From giovanna.pellecchia at camhpet.ca Wed Sep 9 14:51:44 2009 From: giovanna.pellecchia at camhpet.ca (Giovanna Pellecchia) Date: Wed, 9 Sep 2009 14:51:44 -0400 Subject: [MINC-users] mni_autoreg 0.99.6 Message-ID: Hi, I have encountered what seems to be a bug in release 0.99.6. When minctracc is called with the -vr option, it fails with the following error: minctracc -vr AC_mri.mnc AC_mri.mnc test.xfm COG of v1: -1.718248 29.835024 2.200544 COG of v2: -1.718248 29.835024 2.200544 [trans] = 0.000000 0.000000 0.000000 Error in minctracc in file segment_table.c, line 34 Currently an unsupported data type (8). Version 0.99.3 on the same system works correctly. The system is ubuntu ibex (2.6.27-14-generic #1 SMP Fri Jul 24 23:49:25 UTC 2009 x86_64 GNU/Linux), but I do not know whether this problem is restricted to the x86_64. All the minc tools have been compiled from the latest source packages from the bic, except for HDF5: libminc: 2.0.18 netcdf : 3.5.0 HDF5 : 1.6.9 Also, with the mni_autoreg version 0.99.6 the MRI to PET coregistrations seem to be quite off their targets. This is corrected in the 0.99.3 version (this might or might not be related to the bug above). I apologize if this issue is already known. Cheers, Giovanna. From sorench at gmail.com Thu Sep 10 07:38:30 2009 From: sorench at gmail.com (Soren Christensen) Date: Thu, 10 Sep 2009 21:38:30 +1000 Subject: [MINC-users] in plane Message-ID: Hi, I am trying to correct some dynamic perfusion CT data for motion. The slices are relatively thick at 12 mm and there are only 2 of them so coverage is sparse. It seems the main components of the motion are around the z axis so I am trying to constrain the registration to in-plane rotations (that way there is some data left to analyze as well). I am not sure if there is any straightforward way to do this with the MINC tools so I tried to add some lines to mritoself to pass through w_translations and w_rotations to minctracc. I would think that setting the following should achieve in plane translations and rotations only -w_rotations 0 0 0.017 -w_translations 1 1 0 But when I check the resulting xfm file that is not the case (verbose listing from mritoself at the end of this mail): xfm2param 18t00.xfm after parameter extraction -center 0.00000 0.00000 0.00000 -translation -1.60969 0.41978 -0.04529 -rotation 0.00000 0.00000 0.50024 -scale 1.00000 1.00000 1.00000 -shear 0.00000 0.00000 0.00000 The rotation bit seemed to work - but not translation. So where am I going wrong - and is there a way to do what I want? Thanks, Soren Verbose output from mritoself: pc-mugin /NEWCASTLE/mc_corr_tests# mymritoself -resample t.mnc -w_rotations 0 0 0.0174533 -w_translations 1 1 0 -keeptmp -clobber -far -verbose -nothreshold frame18.mnc frame00.mnc 18t00.xfm [mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10 21:28:57] /usr/local/mni2/bin/autocrop -clobber frame18.mnc /usr/tmp/mymritoself_16343//frame18_crop.mnc -step -0.4921875 -0.4921875 11.817999999999999616 -extend 0,0 0,0 0,0 -byte [autocrop] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10 21:28:57] /usr/local/mni2/bin/mincreshape -clobber -byte frame18.mnc /usr/tmp/mymritoself_16343//frame18_crop.mnc -start 0,0,-1 -count 2,512,513 Copying chunks:..Done. [mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10 21:28:57] /usr/local/mni2/bin/autocrop -clobber frame00.mnc /usr/tmp/mymritoself_16343//frame00_crop.mnc -step -0.4921875 -0.4921875 11.817999999999999616 -extend 0,0 0,0 0,0 -byte [autocrop] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10 21:28:57] /usr/local/mni2/bin/mincreshape -clobber -byte frame00.mnc /usr/tmp/mymritoself_16343//frame00_crop.mnc -start 0,0,-1 -count 2,512,513 Copying chunks:..Done. [mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10 21:28:57] /usr/local/mni2/bin/minctracc -clobber /usr/tmp/mymritoself_16343//frame18_crop.mnc /usr/tmp/mymritoself_16343//frame00_crop.mnc /usr/tmp/mymritoself_16343//18t00_tmp1.xfm -est_center -est_translations -lsq6 -mi -groups 256 -w_rotations 0 0 0.0174533 -w_translations 1 1 0 -step 7.3 7.3 7.3 -simplex 10 COG of v1: 3.561098 -68.172920 -620.482849 COG of v2: 1.893397 -68.351616 -620.528137 [trans] = -1.667701 -0.178696 -0.045288 Only center & trans required, now returning from init_transformation Initial objective function val = -1.36852753 Final objective function value = -1.41425633 [mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10 21:28:57] /usr/local/mni2/bin/minctracc -clobber /usr/tmp/mymritoself_16343//frame18_crop.mnc /usr/tmp/mymritoself_16343//frame00_crop.mnc 18t00.xfm -est_center -transformation /usr/tmp/mymritoself_16343//18t00_tmp1.xfm -lsq6 -mi -groups 256 -w_rotations 0 0 0.0174533 -w_translations 1 1 0 -step 4.3 4.3 4.3 -simplex 1.5 Initial objective function val = -1.41286337 Final objective function value = -1.41485536 [mymritoself] [soren at pc-mugin:/NEWCASTLE/mc_corr_tests] [2009-09-10 21:28:58] /usr/local/mni2/bin/mincresample -clobber frame18.mnc t.mnc -byte -transform 18t00.xfm -like /usr/tmp/mymritoself_16343//frame00_crop.mnc Transforming slices:..Done From a.janke at gmail.com Thu Sep 10 07:50:27 2009 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 10 Sep 2009 21:50:27 +1000 Subject: [MINC-users] in plane In-Reply-To: References: Message-ID: Hi Soren, > ?I am trying to correct some dynamic perfusion CT data for motion. > The slices are relatively thick at 12 mm and there are only 2 of them > so coverage is sparse. It seems the main components of the motion are > around the z axis so I am trying to constrain the registration to > in-plane rotations > > I am not sure if there is any straightforward way to do this with the > MINC tools so I tried to add some lines to mritoself to pass through > w_translations and w_rotations to minctracc. > > I would think that setting the following should achieve in plane > translations and rotations only > -w_rotations 0 0 0.017 > -w_translations 1 1 0 > > The rotation bit seemed to work - but not translation. > So where am I going wrong - and is there a way to do what I want? You certainly are on the right track and if you mess about with the weights enough it will eventually work... That said minctracc really is optimised for 3D only. So another approach I have used in these cases is to fake 3D data. In your case simply making the slices a whole lot thicker than they are and adding a blank slice top and bottom should make minctracc do what you want. (just run it as is without weights). The blank slices top and bottom are actually very important as it will give minctracc a bounds to work to. It may even work by simply doing this to your volumes: $ mincresample -dimrange zspace=-1,4 in.mnc out.mnc Once this is done then just pull the bits out the xfm that you want using xfm2param and make another using param2xfm. Another approach if you have single slice data is to duplicate the slice to make a "cylinder" of data. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From M.Bahri at ulg.ac.be Thu Sep 10 08:14:36 2009 From: M.Bahri at ulg.ac.be (Mohamed Ali Bahri) Date: Thu, 10 Sep 2009 14:14:36 +0200 Subject: [MINC-users] Siemens MicroCT image format to dicom ( .dcm) image format Message-ID: <4AA8EDAC.1000805@ulg.ac.be> Hi All, Are there any free software which read micrCT image format and convert it to dicom .dcm format? Thanks Mohamed From sorench at gmail.com Fri Sep 11 04:27:49 2009 From: sorench at gmail.com (Soren Christensen) Date: Fri, 11 Sep 2009 18:27:49 +1000 Subject: [MINC-users] in plane In-Reply-To: References: Message-ID: Thanks Andrew, That seems to work quite well when using the padding (with mincreshape) - much appreciated! In case others should ever struggle with this: I first padded as Andrew suggested, then forced the cosines to be aligned with world space (so voxel and world spaces are aligned). Then every padded frame was registered to a manually selected (also padded of course) target using xcorr (that seemed to make a noticeable difference to mi actually). I used w_translations and w_rotations as described below. I figure that if the cosines are not aligned with world space, then w_translations and w_rotations may not have the desired effect - not sure if this is correct, but it appeared to be the case. Then the original, non padded frames are resampled using the estimated xfms - I did not have to zero out any out of plane contributions as the w_translations and w_rotations did their job setting these contributions to zero. In the 20 cases I ran the correction did a good job. In some cases, judging from the skull thickness , there was out of plane motion and that can of course not be solved. I guess interpolating such frames temporally is the best option. Regards Soren On Thu, Sep 10, 2009 at 9:50 PM, Andrew Janke wrote: > Hi Soren, > >> ?I am trying to correct some dynamic perfusion CT data for motion. >> The slices are relatively thick at 12 mm and there are only 2 of them >> so coverage is sparse. It seems the main components of the motion are >> around the z axis so I am trying to constrain the registration to >> in-plane rotations >> >> I am not sure if there is any straightforward way to do this with the >> MINC tools so I tried to add some lines to mritoself to pass through >> w_translations and w_rotations to minctracc. >> >> I would think that setting the following should achieve in plane >> translations and rotations only >> -w_rotations 0 0 0.017 >> -w_translations 1 1 0 >> >> The rotation bit seemed to work - but not translation. >> So where am I going wrong - and is there a way to do what I want? > > You certainly are on the right track and if you mess about with the > weights enough it will eventually work... That said minctracc really > is optimised for 3D only. So another approach I have used in these > cases is to fake 3D data. > > In your case simply making the slices a whole lot thicker than they > are and adding a blank slice top and bottom should make minctracc do > what you want. ?