From penhunelab at gmail.com Tue Jun 3 15:54:37 2008 From: penhunelab at gmail.com (Penhune Lab) Date: Tue, 3 Jun 2008 15:54:37 -0400 Subject: [MINC-users] Multistat error - ??? Maximum variable size allowed by the program is exceeded. Message-ID: Greetings! I am getting the following error from a multistat script that I have successfully used for ... about 15 other analyses. Any ideas? Cheers, Chris ??? Maximum variable size allowed by the program is exceeded. Error in ==> multistat>regularized_df at 809 ker_x=exp(-(-ceil(fwhm_x):ceil(fwhm_x)).^2*4*log(2)/fwhm_x^2); Error in ==> multistat at 418 [df, ker_x, ker_y, K]=regularized_df(fwhm_varatio,D,Steps,numslices,df,fwhm_data); All I am doing is averaging three files with the following code: (each of the three files is the result of a covariation analysis of 15 Ss with their Bx scores) input_files_effect = ['Lonlycov_PCOR_d1r1_ef.mnc';'Lonlycov_PCOR_d1r2_ef.mnc';'Lonlycov_PCOR_d1r3_ef.mnc']; input_files_sdeffect = ['Lonlycov_PCOR_d1r1_sd.mnc';'Lonlycov_PCOR_d1r2_sd.mnc';'Lonlycov_PCOR_d1r3_sd.mnc']; x = [ones(size(input_files_effect,1),1)] contrast = [1]; input_files_df = []; input_files_fwhm = []; which_stats = '_t _ef _sd _fwhm'; fwhm_varatio = -100; df = multistat(input_files_effect, input_files_sdeffect, input_files_df, input_files_fwhm, x, contrast, output_file_base, which_stats, fwhm_varatio); -- Laboratory for Motor Learning and Neural Plasticity Directed by Dr. Virginia Penhune Department of Psychology, Concordia University SP-A 244, 7141 Sherbrooke St. W Montreal, QC H4B 1R6 Canada (514)848-2424 ext. 7567 http://psychology.concordia.ca/fac/penhune/winindex.html From a.janke at gmail.com Wed Jun 4 17:32:55 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 5 Jun 2008 07:32:55 +1000 Subject: [MINC-users] Multistat error - ??? Maximum variable size allowed by the program is exceeded. In-Reply-To: References: Message-ID: Hi, This really is one for Keith Worsley given that fmristat is his baby, I am unsure if he still reads this list so perhaps send him an email directly. a On Wed, Jun 4, 2008 at 5:54 AM, Penhune Lab wrote: > Greetings! > > I am getting the following error from a multistat script that I have > successfully used for ... about 15 other analyses. Any ideas? > > Cheers, > Chris > > ??? Maximum variable size allowed by the program is exceeded. > > Error in ==> multistat>regularized_df at 809 > ker_x=exp(-(-ceil(fwhm_x):ceil(fwhm_x)).^2*4*log(2)/fwhm_x^2); > > Error in ==> multistat at 418 > [df, ker_x, ker_y, > K]=regularized_df(fwhm_varatio,D,Steps,numslices,df,fwhm_data); > > All I am doing is averaging three files with the following code: (each of > the three files is the result of a covariation analysis of 15 Ss with their > Bx scores) > > input_files_effect = > ['Lonlycov_PCOR_d1r1_ef.mnc';'Lonlycov_PCOR_d1r2_ef.mnc';'Lonlycov_PCOR_d1r3_ef.mnc']; > input_files_sdeffect = > ['Lonlycov_PCOR_d1r1_sd.mnc';'Lonlycov_PCOR_d1r2_sd.mnc';'Lonlycov_PCOR_d1r3_sd.mnc']; > > x = [ones(size(input_files_effect,1),1)] > contrast = [1]; > input_files_df = []; > input_files_fwhm = []; > which_stats = '_t _ef _sd _fwhm'; > fwhm_varatio = -100; > df = multistat(input_files_effect, input_files_sdeffect, input_files_df, > input_files_fwhm, x, contrast, output_file_base, which_stats, fwhm_varatio); > > -- > Laboratory for Motor Learning and Neural Plasticity > Directed by Dr. Virginia Penhune > Department of Psychology, Concordia University > SP-A 244, 7141 Sherbrooke St. W > Montreal, QC H4B 1R6 Canada > (514)848-2424 ext. 7567 > http://psychology.concordia.ca/fac/penhune/winindex.html > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From mferre at bic.mni.mcgill.ca Wed Jun 4 17:46:32 2008 From: mferre at bic.mni.mcgill.ca (Michael Ferreira) Date: Wed, 04 Jun 2008 17:46:32 -0400 Subject: [MINC-users] Multistat error - ??? Maximum variable size allowed by the program is exceeded. In-Reply-To: References: Message-ID: <48470D38.1040405@bic.mni.mcgill.ca> Hi Chris, Ditto to what Andrew said. I don't see anything wrong w/ your code. And I've never come across that error before. So this is certainly one for Prof. Worsley. mike Andrew Janke wrote: > Hi, > > This really is one for Keith Worsley given that fmristat is his baby, > I am unsure if he still reads this list so perhaps send him an email > directly. > > > a > > On Wed, Jun 4, 2008 at 5:54 AM, Penhune Lab wrote: > >>Greetings! >> >>I am getting the following error from a multistat script that I have >>successfully used for ... about 15 other analyses. Any ideas? >> >>Cheers, >>Chris >> >>??? Maximum variable size allowed by the program is exceeded. >> >>Error in ==> multistat>regularized_df at 809 >> ker_x=exp(-(-ceil(fwhm_x):ceil(fwhm_x)).