, > > Very nice work building these packages! > > I installed and ran the test on OSX Lion, and it looks like the > classification tag files are missing/misnamed/mislocated in your test > pipeline: > > /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_ntags_1000_bg.tag > does not exist > /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_ntags_1000_prob_90_nobg.tag > does not exist > > However these two: > > /opt/minc/share/classify/ntags_1000_bg.tag > /opt/minc/share/classify/ntags_1000_prob_90_nobg.tag > > do exist > > -- A > > On Sat, Apr 21, 2012 at 1:02 PM, Vladimir S. FONOV > wrote: >> Hello Everybody, >> >> it turns out that test suit /opt/minc/run_tests.sh is incompatible >> with dash (Ubuntu replacement for bash), so to run it on ubuntu you >> might have to execute it using bash explicitly i.e: >> >> bash /opt/minc/run_tests.sh >> >> On Fri, Apr 20, 2012 at 7:49 PM, Vladimir S. FONOV >> wrote: >>> Hello Everybody, >>> >>> I've created a binary destribution of most of commonly used minc tools >>> in a single package: >>> >>> for Ubuntu 11.04 (will work on newer versions as well, Andrew Janke >>> also succesfully installed it on Ubuntu 10.10) >>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Ubuntu_11.04-x86_64.deb >>> >>> for Debian 6: >>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Debian_6.0-x86_64.deb >>> >>> for MacOS X 10.7: >>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Darwin-x86_64.dmg >>> >>> It includes most of the standard minc tools, Display, Register and a >>> basic image processing pipeline based on the one developed for NIHPD >>> project ( standard_pipeline.pl) Everything is currently installed in >>> /opt/minc , to avoid conflict with standard /usr/local/bic location. >>> To use , source evironment in /opt/minc/minc-toolkit-config.sh for >>> bash or /opt/minc/minc-toolkit-config.csh for tcsh >>> >>> Unfortunately, Display and Register ?show everything in pink on MacOS X - maybe >>> somebody with mac knowledge could take a look at it. >>> >>> The package is based on minc-toolkit superbuild package hosted on github: >>> >>> https://github.com/BIC-MNI/minc-toolkit >>> >>> If you feel like build it, read ?README.txt at the bottom of github page >>> >>> >>> Also, available collection of anatomical templates ( ICBM 152 >>> Nonlinear atlases version 2009 ): >>> >>> For Debian/Ubuntu: >>> http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.deb >>> >>> For MacOS X: >>> http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.dmg >>> >>> anatomical templates will be installed in >>> /opt/minc/share/icbm152_model_09a and >>> /opt/minc/share/icbm152_model_09c >>> >>> I have also made a package for testing installation, right now it is >>> running a standard pipeline on two (supplied ) ICBM subjects: >>> >>> For Debian/Ubuntu: >>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.deb >>> >>> For MacOS X: >>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.dmg >>> >>> Test data is installed in /opt/minc/share/testsuit/ , to run the test >>> execute /opt/minc/run_tests.sh , it will take around >>> 30minutes on modern computer , the output will be in >>> /00200 ?and /00201 and the log file will be saved in >>> /minc-toolkit-test-.log >>> >>> It would be great if somebody with a Mac could install the package and >>> execute the test suite , to make sure it works as expected (I didn't >>> have a chance). >> >> >> >> -- >> Best regards, >> >> ?Vladimir S. Fonov ~ vladimir fonov gmail com >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- Best regards, ?Vladimir S. Fonov ~ vladimir fonov gmail com From vladimir.fonov at gmail.com Tue Apr 24 21:06:03 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Tue, 24 Apr 2012 21:06:03 -0400 Subject: [MINC-users] new minc-toolkit binary package In-Reply-To: References: Message-ID: Hello Everybody, we (me and Louis) have created an official page for minc-tollkit : http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit It contains links to latest versions of binary packages. Also, I have included pre-compiled third-party binary packages of ITK-SNAP with minc support and elastix also with minc support. On Sun, Apr 22, 2012 at 12:04 AM, Vladimir S. FONOV wrote: > Hello Everybody, > > thank you for testing, I've updated my test package and models > package, here are the new versions for Debian/Ubuntu: > http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.1-20120421.deb > http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.1-20120421.deb > > And for Mac OS X: > http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.1-20120421.dmg > http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.1-20120421.dmg > > > On Sat, Apr 21, 2012 at 1:19 PM, Alex Zijdenbos wrote: >> Hi Vlad, >> >> Very nice work building these packages! >> >> I installed and ran the test on OSX Lion, and it looks like the >> classification tag files are missing/misnamed/mislocated in your test >> pipeline: >> >> /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_ntags_1000_bg.tag >> does not exist >> /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_ntags_1000_prob_90_nobg.tag >> does not exist >> >> However these two: >> >> /opt/minc/share/classify/ntags_1000_bg.tag >> /opt/minc/share/classify/ntags_1000_prob_90_nobg.tag >> >> do exist >> >> -- A >> >> On Sat, Apr 21, 2012 at 1:02 PM, Vladimir S. FONOV >> wrote: >>> Hello Everybody, >>> >>> it turns out that test suit /opt/minc/run_tests.sh is incompatible >>> with dash (Ubuntu replacement for bash), so to run it on ubuntu you >>> might have to execute it using bash explicitly i.e: >>> >>> bash /opt/minc/run_tests.sh >>> >>> On Fri, Apr 20, 2012 at 7:49 PM, Vladimir S. FONOV >>> wrote: >>>> Hello Everybody, >>>> >>>> I've created a binary destribution of most of commonly used minc tools >>>> in a single package: >>>> >>>> for Ubuntu 11.04 (will work on newer versions as well, Andrew Janke >>>> also succesfully installed it on Ubuntu 10.10) >>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Ubuntu_11.04-x86_64.deb >>>> >>>> for Debian 6: >>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Debian_6.0-x86_64.deb >>>> >>>> for MacOS X 10.7: >>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-0.3.5-20120419-Darwin-x86_64.dmg >>>> >>>> It includes most of the standard minc tools, Display, Register and a >>>> basic image processing pipeline based on the one developed for NIHPD >>>> project ( standard_pipeline.pl) Everything is currently installed in >>>> /opt/minc , to avoid conflict with standard /usr/local/bic location. >>>> To use , source evironment in /opt/minc/minc-toolkit-config.sh for >>>> bash or /opt/minc/minc-toolkit-config.csh for tcsh >>>> >>>> Unfortunately, Display and Register ?show everything in pink on MacOS X - maybe >>>> somebody with mac knowledge could take a look at it. >>>> >>>> The package is based on minc-toolkit superbuild package hosted on github: >>>> >>>> https://github.com/BIC-MNI/minc-toolkit >>>> >>>> If you feel like build it, read ?README.txt at the bottom of github page >>>> >>>> >>>> Also, available collection of anatomical templates ( ICBM 152 >>>> Nonlinear atlases version 2009 ): >>>> >>>> For Debian/Ubuntu: >>>> http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.deb >>>> >>>> For MacOS X: >>>> http://www.bic.mni.mcgill.ca/~vfonov/software/bic-mni-models-0.1.0-20120420.dmg >>>> >>>> anatomical templates will be installed in >>>> /opt/minc/share/icbm152_model_09a and >>>> /opt/minc/share/icbm152_model_09c >>>> >>>> I have also made a package for testing installation, right now it is >>>> running a standard pipeline on two (supplied ) ICBM subjects: >>>> >>>> For Debian/Ubuntu: >>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.deb >>>> >>>> For MacOS X: >>>> http://www.bic.mni.mcgill.ca/~vfonov/software/minc-toolkit-testsuit-0.1.0-20120420.dmg >>>> >>>> Test data is installed in /opt/minc/share/testsuit/ , to run the test >>>> execute /opt/minc/run_tests.sh , it will take around >>>> 30minutes on modern computer , the output will be in >>>> /00200 ?and /00201 and the log file will be saved in >>>> /minc-toolkit-test-.log >>>> >>>> It would be great if somebody with a Mac could install the package and >>>> execute the test suite , to make sure it works as expected (I didn't >>>> have a chance). >>> >>> >>> >>> -- >>> Best regards, >>> >>> ?Vladimir S. Fonov ~ vladimir fonov gmail com >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > -- > Best regards, > > ?Vladimir S. Fonov ~ vladimir fonov gmail com -- Best regards, ?Vladimir S. Fonov ~ vladimir fonov gmail com From jon.pipitone at utoronto.ca Wed Apr 25 10:12:47 2012 From: jon.pipitone at utoronto.ca (jon pipitone) Date: Wed, 25 Apr 2012 10:12:47 -0400 Subject: [MINC-users] NMI for minc volumes Message-ID: Hey MINC Users, I'm wondering if anyone here