(just run it as is without weights). > > The blank slices top and bottom are actually very important as it will > give minctracc a bounds to work to. It may even work by simply doing > this to your volumes: > > ? $ mincresample -dimrange zspace=-1,4 in.mnc out.mnc > > Once this is done then just pull the bits out the xfm that you want > using xfm2param and make another using param2xfm. > > Another approach if you have single slice data is to duplicate the > slice to make a "cylinder" of data. > > > -- > Andrew Janke > (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia ? ?+61 (402) 700 883 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From mishkind at gmail.com Sat Sep 12 02:09:17 2009 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Sat, 12 Sep 2009 02:09:17 -0400 Subject: [MINC-users] add a dimension to a minc file Message-ID: <9c5abb60909112309s4af7c6cao7e58ee380ac4971f@mail.gmail.com> Hello list, Is there a way to add a dimension (zspace) to a mincfile? I tried mincedit, but couldn't get it to save the header without errors. Example data: http://www.bic.mni.mcgill.ca/users/mishkin/no_zspace.mnc.gz I ask because I'm trying to resample one minc file to be like another, however, the minc files only have 2 dimensions (xspace,yspace), so mincresample doesn't work. Is there another way to accomplish "mincresample -like"? thanks, mishkin From a.janke at gmail.com Sat Sep 12 03:30:10 2009 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 12 Sep 2009 17:30:10 +1000 Subject: [MINC-users] add a dimension to a minc file In-Reply-To: <9c5abb60909112309s4af7c6cao7e58ee380ac4971f@mail.gmail.com> References: <9c5abb60909112309s4af7c6cao7e58ee380ac4971f@mail.gmail.com> Message-ID: > Is there a way to add a dimension (zspace) to a mincfile? I tried > mincedit, but couldn't get it to save the header without errors. Probably not easily... > I ask because I'm trying to resample one minc file to be like another, > however, the minc files only have 2 dimensions (xspace,yspace), so > mincresample doesn't work. Is there another way to accomplish > "mincresample -like"? I'd do this: mincconcat -concat_dimension zspace -start 0 -step 1 in.mnc in_z.mnc -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From mishkind at gmail.com Sat Sep 12 04:02:54 2009 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Sat, 12 Sep 2009 04:02:54 -0400 Subject: [MINC-users] add a dimension to a minc file In-Reply-To: References: <9c5abb60909112309s4af7c6cao7e58ee380ac4971f@mail.gmail.com> Message-ID: <9c5abb60909120102y73b9881en9170fad21d11bb70@mail.gmail.com> On Sat, Sep 12, 2009 at 3:30 AM, Andrew Janke wrote: >> Is there a way to add a dimension (zspace) to a mincfile? I tried >> mincedit, but couldn't get it to save the header without errors. > > Probably not easily... > >> I ask because I'm trying to resample one minc file to be like another, >> however, the minc files only have 2 dimensions (xspace,yspace), so >> mincresample doesn't work. Is there another way to accomplish >> "mincresample -like"? > > I'd do this: > > mincconcat -concat_dimension zspace -start 0 -step 1 in.mnc in_z.mnc mincconcat!!! seems there is always a minc* that I don't know about. That gets me the zspace direction (for which I am grateful), but sadly mincresample -like doesn't seem to work (produces an empty image). The -like file that goes along with the no_zspace.mnc.gz is here: http://www.bic.mni.mcgill.ca/users/mishkin/like.mnc.gz > > > -- > Andrew Janke > (a.janke at gmail.com || http://a.janke.googlepages.com/) > Canberra->Australia ? ?+61 (402) 700 883 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Sat Sep 12 04:43:39 2009 From: a.janke at gmail.com (Andrew Janke) Date: Sat, 12 Sep 2009 18:43:39 +1000 Subject: [MINC-users] add a dimension to a minc file In-Reply-To: <9c5abb60909120102y73b9881en9170fad21d11bb70@mail.gmail.com> References: <9c5abb60909112309s4af7c6cao7e58ee380ac4971f@mail.gmail.com> <9c5abb60909120102y73b9881en9170fad21d11bb70@mail.gmail.com> Message-ID: > That gets me the zspace direction (for which I am grateful), but sadly > mincresample -like doesn't seem to work (produces an empty image). > > The -like file that goes along with the no_zspace.mnc.gz is here: > http://www.bic.mni.mcgill.ca/users/mishkin/like.mnc.gz Well your like files zspace starts at 60 with a step of 3 and has one slice so it would only range between 60 and 63 in world zspace. Remember that mincreshape works in world co-ordinates so you'd have to make sure your data falls in this range. In other words: mincconcat -concat_dimension zspace start 60.7704 -step 3 in.mnc in_z.mnc -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From giovanna.pellecchia at camhpet.ca Tue Sep 15 13:25:24 2009 From: giovanna.pellecchia at camhpet.ca (Giovanna Pellecchia) Date: Tue, 15 Sep 2009 13:25:24 -0400 Subject: [MINC-users] mni_autoreg 0.99.6 In-Reply-To: <4aae6b55.4d44f10a.2377.ffffdbb6SMTPIN_ADDED@mx.google.com> References: <4aae6b55.4d44f10a.2377.ffffdbb6SMTPIN_ADDED@mx.google.com> Message-ID: <0794bb104ffc7898add41b656f8b4783@camhpet.ca> > This is not necessarily a bug but a (unnecessary) limitation. > That part of the code (which is used only with -vr) is identical > in 0.99.3 and 0.99.6. Thanks for the feedback - still, if the code is identical, then I do not understand why it fails in one case and not the other. Something must have changed between the two versions - my understanding is that the -vr option is seldom used, so probably it escaped notice so far. > Can you do a mincinfo on your mnc file? If it says float or > double, that's the problem. For the purpose of registration, > you can convert it to unsigned short (use mincreshape -unsigned > -short). If the problem persists, let me know. I know that > there was a recent change to convert the image values to float > internally, but I think this happens later in the code. > > bye > > Claude > I checked my images and they're all signed short. After switching back to minctracc version 0.99.3, they work without problems. Thanks, Giovanna. >>> I have encountered what seems to be a bug in release >>> 0.99.6. When >>> minctracc is called with the -vr option, it fails with the >>> following >>> error: >>> >>> minctracc -vr AC_mri.mnc AC_mri.mnc test.xfm >>> COG of v1: -1.718248 29.835024 2.200544 >>> COG of v2: -1.718248 29.835024 2.200544 >>> [trans] = 0.000000 0.000000 0.000000 >>> >>> Error in minctracc in file segment_table.c, line 34 >>> Currently an unsupported data type (8). >>> >>> Version 0.99.3 on the same system works correctly. >>> The system is ubuntu ibex (2.6.27-14-generic #1 SMP Fri Jul >>> 24 23:49:25 >>> UTC 2009 x86_64 GNU/Linux), but I do not know whether this >>> problem is >>> restricted to the x86_64. All the minc tools have been >>> compiled from >>> the latest source packages from the bic, except for HDF5: >>> libminc: 2.0.18 >>> netcdf : 3.5.0 >>> HDF5 : 1.6.9 >>> >>> Also, with the mni_autoreg version 0.99.6 the MRI to PET >>> coregistrations seem to be quite off their targets. This is >>> corrected >>> in the 0.99.3 version (this might or might not be related >>> to the bug >>> above). _________________________ Giovanna Pellecchia Research Analyst Toronto Western Hospital & CAMH-PET Imaging Center 250 College Street Toronto, Ontario Canada M5T 1R8 Ph: 416-535-8501x7395 Fax: 416-979-3855 Email: giovanna.pellecchia at camhpet.ca From eavanih at email.chop.edu Wed Sep 16 10:07:14 2009 From: eavanih at email.chop.edu (Harini Eavani) Date: Wed, 16 Sep 2009 10:07:14 -0400 Subject: [MINC-users] Installation issues - make check fails Message-ID: <4AB0B8D2020000FA0000D86A@email.chop.edu> Hello list-users, I am having trouble with one of the binaries in the N3 software. make check fails on test 8 and passes successfully on the other 7 tests. I have installed: N3-1.11.0 EBTKS-1.6.2 MINC-2.0.12 NetCDF-4.0.1 HDF5-1.8.3 Here is the relevant portion of test.log : Running test #8 nu_estimate_np_and_em -distance 100 -b_spline 1 -spline_subsample 2 -auto_mask -iterations 2 -stop 0.001 -shrink 2 -sharpen 0.15 0.01 -parzen ./brain.mnc.gz /usr/tmp/do_test_10495//brain.imp -verbose [root at cortex:/usr/local/N3-1.11.0/testing/] [2009-09-16 09:53:24] running: /usr/local/mni/bin/nu_estimate_np_and_em -distance 100 -b_spline 1 -spline_subsample 2 -auto_mask -iterations 2 -stop 0.001 -shrink 2 -sharpen 0.15 0.01 -parzen ./brain.mnc.gz /usr/tmp/do_test_10495//brain.imp -verbose Uncorrected volume (input): ./brain.mnc.gz Intensity mapping (output): /usr/tmp/do_test_10495//brain.imp # Start of NU estimation algorithm [nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincresample -clobber -verbose -nearest_neighbour -nelements 46 55 46 -step 4 4 4 ./brain.mnc.gz /usr/tmp/nu_estimate_np_and_em_10558/brain.mnc Transforming slices:..............................................Done [nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincmath -clobber -verbose -clamp -const2 1 1.7e+308 /usr/tmp/nu_estimate_np_and_em_10558/brain.mnc /usr/tmp/nu_estimate_np_and_em_10558/brain_log.mnc.temp Processing:..............................................Done [nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincmath -clobber -verbose -zero -log /usr/tmp/nu_estimate_np_and_em_10558/brain_log.mnc.temp /usr/tmp/nu_estimate_np_and_em_10558/brain_log.mnc Processing:..............................................Done [nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /bin/rm /usr/tmp/nu_estimate_np_and_em_10558/brain_log.mnc.temp [nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincinfo -attvalue xspace:spacetype -attvalue yspace:spacetype -attvalue zspace:spacetype /usr/tmp/nu_estimate_np_and_em_10558/brain.mnc # input volume is in Talairach space # thresholding background [nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincmath -clobber -verbose -short -zero -gt -const 1 /usr/tmp/nu_estimate_np_and_em_10558/brain.mnc /usr/tmp/nu_estimate_np_and_em_10558/brain_bkg.mnc Processing:..............................................Done # using average brain mask to remove background Resampling /usr/local/mni/bin/../share/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz like /usr/tmp/nu_estimate_np_and_em_10558/brain_bkg.mnc [nu_estimate_np_and_em] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/resample_labels -clobber -verbose -resample '-like /usr/tmp/nu_estimate_np_and_em_10558/brain_bkg.mnc' /usr/local/mni/bin/../share/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz /usr/tmp/nu_estimate_np_and_em_10558/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.temp [resample_labels] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/mincresample /usr/local/mni/bin/../share/N3/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.gz /usr/tmp/resample_labels_10573/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc_rsl.mnc -trilinear -byte -like /usr/tmp/nu_estimate_np_and_em_10558/brain_bkg.mnc Transforming slices:..............................................Done [resample_labels] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/extracttag /usr/tmp/resample_labels_10573/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc_rsl.mnc -volume /usr/tmp/nu_estimate_np_and_em_10558/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.temp -threshold 0.5 1.1 -label 1 -maxtags 0 Updating history (from miopen): Can't write compressed file ncredef: ncid -1: NetCDF: Not a valid ID ncattput: ncid -1: NetCDF: Not a valid ID ncclose: ncid -1: NetCDF: Not a valid ID resample_labels: crashed while running minc_modify_header (termination status=768) nu_estimate_np_and_em: crashed while running resample_labels (termination status=768) -------------------------------------------------------- Test #8 suffered a fatal error. Consult the file N3/testing/test.log for details and compare with N3/testing/test_ref.log, a log from a sucessful run of the test suite. Any help is appreciated. Thanks! Harini Eavani Research Data Analyst Center for Autism Research Children's Hospital of Philadelphia 3535 Market Street, Suite 860 Philadelphia, PA 19104 From claude at bic.mni.mcgill.ca Wed Sep 16 10:26:45 2009 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Wed, 16 Sep 2009 10:26:45 -0400 Subject: [MINC-users] Installation issues - make check fails In-Reply-To: <4AB0B8D2020000FA0000D86A@email.chop.edu> Message-ID: <200909161426.n8GEQjaB027486@grumio.bic.mni.mcgill.ca> Hi, > I am having trouble with one of the binaries in the N3 software. make check fails on test 8 and passes successfully on the other 7 tests. > > I have installed: > N3-1.11.0 > EBTKS-1.6.2 > MINC-2.0.12 > NetCDF-4.0.1 > HDF5-1.8.3 > > Here is the relevant portion of test.log : > > [resample_labels] [root at cortex:/usr/local/N3-1.11.0/testing] [2009-09-16 09:53:24] /usr/local/mni/bin/extracttag /usr/tmp/resample_labels_10573/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc_rsl.mnc -volume /usr/tmp/nu_estimate_np_and_em_10558/icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc.temp -threshold 0.5 1.1 -label 1 -maxtags 0 > Updating history > (from miopen): Can't write compressed file > ncredef: ncid -1: NetCDF: Not a valid ID > ncattput: ncid -1: NetCDF: Not a valid ID > ncclose: ncid -1: NetCDF: Not a valid ID > resample_labels: crashed while running minc_modify_header (termination status=768) > nu_estimate_np_and_em: crashed while running resample_labels (termination status=768) I don't know if this will solve the problem, but netcdf-4 has not been tested with minc. The API changed from version 3 to 4, so there might be some incompatibilities. I suggest you link with netcdf 3.6.1 (which I know works). Similarly, we use hdf5 1.6.6. I haven't tested 1.8.X. And while you are at it, why not use minc-2.0.18? 2.0.12 is old and many bugs have been fixed since then. Moreover, 2.0.18 offers much better/faster internal compression. Make sure to activate minc2 compression using the shell environment variables MINC_FORCE_V2=1 and MINC_COMPRESS=4. Let me know if this works. Claude From sean at rogue-research.com Wed Sep 16 10:36:25 2009 From: sean at rogue-research.com (Sean McBride) Date: Wed, 16 Sep 2009 10:36:25 -0400 Subject: [MINC-users] Installation issues - make check fails In-Reply-To: <200909161426.n8GEQjaB027486@grumio.bic.mni.mcgill.ca> References: <4AB0B8D2020000FA0000D86A@email.chop.edu> <200909161426.n8GEQjaB027486@grumio.bic.mni.mcgill.ca> Message-ID: <20090916143625.1099197234@kingu.local> On 9/16/09 10:26 AM, Claude LEPAGE said: >I don't know if this will solve the problem, but netcdf-4 has not been >tested with minc. The API changed from version 3 to 4, so there might be >some incompatibilities. I suggest you link with netcdf 3.6.1 (which I >know works). Similarly, we use hdf5 1.6.6. I haven't tested 1.8.X. NetCDF 4.0.1 is working well for me, one minor codechange was needed, which I believe is now in MINC CVS. >And while you are at it, why not use minc-2.0.18? 