^2*4*log(2)/fwhm_x^2); >> >>Error in ==> multistat at 418 >> [df, ker_x, ker_y, >>K]=regularized_df(fwhm_varatio,D,Steps,numslices,df,fwhm_data); >> >>All I am doing is averaging three files with the following code: (each of >>the three files is the result of a covariation analysis of 15 Ss with their >>Bx scores) >> >>input_files_effect = >>['Lonlycov_PCOR_d1r1_ef.mnc';'Lonlycov_PCOR_d1r2_ef.mnc';'Lonlycov_PCOR_d1r3_ef.mnc']; >>input_files_sdeffect = >>['Lonlycov_PCOR_d1r1_sd.mnc';'Lonlycov_PCOR_d1r2_sd.mnc';'Lonlycov_PCOR_d1r3_sd.mnc']; >> >>x = [ones(size(input_files_effect,1),1)] >>contrast = [1]; >>input_files_df = []; >>input_files_fwhm = []; >>which_stats = '_t _ef _sd _fwhm'; >>fwhm_varatio = -100; >>df = multistat(input_files_effect, input_files_sdeffect, input_files_df, >>input_files_fwhm, x, contrast, output_file_base, which_stats, fwhm_varatio); >> >>-- >>Laboratory for Motor Learning and Neural Plasticity >>Directed by Dr. Virginia Penhune >>Department of Psychology, Concordia University >>SP-A 244, 7141 Sherbrooke St. W >>Montreal, QC H4B 1R6 Canada >>(514)848-2424 ext. 7567 >>http://psychology.concordia.ca/fac/penhune/winindex.html >>_______________________________________________ >>MINC-users at bic.mni.mcgill.ca >>http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > > From bouffard at bic.mni.mcgill.ca Thu Jun 5 09:00:47 2008 From: bouffard at bic.mni.mcgill.ca (Marc BOUFFARD) Date: Thu, 5 Jun 2008 09:00:47 -0400 Subject: [MINC-users] Multistat error - ??? Maximum variable size allowed by the program is exceeded. In-Reply-To: <48470D38.1040405@bic.mni.mcgill.ca> References: <48470D38.1040405@bic.mni.mcgill.ca> Message-ID: Hi Chris, I have encountered this error before: try fwhm_varatio = inf instead of -100 which gives a fixed effects analysis which seems to be what the error is telling you in this case. I think (to be confirmed) that this is a bug whithin multistat. It is related to this section of the code in multistat: ******************************************************************* if fwhm_varatio<0 % find fwhm to achieve target df: df_target=-fwhm_varatio; fwhm_varatio_limit=50; ff=0:1:100; dfs=[]; for f=ff; df=regularized_df(f,D,Steps,numslices,df,fwhm_data); dfs=[dfs df.t]; end fwhm_varatio=interp1(dfs,ff,df_target); if isnan(fwhm_varatio) | fwhm_varatio > fwhm_varatio_limit fwhm_varatio=Inf; varatio_vol=zeros(numpix,numslices); end fwhm_varatio end [df, ker_x, ker_y, K]=regularized_df(fwhm_varatio,D,Steps,numslices,df,fwhm_data); df.rfx=round(df.rfx); df.t=round(df.t); if fwhm_varatio>0 & fwhm_varatio fwhm_varatio_limit it tries to calculate regularized_df which gives an error. Instead it should go directly to: else df.rfx=Inf; df.t=df.fixed; end On Wed, 4 Jun 2008, Michael Ferreira wrote: > Hi Chris, > > Ditto to what Andrew said. > > I don't see anything wrong w/ your code. And I've never come across > that error before. So this is certainly one for Prof. Worsley. > > mike > > > Andrew Janke wrote: > > Hi, > > > > This really is one for Keith Worsley given that fmristat is his baby, > > I am unsure if he still reads this list so perhaps send him an email > > directly. > > > > > > a > > > > On Wed, Jun 4, 2008 at 5:54 AM, Penhune Lab wrote: > > > >>Greetings! > >> > >>I am getting the following error from a multistat script that I have > >>successfully used for ... about 15 other analyses. Any ideas? > >> > >>Cheers, > >>Chris > >> > >>??? Maximum variable size allowed by the program is exceeded. > >> > >>Error in ==> multistat>regularized_df at 809 > >> ker_x=exp(-(-ceil(fwhm_x):ceil(fwhm_x)).^2*4*log(2)/fwhm_x^2); > >> > >>Error in ==> multistat at 418 > >> [df, ker_x, ker_y, > >>K]=regularized_df(fwhm_varatio,D,Steps,numslices,df,fwhm_data); > >> > >>All I am doing is averaging three files with the following code: (each of > >>the three files is the result of a covariation analysis of 15 Ss with their > >>Bx scores) > >> > >>input_files_effect = > >>['Lonlycov_PCOR_d1r1_ef.mnc';'Lonlycov_PCOR_d1r2_ef.mnc';'Lonlycov_PCOR_d1r3_ef.mnc']; > >>input_files_sdeffect = > >>['Lonlycov_PCOR_d1r1_sd.mnc';'Lonlycov_PCOR_d1r2_sd.mnc';'Lonlycov_PCOR_d1r3_sd.mnc']; > >> > >>x = [ones(size(input_files_effect,1),1)] > >>contrast = [1]; > >>input_files_df = []; > >>input_files_fwhm = []; > >>which_stats = '_t _ef _sd _fwhm'; > >>fwhm_varatio = -100; > >>df = multistat(input_files_effect, input_files_sdeffect, input_files_df, > >>input_files_fwhm, x, contrast, output_file_base, which_stats, fwhm_varatio); > >> > >>-- > >>Laboratory for Motor Learning and Neural Plasticity > >>Directed by Dr. Virginia Penhune > >>Department of Psychology, Concordia University > >>SP-A 244, 7141 Sherbrooke St. W > >>Montreal, QC H4B 1R6 Canada > >>(514)848-2424 ext. 7567 > >>http://psychology.concordia.ca/fac/penhune/winindex.html > >>_______________________________________________ > >>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 mishkind at gmail.com Thu Jun 5 17:05:10 2008 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Thu, 5 Jun 2008 17:05:10 -0400 Subject: [MINC-users] nu_correct directory problems Message-ID: <9c5abb60806051405r4ba29de3k7a6c9bfbb2858029@mail.gmail.com> Hi, I am trying to call nu_correct from perl: ie. #! /usr/bin/perl chdir("/mydir/"); system("nu_correct -iter 150 -stop 5e-05 -normalize_field file_nu_0.mnc.gz file_nu_1.mnc"); If I run this from the command line, ie. opus[~]$ cd /mydir opus[/mydir]$ nu_correct -iter 150 -stop 5e-05 -normalize_field file_nu_0.mnc.gz file_nu_1.mnc Then everything works fine. If however, I do this: opus[~]$ ./perlscript.pl Then I always get the same error: Cannot open .imp file: file_nu_1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) The problem seems to be that the .imp file is getting saved to the directory I was in before I ran my perl script, and not to /mydir. I suspect this has something to do with using chdir() in perl, and to how nu_correct is calculating what its current directory. Any tips? thanks, mishkin opus[~]$ `which nu_correct` -version Program nu_correct, built from: Package MNI N3, version 1.10.1, compiled by rotor at ben (x86_64-unknown-linux-gnu) on 2007-11-07 at 11:54:01 From a.janke at gmail.com Thu Jun 5 17:16:44 2008 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 6 Jun 2008 07:16:44 +1000 Subject: [MINC-users] nu_correct directory problems In-Reply-To: <9c5abb60806051405r4ba29de3k7a6c9bfbb2858029@mail.gmail.com> References: <9c5abb60806051405r4ba29de3k7a6c9bfbb2858029@mail.gmail.com> Message-ID: Hi Mishkin, On Fri, Jun 6, 2008 at 7:05 AM, Mishkin Derakhshan wrote: > Hi, > I am trying to call nu_correct from perl: > ie. > #! /usr/bin/perl > chdir("/mydir/"); > system("nu_correct -iter 150 -stop 5e-05 -normalize_field > file_nu_0.mnc.gz file_nu_1.mnc"); > > If however, I do this: > opus[~]$ ./perlscript.pl > > Then I always get the same error: > Cannot open .imp file: file_nu_1.imp > nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) You are right that the chdir/system interaction is biting you (I think). My first suggestion is why use chdir? It typically makes things more fragile. Why not just this: system("nu_correct -iter 150 -stop 5e-05 -normalize_field \ $indir/file_nu_0.mnc.gz $indir/file_nu_1.mnc"); You may also be being bitten by the .gz on the file but I dont think so. My other suggestion (which will not be causing the problem) is to use system as an array, this tends to work better with filenames with spaces in them. ie: system("nu_correct", '-iter', 150, '-stop', 5e-05, '-normalize_field', "$indir/file_nu_0.mnc.gz", "$indir/file_nu_1.mnc") == 0 or die "I tried but couldnt\n"; I have also added a check for the status of the command a From mishkind at gmail.com Thu Jun 5 17:16:56 2008 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Thu, 5 Jun 2008 17:16:56 -0400 Subject: [MINC-users] nu_correct directory problems In-Reply-To: <9c5abb60806051405r4ba29de3k7a6c9bfbb2858029@mail.gmail.com> References: <9c5abb60806051405r4ba29de3k7a6c9bfbb2858029@mail.gmail.com> Message-ID: <9c5abb60806051416qde557f4iecb5e5a70e048ab7@mail.gmail.com> Seems I found the problem. chdir() in perl does not set the PWD environment variable, and I'm assuming that is what nu_correct uses to determine where to write its output files. So what I thought might have been a bug at first, can be remedied with: #! /usr/bin/perl chdir("/mydir/"); $ENV{'PWD'} = "/mydir/"; system("nu_correct -iter 150 -stop 5e-05 -normalize_field file_nu_0.mnc.gz file_nu_1.mnc"); unless there are other suggestions? On Thu, Jun 5, 2008 at 5:05 PM, Mishkin Derakhshan wrote: > Hi, > I am trying to call nu_correct from perl: > ie. > #! /usr/bin/perl > chdir("/mydir/"); > system("nu_correct -iter 150 -stop 5e-05 -normalize_field > file_nu_0.mnc.gz file_nu_1.mnc"); > > > If I run this from the command line, ie. > opus[~]$ cd /mydir > opus[/mydir]$ nu_correct -iter 150 -stop 5e-05 -normalize_field > file_nu_0.mnc.gz file_nu_1.mnc > > Then everything works fine. > > If however, I do this: > opus[~]$ ./perlscript.pl > > Then I always get the same error: > Cannot open .imp file: file_nu_1.imp > nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) > > The problem seems to be that the .imp file is getting saved to the > directory I was in before I ran my perl script, and not to /mydir. > > I suspect this has something to do with using chdir() in perl, and to > how nu_correct is calculating what its current directory. > > Any tips? > thanks, > mishkin > > opus[~]$ `which nu_correct` -version > Program nu_correct, built from: > Package MNI N3, version 1.10.1, compiled by rotor at ben > (x86_64-unknown-linux-gnu) on 2007-11-07 at 11:54:01 > From penhunelab at gmail.com Mon Jun 9 23:36:57 2008 From: penhunelab at gmail.com (Penhune Lab) Date: Mon, 9 Jun 2008 23:36:57 -0400 Subject: [MINC-users] Multistat error - ??? Maximum variable size allowed by the program is exceeded. In-Reply-To: References: <48470D38.1040405@bic.mni.mcgill.ca> Message-ID: Thank you for your input. I also sent this to Dr. Worsley and he replied with basically the same answer that Marc has given here - which works just fine :). This has been corrected in multistat by Dr. Worsley. Cheers, Chris On Thu, Jun 5, 2008 at 9:00 AM, Marc BOUFFARD wrote: > Hi Chris, > > I have encountered this error before: > > try > > fwhm_varatio = inf > > instead of -100 > > which gives a fixed effects analysis which seems to be what the error is > telling you in this case. I think (to be confirmed) that this is a bug > whithin multistat. It is related to this section of the code in > multistat: > ******************************************************************* > > if fwhm_varatio<0 > % find fwhm to achieve target df: > df_target=-fwhm_varatio; > fwhm_varatio_limit=50; > ff=0:1:100; > dfs=[]; > for f=ff; > df=regularized_df(f,D,Steps,numslices,df,fwhm_data); > dfs=[dfs df.t]; > end > fwhm_varatio=interp1(dfs,ff,df_target); > if isnan(fwhm_varatio) | fwhm_varatio > fwhm_varatio_limit > fwhm_varatio=Inf; > varatio_vol=zeros(numpix,numslices); > end > fwhm_varatio > end > > [df, ker_x, ker_y, > K]=regularized_df(fwhm_varatio,D,Steps,numslices,df,fwhm_data); > df.rfx=round(df.rfx); > df.t=round(df.t); > > if fwhm_varatio>0 & fwhm_varatio % Smoothing varatio in slice is done using conv2 with a kernel > ker_xy. > for slice=1:numslices > varatio_slice=reshape(varatio_vol(:,slice),numxs,numys); > > > varatio_vol(:,slice)=reshape(conv2(ker_x,ker_y,varatio_slice,'same'),numpix,1); > end > % Smoothing betwen slices is done by straight matrix > multiplication > % by a toeplitz matrix K normalized so that the column sums are > 1. > varatio_vol=varatio_vol*K; > end > > else > df.rfx=Inf; > df.t=df.fixed; > end > > ************************************************************* > In the case where fwhm_variatio > fwhm_varatio_limit it tries to calculate > regularized_df which gives an error. Instead it should go directly to: > > else > df.rfx=Inf; > df.t=df.fixed; > end > > > > > On Wed, 4 Jun 2008, Michael Ferreira wrote: > > > Hi Chris, > > > > Ditto to what Andrew said. > > > > I don't see anything wrong w/ your code. And I've never come across > > that error before. So this is certainly one for Prof. Worsley. > > > > mike > > > > > > Andrew Janke wrote: > > > Hi, > > > > > > This really is one for Keith Worsley given that fmristat is his baby, > > > I am unsure if he still reads this list so perhaps send him an email > > > directly. > > > > > > > > > a > > > > > > On Wed, Jun 4, 2008 at 5:54 AM, Penhune Lab > wrote: > > > > > >>Greetings! > > >> > > >>I am getting the following error from a multistat script that I have > > >>successfully used for ... about 15 other analyses. Any ideas? > > >> > > >>Cheers, > > >>Chris > > >> > > >>??? Maximum variable size allowed by the program is exceeded. > > >> > > >>Error in ==> multistat>regularized_df at 809 > > >> ker_x=exp(-(-ceil(fwhm_x):ceil(fwhm_x)).^2*4*log(2)/fwhm_x^2); > > >> > > >>Error in ==> multistat at 418 > > >> [df, ker_x, ker_y, > > >>K]=regularized_df(fwhm_varatio,D,Steps,numslices,df,fwhm_data); > > >> > > >>All I am doing is averaging three files with the following code: (each > of > > >>the three files is the result of a covariation analysis of 15 Ss with > their > > >>Bx scores) > > >> > > >>input_files_effect = > > > >>['Lonlycov_PCOR_d1r1_ef.mnc';'Lonlycov_PCOR_d1r2_ef.mnc';'Lonlycov_PCOR_d1r3_ef.mnc']; > > >>input_files_sdeffect = > > > >>['Lonlycov_PCOR_d1r1_sd.mnc';'Lonlycov_PCOR_d1r2_sd.mnc';'Lonlycov_PCOR_d1r3_sd.mnc']; > > >> > > >>x = [ones(size(input_files_effect,1),1)] > > >>contrast = [1]; > > >>input_files_df = []; > > >>input_files_fwhm = []; > > >>which_stats = '_t _ef _sd _fwhm'; > > >>fwhm_varatio = -100; > > >>df = multistat(input_files_effect, input_files_sdeffect, > input_files_df, > > >>input_files_fwhm, x, contrast, output_file_base, which_stats, > fwhm_varatio); > > >> > > >>-- > > >>Laboratory for Motor Learning and Neural Plasticity > > >>Directed by Dr. Virginia Penhune > > >>Department of Psychology, Concordia University > > >>SP-A 244, 7141 Sherbrooke St. W > > >>Montreal, QC H4B 1R6 Canada > > >>(514)848-2424 ext. 7567 > > >>http://psychology.concordia.ca/fac/penhune/winindex.html > > >>_______________________________________________ > > >>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 > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Laboratory for Motor Learning and Neural Plasticity Directed by Dr. Virginia Penhune Department of Psychology, Concordia University SP-A 244, 7141 Sherbrooke St. W Montreal, QC H4B 1R6 Canada (514)848-2424 ext. 7567 http://psychology.concordia.ca/fac/penhune/winindex.html From john at absherneurology.com Tue Jun 10 18:38:49 2008 From: john at absherneurology.com (John Absher) Date: Tue, 10 Jun 2008 18:38:49 -0400 Subject: [MINC-users] libppm.so.9 error In-Reply-To: Message-ID: Running ubuntu, gutsy gibbon, I get a "libppm.so.9 not found" error when trying to run the Display program, downloaded and installed from the packages.bic.mni.mcgill.ca site. What am I missing? Thanks, John From alex at bic.mni.mcgill.ca Tue Jun 10 20:00:14 2008 From: alex at bic.mni.mcgill.ca (Alex Zijdenbos) Date: Tue, 10 Jun 2008 20:00:14 -0400 Subject: [MINC-users] libppm.so.9 error In-Reply-To: References: Message-ID: Hi John, My guess is that apt-get install libnetpbm9 will solve your problem. You could also install the apt-file package which will easily let you search for these kinds of things ("apt-file search libppm" would tell you which packages provide libppm). -- A On Tue, Jun 10, 2008 at 6:38 PM, John Absher wrote: > Running ubuntu, gutsy gibbon, I get a "libppm.so.9 not found" error when > trying to run the Display program, downloaded and installed from the > packages.bic.mni.mcgill.ca site. What am I missing? > > Thanks, > John > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From a.janke at gmail.com Tue Jun 10 20:39:27 2008 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 11 Jun 2008 10:39:27 +1000 Subject: [MINC-users] libppm.so.9 error In-Reply-To: References: Message-ID: > My guess is that > > apt-get install libnetpbm9 > > will solve your problem. You could also install the apt-file package > which will easily let you search for these kinds of things ("apt-file > search libppm" would tell you which packages provide libppm). Alex is on the money. Here is the prereq list I use for gutsy when building MINC2 apps. netcdfg-dev libhdf5-serial-dev libnetpbm9-dev fftw-dev libgsl0-dev libgetopt-tabular-perl libmni-perllib-perl libxext-dev glutg3-dev libsoqt-dev a From alex at bic.mni.mcgill.ca Tue Jun 10 22:46:42 2008 From: alex at bic.mni.mcgill.ca (Alex Zijdenbos) Date: Tue, 10 Jun 2008 22:46:42 -0400 Subject: [MINC-users] libppm.so.9 error In-Reply-To: References: Message-ID: This is probably a naive question but I will ask it anyway: the 'normal' "apt-get install X" call will automagically draw in any packages prerequisite to X that are not already installed. Why does this not work with the minc deb packages? Ideally, John would not need to ask this question (which is definitely a FAQ) because his apt-get-ting would have selected libnetpbm by itself. -- A On Tue, Jun 10, 2008 at 8:39 PM, Andrew Janke wrote: >> My guess is that >> >> apt-get install libnetpbm9 >> >> will solve your problem. You could also install the apt-file package >> which will easily let you search for these kinds of things ("apt-file >> search libppm" would tell you which