knows about, or has written, some code to compute the normalised mutual information of two minc volumes[1]? I see that minctracc uses nmi, and has a -measure option to output various objective functions[2], except not NMI. I'm hoping that there is a magical utility out there to do this already that I'm just not aware of. Otherwise, I figure I'd dip into the minctracc code and see if I can expose the measure either through the -measure flag, or as a separate utility (a la xcorr_vol). If I go this route and anyone has helpful pointers or gotchas, let me know. Thanks all, Jon Pipitone Research Imaging Centre Centre for Addiction and Mental Health Toronto, Ontario [1] I've found one other person asking about this way back: http://www.bic.mni.mcgill.ca/pipermail/minc-users/2005-August/000805.html [2] But I'm wary of the quality of the output: http://www.bic.mni.mcgill.ca/pipermail/minc-users/2007-September/001705.html From andrew at biospective.com Wed Apr 25 10:20:16 2012 From: andrew at biospective.com (Andrew Wood) Date: Wed, 25 Apr 2012 10:20:16 -0400 Subject: [MINC-users] HDF5-1.8.5 vs HDF5-1.8.5-patch1 Message-ID: Hi All, I ran into a problem running minc commands on gzipped files (I'm using a locally-built MINC 2.1 and HDF5-1.8.5-patch1): $ mincinfo icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz (from miexpand_file): Cannot uncompress the file mincinfo: Error expanding file "icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz" The interesting thing is that when I rebuilt minc against hdf5-1.8.5 (without the patch), things run as they should: $ mincinfo icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz file: icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz image: unsigned short 0 to 65535 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 193 1 -74 yspace 229 1 -132 xspace 193 1 -96 Maybe a minc bug? Maybe something broke in hdf5? I thought it was worth mentioning in either case. Regards, Andrew From vladimir.fonov at gmail.com Wed Apr 25 11:32:18 2012 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Wed, 25 Apr 2012 11:32:18 -0400 Subject: [MINC-users] NMI for minc volumes In-Reply-To: References: Message-ID: <4F981902.4080506@gmail.com> Hello, I've been using a wrapper around ITK cost functions to achieve this. Right now it's not distributed as part of any package, but it is not difficult to compile. On 25/04/2012 10:12 AM, jon pipitone wrote: > Hey MINC Users, > > I'm wondering if anyone here knows about, or has written, some code to > compute the normalised mutual information of two minc volumes[1]? > > I see that minctracc uses nmi, and has a -measure option to output various > objective functions[2], except not NMI. I'm hoping that there is a magical > utility out there to do this already that I'm just not aware of. > > Otherwise, I figure I'd dip into the minctracc code and see if I can expose > the measure either through the -measure flag, or as a separate utility (a > la xcorr_vol). If I go this route and anyone has helpful pointers or > gotchas, let me know. > > Thanks all, > > Jon Pipitone > Research Imaging Centre > Centre for Addiction and Mental Health > Toronto, Ontario > > > [1] I've found one other person asking about this way back: > http://www.bic.mni.mcgill.ca/pipermail/minc-users/2005-August/000805.html > > [2] But I'm wary of the quality of the output: > http://www.bic.mni.mcgill.ca/pipermail/minc-users/2007-September/001705.html > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com From jon.pipitone at utoronto.ca Wed Apr 25 12:30:45 2012 From: jon.pipitone at utoronto.ca (jon pipitone) Date: Wed, 25 Apr 2012 12:30:45 -0400 Subject: [MINC-users] NMI for minc volumes Message-ID: Ah, excellent idea. Vlad, do you mind sharing your code to do this? Jon. Date: Wed, 25 Apr 2012 11:32:18 -0400 > From: "Vladimir S. Fonov" > To: minc-users at bic.mni.mcgill.ca > Subject: Re: [MINC-users] NMI for minc volumes > Message-ID: <4F981902.4080506 at gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello, > > I've been using a wrapper around ITK cost functions to achieve this. > Right now it's not distributed as part of any package, but it is not > difficult to compile. > > On 25/04/2012 10:12 AM, jon pipitone wrote: > > Hey MINC Users, > > > > I'm wondering if anyone here knows about, or has written, some code to > > compute the normalised mutual information of two minc volumes[1]? > > > > I see