2.0.12 is old and many >bugs have been fixed since then. Moreover, 2.0.18 offers much better/faster >internal compression. Make sure to activate minc2 compression using the >shell environment variables MINC_FORCE_V2=1 and MINC_COMPRESS=4. Maybe because 2.0.12 is the newest version listed! :( See -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From a.janke at gmail.com Wed Sep 16 22:35:39 2009 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 17 Sep 2009 12:35:39 +1000 Subject: [MINC-users] Installation issues - make check fails In-Reply-To: <4AB0B8D2020000FA0000D86A@email.chop.edu> References: <4AB0B8D2020000FA0000D86A@email.chop.edu> Message-ID: Hi Harini, On Thu, Sep 17, 2009 at 00:07, Harini Eavani wrote: > I am having trouble with one of the binaries in the N3 software. make check fails on test 8 and passes successfully on the other 7 tests. > > Updating history > (from miopen): Can't write compressed file > ncredef: ncid -1: NetCDF: Not a valid ID > ncattput: ncid -1: NetCDF: Not a valid ID > ncclose: ncid -1: NetCDF: Not a valid ID > resample_labels: crashed while running minc_modify_header (termination status=768) > nu_estimate_np_and_em: crashed while running resample_labels (termination status=768) You can safely ignore this error, it has been fixed in CVS for a while but we haven't made a new release of N3. The bug was a compressed file that shouldn't have been. Andrew From davids at bic.mni.mcgill.ca Thu Sep 17 18:28:50 2009 From: davids at bic.mni.mcgill.ca (David Seminowicz) Date: Thu, 17 Sep 2009 18:28:50 -0400 Subject: [MINC-users] philips PAR REC to minc Message-ID: <001801ca37e6$4fcf9390$ef6ebab0$@mni.mcgill.ca> Hello, does anyone have a good way to convert Philips .PAR/.REC files to minc? I?ve been using r2agui ? a matlab program ? but I?m having problems with it. Thanks, Dave ______________________ David A. Seminowicz, Ph.D. Postdoctoral Fellow Alan Edwards Centre for Research on Pain McGill University Rm M/19 Strathcona Anatomy & Dentistry 3640 University St. Montreal, Quebec H3A 2B2 ? Ph: 514.398.1271 Fax: 514.398.7464 From dcb210 at psu.edu Fri Sep 18 13:39:43 2009 From: dcb210 at psu.edu (Don Bigler) Date: Fri, 18 Sep 2009 13:39:43 -0400 Subject: [MINC-users] philips PAR REC to minc Message-ID: David, I haven't used the MINC tools in a long time, but I still happen to be on the users list. You could use ITK to create a converter. ITK supports reading PAR/REC (http://www.itk.org/cgi-bin/viewcvs.cgi/Code/Review/itkPhilipsRECImageIO.h?root=Insight&view=markup ) and I believe read/write to minc2 (http://www.itk.org/cgi-bin/viewcvs.cgi/Code/Review/itkMINC2ImageIO.h?root=Insight&view=markup ). An example of how to create a reader and writer using C++ is given in the ITK user's guide (http://www.itk.org/ItkSoftwareGuide.pdf). I hope this helps! Don Bigler From mccreedy at mail.nih.gov Fri Sep 18 15:34:09 2009 From: mccreedy at mail.nih.gov (McCreedy, Evan (NIH/CIT) [E]) Date: Fri, 18 Sep 2009 15:34:09 -0400 Subject: [MINC-users] philips PAR REC to minc In-Reply-To: References: Message-ID: Hello David, You might want to give our software, MIPAV, a try (a Java-based image processing application at http://mipav.cit.nih.gov). We support reading most Par/Rec files and writing to Minc 1 or Minc 2. A couple of caveats: our Minc writer support is currently limited to 3D volumes and only the basic image meta-information will make it over to the Minc file (origin, resolutions, orientation, etc.) Let me know if you have any questions. Evan ------ Evan McCreedy Computer Scientist BIRSS/ISL/DCB/CIT/NIH From rupert.brooks at gmail.com Tue Sep 22 07:21:47 2009 From: rupert.brooks at gmail.com (Rupert Brooks) Date: Tue, 22 Sep 2009 07:21:47 -0400 Subject: [MINC-users] philips PAR REC to minc In-Reply-To: References: Message-ID: <1c32ff3d0909220421x9669126vffbef4929c5f4c24@mail.gmail.com> hi Dave, Did you find a solution to your conversion problem? If not I can hook you up with ITK based code i wrote during my thesis, which can use the ITK conversion ability. However, the ITK minc converter had certain limitations last i used it (a year ago, in fairness) and so MIPAV might be the better solution for you. If you are still stuck though, let me know - quicker than writing your own unless you know ITK well. Cheers, Rupert -------------------------------------------------------------- Rupert Brooks rupert.brooks at gmail.com On Fri, Sep 18, 2009 at 13:39, Don Bigler wrote: > David, > ? ? ? ?I haven't used the MINC tools in a long time, but I still happen to > be on the users list. ?You could use ITK to create a converter. ?ITK > supports reading PAR/REC (http://www.itk.org/cgi-bin/viewcvs.cgi/Code/Review/itkPhilipsRECImageIO.h?root=Insight&view=markup > ) and I believe read/write to minc2 (http://www.itk.org/cgi-bin/viewcvs.cgi/Code/Review/itkMINC2ImageIO.h?root=Insight&view=markup > ). > ? ? ? ?An example of how to create a