packages provide libppm). > > Alex is on the money. Here is the prereq list I use for gutsy when > building MINC2 apps. > > netcdfg-dev libhdf5-serial-dev libnetpbm9-dev fftw-dev libgsl0-dev > libgetopt-tabular-perl libmni-perllib-perl libxext-dev glutg3-dev > libsoqt-dev > > > a > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From a.janke at gmail.com Wed Jun 11 00:01:27 2008 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 11 Jun 2008 14:01:27 +1000 Subject: [MINC-users] libppm.so.9 error In-Reply-To: References: Message-ID: On Wed, Jun 11, 2008 at 12:46, Alex Zijdenbos wrote: > This is probably a naive question but I will ask it anyway: the > 'normal' "apt-get install X" call will automagically draw in any > packages prerequisite to X that are not already installed. Why does > this not work with the minc deb packages? Ideally, John would not need > to ask this question (which is definitely a FAQ) because his > apt-get-ting would have selected libnetpbm by itself. Hi Alex, There are two answers to this one, the short one: "I am slack". The longer one: Initially the package building system I have been using is supposed to be platform agnostic at least with respect to debian/ubuntu. Problem is it wasn't and isn't. So I have had to rethink how we do binary builds if only because the dependencies keep changing names dependant on the target. And to make it more interesting they change names between releases! What this has meant is that I have stripped all the dependencies from the epm-headers (what I build from) if only because it seemed better to me to have some packages as opposed to none. So, what to do. From what I can see the only option is to build for each architecture/release/distro which is what I have been doing, now that I have all the base packages I plan to also release a "mincbundle" package for each architecture that will handle all the dependencies (That I am slowly building a list of via virtual machines). The result is something like this: http://ajanke.selfip.com/minc-beta/mincbundle.deb This is one for Ubuntu Hardy (It might work on other versions but I would doubt it, perhaps debian lenny) and the goal is then that you can install "all of minc" by just doing this: apt-get install mincbundle Of course this will only work if I put this deb in the right directory on packages.bic.mni.mcgill.ca first. I will do this as soon as I have done a bit more testing on this. a From vikingy at gmail.com Thu Jun 12 14:23:48 2008 From: vikingy at gmail.com (vikingy) Date: Fri, 13 Jun 2008 02:23:48 +0800 Subject: [MINC-users] report a wrong package Message-ID: <200806130223462184133@gmail.com> It seems that the package "minc-2.0.15-linux-2.6-amd64.deb" on the http://packages.bic.mni.mcgill.ca/ubuntu-hardy/ is wrong, it's only 421 bytes. when I try to install this, system reports the error info, and I have replaced the same package on the http://packages.bic.mni.mcgill.ca/ubuntu-hardy-prereq/, it's ok. bin lv 2008-06-13 The Key Lab of Complex Systems and Intelligence Science, Institute of Automation, Chinese Academy of Sciences. From dfwang at cse.cuhk.edu.hk Sun Jun 15 13:56:19 2008 From: dfwang at cse.cuhk.edu.hk (dfwang) Date: Mon, 16 Jun 2008 01:56:19 +0800 Subject: [MINC-users] convert mesh from VTK to .obj References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> <470A286F.2020206@hst.aau.dk><1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> <470B55FA.3060606@hst.aau.dk> Message-ID: <006d01c8cf11$20e1c600$a459bd89@PC89164> Dear Simon, May I have the same program running under cygwin? Thanks in advance. Best wishes, Vincent ----- Original Message ----- From: "Simon Fristed Eskildsen" To: "MINC users mailing list" Sent: Tuesday, October 09, 2007 6:20 PM Subject: Re: [MINC-users] convert mesh from VTK to .obj > Did you try the P3 version? > http://www.hst.aau.dk/~se/software/parse.p3fc2 > It should be compatible whether you run 32 or 64 bit xeon. > > Simon > dfwang at cse.cuhk.edu.hk wrote: >> Hi, Simon, >> >> My computer information is as follows, >> >> [dfwang at pc89164 ~]$ cat /proc/cpuinfo >> processor : 0 >> vendor_id : GenuineIntel >> cpu family : 15 >> model : 4 >> model name : Intel(R) Xeon(TM) CPU 3.00GHz >> stepping : 3 >> cpu MHz : 3001.815 >> cache size : 2048 KB >> fdiv_bug : no >> hlt_bug : no >> f00f_bug : no >> coma_bug : no >> fpu : yes >> fpu_exception : yes >> cpuid level : 5 >> wp : yes >> flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca >> cmov pat >> pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni >> monito r ds_cpl cid xtpr >> bogomips : 6004.11 >> >> processor : 1 >> vendor_id : GenuineIntel >> cpu family : 15 >> model : 4 >> model name : Intel(R) Xeon(TM) CPU 3.00GHz >> stepping : 3 >> cpu MHz : 3001.815 >> cache size : 2048 KB >> fdiv_bug : no >> hlt_bug : no >> f00f_bug : no >> coma_bug : no >> fpu : yes >> fpu_exception : yes >> cpuid level : 5 >> wp : yes >> flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca >> cmov pat >> pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe lm constant_tsc pni >> monito r ds_cpl cid xtpr >> bogomips : 5999.43 >> >> [dfwang at pc89164 data]$ uname -a >> Linux pc89164.cse.cuhk.edu.hk 2.6.9-55.0.9.ELsmp #1 SMP Thu Sep 27 >> 18:27:41 EDT >> 2007 i686 i686 i386 GNU/Linux >> >> >> [dfwang at pc89164 data]$ strace ./parse.bin >> execve("./parse.bin", ["./parse.bin"], [/* 64 vars */]) = 0 >> uname({sys="Linux", node="pc89164.cse.cuhk.edu.hk", ...