that minctracc uses nmi, and has a -measure option to output > various > > objective functions[2], except not NMI. I'm hoping that there is a > magical > > utility out there to do this already that I'm just not aware of. > > > > Otherwise, I figure I'd dip into the minctracc code and see if I can > expose > > the measure either through the -measure flag, or as a separate utility (a > > la xcorr_vol). If I go this route and anyone has helpful pointers or > > gotchas, let me know. > > > > Thanks all, > > > > Jon Pipitone > > Research Imaging Centre > > Centre for Addiction and Mental Health > > Toronto, Ontario > > > > > > [1] I've found one other person asking about this way back: > > > http://www.bic.mni.mcgill.ca/pipermail/minc-users/2005-August/000805.html > > > > [2] But I'm wary of the quality of the output: > > > http://www.bic.mni.mcgill.ca/pipermail/minc-users/2007-September/001705.html > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > -- > Best regards, > > Vladimir S. Fonov ~ vladimir fonov gmail com > > From vladimir.fonov at gmail.com Wed Apr 25 14:48:23 2012 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 25 Apr 2012 14:48:23 -0400 Subject: [MINC-users] NMI for minc volumes In-Reply-To: References: Message-ID: Hello, On Wed, Apr 25, 2012 at 12:30 PM, jon pipitone wrote: > Vlad, do you mind sharing your code to do this? I've included it into EZminc package ( https://github.com/BIC-MNI/EZminc develop branch ) To compile it all you will have to install minc from https://github.com/BIC-MNI/minc , minc4itk branch and https://github.com/BIC-MNI/minc4itk the program itself is here: https://github.com/BIC-MNI/EZminc/blob/develop/tools/itk_similarity.cpp >> From: "Vladimir S. Fonov" >> To: minc-users at bic.mni.mcgill.ca >> Subject: Re: [MINC-users] NMI for minc volumes >> Message-ID: <4F981902.4080506 at gmail.com> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hello, >> >> I've been using a wrapper around ITK cost functions to achieve this. >> Right now it's not distributed as part of any package, but it is not >> difficult to compile. >> >> On 25/04/2012 10:12 AM, jon pipitone wrote: >> > Hey MINC Users, >> > >> > I'm wondering if anyone here knows about, or has written, some code to >> > compute the normalised mutual information of two minc volumes[1]? >> > >> > I see that minctracc uses nmi, and has a -measure option to output >> various >> > objective functions[2], except not NMI. ?I'm hoping that there is a >> magical >> > utility out there to do this already that I'm just not aware of. >> > >> > Otherwise, I figure I'd dip into the minctracc code and see if I can >> expose >> > the measure either through the -measure flag, or as a separate utility (a >> > la xcorr_vol). ?If I go this route and anyone has helpful pointers or >> > gotchas, let me know. >> > >> > Thanks all, >> > >> > Jon Pipitone >> > Research Imaging Centre >> > Centre for Addiction and Mental Health >> > Toronto, Ontario >> > >> > >> > [1] I've found one other person asking about this way back: >> > >> http://www.bic.mni.mcgill.ca/pipermail/minc-users/2005-August/000805.html >> > >> > [2] But I'm wary of the quality of the output: >> > >> http://www.bic.mni.mcgill.ca/pipermail/minc-users/2007-September/001705.html >> > _______________________________________________ -- Best regards, ?Vladimir S. Fonov ~ vladimir fonov gmail com From jon.pipitone at utoronto.ca Wed Apr 25 17:03:24 2012 From: jon.pipitone at utoronto.ca (jon pipitone) Date: Wed, 25 Apr 2012 17:03:24 -0400 Subject: [MINC-users] NMI for minc volumes In-Reply-To: References: Message-ID: Nice one! Thank you *so* much Vlad. Jon. On Wed, Apr 25, 2012 at 2:48 PM, Vladimir S. FONOV wrote: > Hello, > > On Wed, Apr 25, 2012 at 12:30 PM, jon pipitone > wrote: > > Vlad, do you mind sharing your code to do this? > > I've included it into EZminc package ( > https://github.com/BIC-MNI/EZminc develop branch ) > > To compile it all you will have to install minc from > https://github.com/BIC-MNI/minc , minc4itk branch and > > https://github.com/BIC-MNI/minc4itk > > the program itself is here: > https://github.com/BIC-MNI/EZminc/blob/develop/tools/itk_similarity.cpp > > > > >> From: "Vladimir S. Fonov" > >> To: minc-users at bic.mni.mcgill.ca > >> Subject: Re: [MINC-users] NMI for minc volumes > >> Message-ID: <4F981902.4080506 at gmail.com> > >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >> > >> Hello, > >> > >> I've