reader and writer using C++ is given in > the ITK user's guide (http://www.itk.org/ItkSoftwareGuide.pdf). > ? ? ? ?I hope this helps! > Don Bigler > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From davids at bic.mni.mcgill.ca Tue Sep 22 13:50:53 2009 From: davids at bic.mni.mcgill.ca (David Seminowicz) Date: Tue, 22 Sep 2009 13:50:53 -0400 Subject: [MINC-users] philips PAR REC to minc In-Reply-To: <1c32ff3d0909220421x9669126vffbef4929c5f4c24@mail.gmail.com> References: <1c32ff3d0909220421x9669126vffbef4929c5f4c24@mail.gmail.com> Message-ID: <002101ca3bad$50aff410$f20fdc30$@mni.mcgill.ca> Thanks Evan, Don, and Rupert. I gave MIPAV a quick try and it works well although I'm having a few issues with orientation, which I haven't had a chance yet to work out (MIPAV looks like a really useful program that I wasn't aware of, so thanks for pointing it out to me). Rupert, I wouldn't mind checking out your ITK code if you don't mind sharing. dave -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Rupert Brooks Sent: Tuesday, September 22, 2009 7:22 AM To: MINC users mailing list Subject: Re: [MINC-users] philips PAR REC to minc hi Dave, Did you find a solution to your conversion problem? If not I can hook you up with ITK based code i wrote during my thesis, which can use the ITK conversion ability. However, the ITK minc converter had certain limitations last i used it (a year ago, in fairness) and so MIPAV might be the better solution for you. If you are still stuck though, let me know - quicker than writing your own unless you know ITK well. Cheers, Rupert -------------------------------------------------------------- Rupert Brooks rupert.brooks at gmail.com On Fri, Sep 18, 2009 at 13:39, Don Bigler wrote: > David, > ? ? ? ?I haven't used the MINC tools in a long time, but I still happen to > be on the users list. ?You could use ITK to create a converter. ?ITK > supports reading PAR/REC (http://www.itk.org/cgi-bin/viewcvs.cgi/Code/Review/itkPhilipsRECImageIO.h?r oot=Insight&view=markup > ) and I believe read/write to minc2 (http://www.itk.org/cgi-bin/viewcvs.cgi/Code/Review/itkMINC2ImageIO.h?root=I nsight&view=markup > ). > ? ? ? ?An example of how to create a reader and writer using C++ is given in > the ITK user's guide (http://www.itk.org/ItkSoftwareGuide.pdf). > ? ? ? ?I hope this helps! > Don Bigler > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From davids at bic.mni.mcgill.ca Tue Sep 22 13:53:31 2009 From: davids at bic.mni.mcgill.ca (David Seminowicz) Date: Tue, 22 Sep 2009 13:53:31 -0400 Subject: [MINC-users] philips PAR REC to minc In-Reply-To: <1c32ff3d0909220421x9669126vffbef4929c5f4c24@mail.gmail.com> References: <1c32ff3d0909220421x9669126vffbef4929c5f4c24@mail.gmail.com> Message-ID: <002201ca3bad$ae1a7170$0a4f5450$@mni.mcgill.ca> Thanks Evan, Don, and Rupert. I gave MIPAV a quick try and it works well although I'm having a few issues with orientation, which I haven't had a chance yet to work out (MIPAV looks like a really useful program that I wasn't aware of, so thanks for pointing it out to me). Rupert, I wouldn't mind checking out your ITK code if you don't mind sharing. dave -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Rupert Brooks Sent: Tuesday, September 22, 2009 7:22 AM To: MINC users mailing list Subject: Re: [MINC-users] philips PAR REC to minc hi Dave, Did you find a solution to your conversion problem? If not I can hook you up with ITK based code i wrote during my thesis, which can use the ITK conversion ability. However, the ITK minc converter had certain limitations last i used it (a year ago, in fairness) and so MIPAV might be the better solution for you. If you are still stuck though, let me know - quicker than writing your own unless you know ITK well. Cheers, Rupert -------------------------------------------------------------- Rupert Brooks rupert.brooks at gmail.com On Fri, Sep 18, 2009 at 13:39, Don Bigler wrote: > David, > ? ? ? ?I haven't used the MINC tools in a long time, but I still happen to > be on the users list. ?You could use ITK to create a converter. ?ITK > supports reading PAR/REC (http://www.itk.org/cgi-bin/viewcvs.cgi/Code/Review/itkPhilipsRECImageIO.h?r oot=Insight&view=markup > ) and I believe read/write to minc2 (http://www.itk.org/cgi-bin/viewcvs.cgi/Code/Review/itkMINC2ImageIO.h?root=I nsight&view=markup > ). > ? ? ? ?An example of how to create a reader and writer using C++ is given in > the ITK user's guide (http://www.itk.org/ItkSoftwareGuide.pdf). > ? ? ? ?I hope this helps! > Don Bigler > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From davids at bic.mni.mcgill.ca Sun Sep 27 17:17:33 2009 From: davids at bic.mni.mcgill.ca (David Seminowicz) Date: Sun, 27 Sep 2009 17:17:33 -0400 Subject: [MINC-users] determinant of non-linear local deformation fields (fwd) In-Reply-To: References: Message-ID: <000c01ca3fb8$037fcd00$0a7f6700$@mni.mcgill.ca> Hi Marc and others, did you ever find a good way to do modulated