been using a wrapper around ITK cost functions to achieve this. > >> Right now it's not distributed as part of any package, but it is not > >> difficult to compile. > >> > >> On 25/04/2012 10:12 AM, jon pipitone wrote: > >> > Hey MINC Users, > >> > > >> > I'm wondering if anyone here knows about, or has written, some code to > >> > compute the normalised mutual information of two minc volumes[1]? > >> > > >> > I see that minctracc uses nmi, and has a -measure option to output > >> various > >> > objective functions[2], except not NMI. I'm hoping that there is a > >> magical > >> > utility out there to do this already that I'm just not aware of. > >> > > >> > Otherwise, I figure I'd dip into the minctracc code and see if I can > >> expose > >> > the measure either through the -measure flag, or as a separate > utility (a > >> > la xcorr_vol). If I go this route and anyone has helpful pointers or > >> > gotchas, let me know. > >> > > >> > Thanks all, > >> > > >> > Jon Pipitone > >> > Research Imaging Centre > >> > Centre for Addiction and Mental Health > >> > Toronto, Ontario > >> > > >> > > >> > [1] I've found one other person asking about this way back: > >> > > >> > http://www.bic.mni.mcgill.ca/pipermail/minc-users/2005-August/000805.html > >> > > >> > [2] But I'm wary of the quality of the output: > >> > > >> > http://www.bic.mni.mcgill.ca/pipermail/minc-users/2007-September/001705.html > >> > _______________________________________________ > > -- > Best regards, > > Vladimir S. Fonov ~ vladimir fonov gmail com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sebastien.proulx2 at mcgill.ca Fri Apr 27 18:44:22 2012 From: sebastien.proulx2 at mcgill.ca (=?ISO-8859-1?Q?S=E9bastien_Proulx?=) Date: Fri, 27 Apr 2012 18:44:22 -0400 Subject: [MINC-users] Convert DICOM EPIs from 3D volumes to 2D slices Message-ID: <4F9B2146.8040101@mcgill.ca> Hello, This may sound unusual, but I have 3D EPI volumes stored in DICOMs (one volume per DICOM file) that I want to convert to 2D EPI slices, keeping the DICOM format (one slice per DICOM file). If it could some how help, I also have the volumes in one MINC file (all volumes of the series in one MINC file), but the goal is really to get an EPI volume stored in multiple DICOM files (one slice of the volume per file). I'm quite a newbie in that file handling business, but so far, I've only seen information on 2D to 3D conversion on the web... and I tried something called Debabeler (http://www.loni.ucla.edu/Software/Debabeler), but could even make it work. Thanks a lot for any suggestion! -- S?bastien Proulx McGill University (514) 398-6644 #00445 From a.janke at gmail.com Fri Apr 27 19:30:31 2012 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 28 Apr 2012 09:30:31 +1000 Subject: [MINC-users] Convert DICOM EPIs from 3D volumes to 2D slices In-Reply-To: <4F9B2146.8040101@mcgill.ca> References: <4F9B2146.8040101@mcgill.ca> Message-ID: Hi S?bastien > This may sound unusual, but I have 3D EPI volumes stored in DICOMs (one > volume per DICOM file) that I want to convert to 2D EPI slices, keeping the > DICOM format (one slice per DICOM file). If it could some how help, I also > have the volumes in one MINC file (all volumes of the series in one MINC > file), but the goal is really to get an EPI volume stored in multiple DICOM > files (one slice of the volume per file). The conversion from 3D MINC to 2D MINC is very straight forward, say you just wanted the 10th Z slice from a MINC volume, you would do this: mincreshape -dimrange zspace=10,0 3d.mnc 2.mnc The conversion to DICOM be it 2D or 3D is more problematic. a a From steve at sumost.ca Sat Apr 28 23:35:42 2012 From: steve at sumost.ca (Steve M. Robbins) Date: Sat, 28 Apr 2012 22:35:42 -0500 Subject: [MINC-users] Convert DICOM EPIs from 3D volumes to 2D slices In-Reply-To: <4F9B2146.8040101@mcgill.ca> References: <4F9B2146.8040101@mcgill.ca> Message-ID: <20120429033542.GL4832@sumost.ca> On Fri, Apr 27, 2012 at 06:44:22PM -0400, S?bastien Proulx wrote: > Hello, > > This may sound unusual, but I have 3D EPI volumes stored in DICOMs > (one volume per DICOM file) that I want to convert to 2D EPI slices, > keeping the DICOM format (one slice per DICOM file). If your input is the so-called "mosaic" format from Siemens, you can load the series back onto the Siemens console and use a tool there to export it in a normal series of 2D slices. Cheers, -Steve