VBM with minc tools? dave -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Marc BOUFFARD Sent: Thursday, August 07, 2008 11:43 AM To: minc-users at bic.mni.mcgill.ca Subject: Re: [MINC-users] determinant of non-linear local deformation fields (fwd) On Fri, 1 Aug 2008, Andrew Janke wrote: > Hi Marc, > > On Wed, Jul 30, 2008 at 01:38, Marc BOUFFARD wrote: > > I have a question about deformation grids obtained from non-linear > > registration using nlpfit. These grids contain the 3D displacements at > > each voxel applied to the source to match the template or to the template > > to match the source? > > (note that this all presumes you did something like this: where > fred.mnc is our input subject) > > bestlinreg fred.mnc template.mnc linear_part.xfm > nlpfit -init_xfm linear_part.xfm fred.mnc template.mnc nonlinear_part.xfm > > If this is so then the nlxfm is from the source to the target. (after > the linear transformation if there is one). This incidentally is why > we calculate a model to individual transformation when we want to > average a number of transformations during building a model. > > > Now if the determinant is calculated from those grids with mincblob and it > > is found that voxel x has a value greater than 1. Does this mean the > > region in the neighborhood of x has expanded relative to the source or > > relative to the target? > > Perhaps best by example: > > 0.5 == the area in question is 50% smaller in the template than the source > 1 == no change > 1.5 == the area in question is 50% larger in the template than the source. > > > In a further step, to obtain modulated VBM data should the standard VBM > > data be multiplied by the determinant of the Jacobian matrix or its > > inverse? > > You lost me, what do you define as "modulated" VBM data? I would take > a punt there are a few different takes on it. > I am trying to apply the method used in SPM VBM but with the minc tools. Assuming we have the gray matter classified images linearly transformed then in "standard VBM" we would just apply the linear model to that and solve for a contrast of interest with glim_image, e.g., group 1 - group 2. Now, if the data is additionally non-linearly transformed another step called modulation can be applied: "in order to preserve the actual amounts of gray matter within each structure, a further processing step that multiplies (modulates) the images by the relative voxel volumes can be incorporated. These relative volumes are simply the Jacobian determinants of the deformation field." (Ashburner and Friston, Neuroimage 11 805-821) So according to that we just need to multiply by the Jacobian determinants but apparently the deformation fields calculated in SPM are relative to the target and not the source like with nlpfit (does that make sense?). So, logically if the deformation fields are relative to the source to the target(as you mention above) we should multiply by the voxel-wise inverse of the Jacobian determinant to get the same effect as with SPM? Marc _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Tue Sep 29 17:32:40 2009 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 30 Sep 2009 07:32:40 +1000 Subject: [MINC-users] determinant of non-linear local deformation fields (fwd) In-Reply-To: <000c01ca3fb8$037fcd00$0a7f6700$@mni.mcgill.ca> References: <000c01ca3fb8$037fcd00$0a7f6700$@mni.mcgill.ca> Message-ID: Hi Dave, On Mon, Sep 28, 2009 at 07:17, David Seminowicz wrote: > Hi Marc and others, did you ever find a good way to do modulated VBM with > minc tools? ?dave I am not quite sure what you mean by a good way. Certainly you can do such an analysis (as described in the previous message). If you mean is there is single button to press to do this then the answer is no. Thanks -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From davids at bic.mni.mcgill.ca Tue Sep 29 19:26:54 2009 From: davids at bic.mni.mcgill.ca (David Seminowicz) Date: Tue, 29 Sep 2009 19:26:54 -0400 Subject: [MINC-users] determinant of non-linear local deformation fields (fwd) In-Reply-To: References: <000c01ca3fb8$037fcd00$0a7f6700$@mni.mcgill.ca> Message-ID: <000301ca415c$69b61de0$3d2259a0$@mni.mcgill.ca> Hi Andrew, just wondering if anyone out there is doing modulated vbm and has step-by-step instructions before I attempt to figure it out. dave -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke Sent: Tuesday, September 29, 2009 5:33 PM To: MINC users mailing list Subject: Re: [MINC-users] determinant of non-linear local deformation fields (fwd) Hi Dave, On Mon, Sep 28, 2009 at 07:17, David Seminowicz wrote: > Hi Marc and others, did you ever find a good way to do modulated VBM with > minc tools? ?dave I am not quite sure what you mean by a good way. Certainly you can do such an analysis (as described in the previous message). If you mean is there is single button to press to do this then the answer is no. Thanks -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users