}) = 0 >> brk(0) = 0x9b99000 >> --- SIGFPE (Floating point exception) @ 0 (0) --- >> +++ killed by SIGFPE +++ >> Process 5227 detached >> >> >> Thanks a lot! >> >> Best wishes, >> Defeng >> >> >> Quoting Simon Fristed Eskildsen : >> >>> Hi Defeng, >>> >>> parse.bin is compiled on a pentium4, and it works also on pentiumM. >>> What CPU are you using? >>> What is the output of >>> cat /proc/cpuinfo >>> uname -a >>> strace ./parse.bin >>> >>> I have compiled it on a pentium3 as well. Maybe that works for you: >>> http://www.hst.aau.dk/~se/software/parse.p3fc2 >>> >>> Simon >>> >>> dfwang at cse.cuhk.edu.hk wrote: >>>> Hi, Simon, >>>> >>>> Thanks for your reply. Yes, my VTK mesh is in triangular. >>>> >>>> My linux system is CentOS 4.4. I downloaded your small parser just now, >>>> and >>>> changed the mode by >>>> >>>> chmod a+x parse.bin >>>> >>>> then run parse.bin, I got the following error, >>>> >>>> Floating point exception >>>> >>>> Could you please tell me how I can run it successfully? >>>> >>>> Best wishes, >>>> Defeng >>>> Quoting Simon Fristed Eskildsen : >>>> >>>>> Hi Defeng, >>>>> >>>>> If you're dealing with triangular mesh and pure ascii, you can try my >>>>> small parser found here: >>>>> 32bit linux: http://www.hst.aau.dk/~se/software/parse.bin >>>>> 64bit linux: http://www.hst.aau.dk/~se/software/parse.bin64 >>>>> >>>>> Also, more information about the .obj format can be found here: >>>>> http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles >>>>> >>>>> Simon >>>>> >>>>> Defeng WANG wrote: >>>>>> Dear MINC Users, >>>>>> >>>>>> I have one mesh in VTK format at hand, and would like to convert it >>>>>> into >>>>> the >>>>>> .obj format in MINC. Which tool can do this? Or any suggestions on >>>>>> the >>> way >>>>>> to convert it? >>>>>> >>>>>> Many thanks! >>>>>> Defeng >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 nikelski at bic.mni.mcgill.ca Sun Jun 15 19:01:21 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Sun, 15 Jun 2008 19:01:21 -0400 Subject: [MINC-users] minc2 API error? Message-ID: Hi all, I've been writing some minc2 code, and have run into a problem when retrieving attributes from a minc2 volume. For example, say that I wanted to get information on attribute "xspace:varid" (just as an example). If I were to start by retrieving the length of the attribute by calling miget_attr_length, I would get a no-find returned since miget_attr_length starts all attribute searches relative to /minc-2.0/info. Any path passed to miget_attr_length is simply appended to /minc-2.0/info. Therefore, call like this : result = miget_attr_length(minc_volume, "/minc-2.0/dimensions/xspace", "varid", &attr_length); ... would result in /minc-2.0/info/minc-2.0/dimensions/xspace being searched for attribute "varid" (and subsequently not found). The code that causes this behaviour can be found in a number of miget_attr_xxx functions, and therefore most other attribute related functions similarly are unable to find requested attributes. Now I know that the API has specialty functions to retrieve all sorts of attributes, however, I had assumed that one should be able to use the miget_attr_xxx functions to retrieve any or all of the attributes -- and not just those in /minc-2.0/info/. Is this assumption incorrect? By the way, I modified some of the miget_attr_xxx functions on my system to respect an absolute path when passed (and not prepend /minc-2.0/info/), which worked ... but broke other things (including the minc2 "make check", amongst other things) ... so beware, as some code assumes the current behaviour. Any comments/suggestions on this stuff would be welcome. -Jim From a.janke at gmail.com Mon Jun 16 02:54:00 2008 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 16 Jun 2008 16:54:00 +1000 Subject: [MINC-users] report a wrong package In-Reply-To: <200806130223462184133@gmail.com> References: <200806130223462184133@gmail.com> Message-ID: Thanks for the report. I have updated the package in question. a On Fri, Jun 13, 2008 at 04:23, vikingy wrote: > It seems that the package "minc-2.0.15-linux-2.6-amd64.deb" on the http://packages.bic.mni.mcgill.ca/ubuntu-hardy/ is wrong, it's only 421 bytes. when I try to install this, system reports the error info, and I have replaced the same package on the http://packages.bic.mni.mcgill.ca/ubuntu-hardy-prereq/, it's ok. > > bin lv > 2008-06-13 > > > > The Key Lab of Complex Systems and Intelligence Science, > Institute of Automation, > Chinese Academy of Sciences. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From se at hst.aau.dk Mon Jun 16 11:04:52 2008 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Mon, 16 Jun 2008 17:04:52 +0200 Subject: [MINC-users] convert mesh from VTK to .obj In-Reply-To: <006d01c8cf11$20e1c600$a459bd89@PC89164> References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> <470A286F.2020206@hst.aau.dk><1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> <470B55FA.3060606@hst.aau.dk> <006d01c8cf11$20e1c600$a459bd89@PC89164> Message-ID: <48568114.9090401@hst.aau.dk> dfwang wrote: > May I have the same program running under cygwin? > Hi Vincent, I have not compiled it for cygwin. Maybe I'll give it a try one of the days. I'll let you know. Cheers, Simon From dfwang at cse.cuhk.edu.hk Sun Jun 22 16:07:53 2008 From: dfwang at cse.cuhk.edu.hk (dfwang) Date: Mon, 23 Jun 2008 04:07:53 +0800 Subject: [MINC-users] convert mesh from VTK to .obj References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> <470A286F.2020206@hst.aau.dk><1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> <470B55FA.3060606@hst.aau.dk><006d01c8cf11$20e1c600$a459bd89@PC89164> <48568114.9090401@hst.aau.dk> Message-ID: <00f801c8d4a3$abb80220$a459bd89@PC89164> Hi, Simon, Thanks in advance. Best wishes, Vincent ----- Original Message ----- From: "Simon Fristed Eskildsen" To: "MINC users mailing list" Sent: Monday, June 16, 2008 11:04 PM Subject: Re: [MINC-users] convert mesh from VTK to .obj > dfwang wrote: >> May I have the same program running under cygwin? >> > Hi Vincent, > I have not compiled it for cygwin. Maybe I'll give it a try one of the > days. I'll let you know. > > Cheers, > Simon > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From se at hst.aau.dk Mon Jun 23 10:58:44 2008 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Mon, 23 Jun 2008 16:58:44 +0200 Subject: [MINC-users] convert mesh from VTK to .obj In-Reply-To: <48568114.9090401@hst.aau.dk> References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> <470A286F.2020206@hst.aau.dk><1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> <470B55FA.3060606@hst.aau.dk> <006d01c8cf11$20e1c600$a459bd89@PC89164> <48568114.9090401@hst.aau.dk> Message-ID: <485FBA24.6040504@hst.aau.dk> Simon Fristed Eskildsen wrote: > I have not compiled it for cygwin. Maybe I'll give it a try one of the > days. I'll let you know. > Here it is: http://www.hst.aau.dk/~se/software/parse.cygwin Enjoy Cheers, Simon From dfwang at cse.cuhk.edu.hk Mon Jun 23 12:09:28 2008 From: dfwang at cse.cuhk.edu.hk (dfwang) Date: Tue, 24 Jun 2008 00:09:28 +0800 Subject: [MINC-users] convert mesh from VTK to .obj References: <160E3DD4FB702C4CB860C65186686E69015F1CA8@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6901145642@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E690114564E@MRZS152229.medizin.uni-leipzig.de> <00a501c80986$22f86170$a459bd89@PC89164> <4709F25D.5030500@hst.aau.dk> <1191835216.4709f650b95ed@webmail.cse.cuhk.edu.hk> <470A286F.2020206@hst.aau.dk><1191850810.470a333a4e6fe@webmail.cse.cuhk.edu.hk> <470B55FA.3060606@hst.aau.dk> <006d01c8cf11$20e1c600$a459bd89@PC89164><48568114.9090401@hst.aau.dk> <485FBA24.6040504@hst.aau.dk> Message-ID: <029201c8d54b$8714f420$a459bd89@PC89164> Dear Simon, Thanks a lot! Best wishes, Vincent ----- Original Message ----- From: "Simon Fristed Eskildsen" To: "MINC users mailing list" Sent: Monday, June 23, 2008 10:58 PM Subject: Re: [MINC-users] convert mesh from VTK to .obj > Simon Fristed Eskildsen wrote: >> I have not compiled it for cygwin. Maybe I'll give it a try one of the >> days. I'll let you know. >> > Here it is: > http://www.hst.aau.dk/~se/software/parse.cygwin > > Enjoy > > Cheers, > Simon > -------------------------------------------------------------------------------- > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From john at absherneurology.com Mon Jun 23 16:21:17 2008 From: john at absherneurology.com (John Absher) Date: Mon, 23 Jun 2008 16:21:17 -0400 Subject: [MINC-users] nii2mnc In-Reply-To: Message-ID: Running nii2mnc under ubuntu gutsy, we are having trouble. We're using spm5, and have tried saving as nii in one .nii file, and also as .img + .hdr file. When we try nii2mnc (on ubunutu), we get an error ... can't find the header. It won't translate into mnc. What are we doing wrong? A second question is whether there is right-left confusion on the nii2mnc conversions, or if the spm5 import takes care of it? We have some analyze format files (created using MRIcro, Chris Rorden's program) that we put into spm5 to do normalization and segmentation, and now we want to get them back into David MacDonald's register and Display programs running under ubuntu. We can get them into spm5, but not safely back again. Thanks, John John R. Absher, MD, FAAN Absher Neurology, PA Alliance for Neuro Research, LLC 274-A Commonwealth Dr. Greenville, SC 29615 864-286-8222 864-286-3356 FAX http://www.absherneurology.com john at absherneurology.com From a.janke at gmail.com Mon Jun 23 20:12:29 2008 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 24 Jun 2008 10:12:29 +1000 Subject: [MINC-users] nii2mnc In-Reply-To: References: Message-ID: Hi John, On Tue, Jun 24, 2008 at 06:21, John Absher wrote: > Running nii2mnc under ubuntu gutsy, we are having trouble. We're using > spm5, and have tried saving as nii in one .nii file, and also as .img + .hdr > file. When we try nii2mnc (on ubunutu), we get an error ... can't find the > header. It won't translate into mnc. What are we doing wrong? Which header is it complaining about? as in a library link error or the nifti "header"? Can you please copy and paste the command (and error) that you get? > A second question is whether there is right-left confusion on the nii2mnc > conversions, or if the spm5 import takes care of it? We have some analyze > format files (created using MRIcro, Chris Rorden's program) that we put into > spm5 to do normalization and segmentation, and now we want to get them back > into David MacDonald's register and Display programs running under ubuntu. > We can get them into spm5, but not safely back again. Ah, orientation.. :) First things first, MINC does not "do" radio vs neurological "format", this was as abomination forced upon us by certain other packages who shall remain nameless. In short this this should be a viewing convention only. In the case of the BIC software all the tools that I know of view in neuro orientation. (register for one) That said other packages do not do this and even go to the extents of flipping data on disk and defining global "orientation flags". So in short I can guarantee nothing regarding orientation and files. The only way to be sure of this is to use a fiducial marker in an image and track it through your entire processing chain. mnc2nii follows the Nifti standard so I believe that a conversion to Nifti and then into FSL will not result in orientation issues. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From alex at bic.mni.mcgill.ca Mon Jun 23 22:59:32 2008 From: alex at bic.mni.mcgill.ca (Alex Zijdenbos) Date: Mon, 23 Jun 2008 22:59:32 -0400 Subject: [MINC-users] libppm.so.9 error In-Reply-To: References: Message-ID: Hi Andrew, I think the mincbundle thing would be very useful - but so far it seems to be somewhat broken. I just added deb http://packages.bic.mni.mcgill.ca/ubuntu-hardy/ ./ to /etc/apt/sources.list, then ran apt-get update apt-get install mincbundle and got The following packages have unmet dependencies: mincbundle: Depends: glim_image but it is not installable Depends: mni_autoreg but it is not installable Depends: mni-models_average305-lin but it is not installable Depends: mni-models_colin27-lin but it is not installable Depends: mni-models_icbm152-lin but it is not installable Depends: Display but it is not installable Depends: Register but it is not installable Depends: ray_trace but it is not installable Depends: N3 but it is not installable Depends: oobicpl but it is not going to be installed E: Broken packages Should this have worked, or did I miss something? When I try to separately install one or more of the unmet dependencies, like mni-autoreg, I get: Err http://packages.bic.mni.mcgill.ca ./ minc 2.0.15 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ mni-autoreg 0.99.3 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//minc-2.0.15-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mni-autoreg-0.99.3-linux-2.6-i386.deb 404 Not Found Something tells me that /data/home/rotor/data/epm-build/etc doesn't actually belong there :) (I'm running Hardy i386) Thanks, -- A On Wed, Jun 11, 2008 at 12:01 AM, Andrew Janke wrote: > On Wed, Jun 11, 2008 at 12:46, Alex Zijdenbos wrote: >> This is probably a naive question but I will ask it anyway: the >> 'normal' "apt-get install X" call will automagically draw in any >> packages prerequisite to X that are not already installed. Why does >> this not work with the minc deb packages? Ideally, John would not need >> to ask this question (which is definitely a FAQ) because his >> apt-get-ting would have selected libnetpbm by itself. > > Hi Alex, > > There are two answers to this one, the short one: "I am slack". The > longer one: Initially the package building system I have been using is > supposed to be platform agnostic at least with respect to > debian/ubuntu. Problem is it wasn't and isn't. So I have had to > rethink how we do binary builds if only because the dependencies keep > changing names dependant on the target. And to make it more > interesting they change names between releases! What this has meant is > that I have stripped all the dependencies from the epm-headers (what I > build from) if only because it seemed better to me to have some > packages as opposed to none. > > So, what to do. From what I can see the only option is to build for > each architecture/release/distro which is what I have been doing, now > that I have all the base packages I plan to also release a > "mincbundle" package for each architecture that will handle all the > dependencies (That I am slowly building a list of via virtual > machines). The result is something like this: > > http://ajanke.selfip.com/minc-beta/mincbundle.deb > > This is one for Ubuntu Hardy (It might work on other versions but I > would doubt it, perhaps debian lenny) and the goal is then that you > can install "all of minc" by just doing this: > > apt-get install mincbundle > > Of course this will only work if I put this deb in the right directory > on packages.bic.mni.mcgill.ca first. I will do this as soon as I have > done a bit more testing on this. > > > a > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From Michel.Audette at medizin.uni-leipzig.de Wed Jun 25 07:07:05 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Wed, 25 Jun 2008 13:07:05 +0200 Subject: [MINC-users] optizing minctracc parameters for heart data References: A<160E3DD4FB702C4CB860C65186686E6902886E23@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E6902425013@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E69029C1E9E@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de> Hi all, after registering inner ear data, I'm now playing with cardiac data. I have preop CT and DynaCT data to register. Can anyone comment about the appropriateness of the default w_translations w_rotations and step parameters appropriate for this anatomy? One of the two data sets spans a good part of the chest, but the registration can probably be determined by the heart and aorta alone, and perhaps incrementally improved with masks based on the coronary arteries and aorta. Cheers, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 From Michel.Audette at medizin.uni-leipzig.de Wed Jun 25 10:42:42 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Wed, 25 Jun 2008 16:42:42 +0200 Subject: [MINC-users] win32 versions of register and Display In-Reply-To: <160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de> References: A<160E3DD4FB702C4CB860C65186686E6902886E23@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6902425013@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69029C1E9E@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E6902425014@MRZS152229.medizin.uni-leipzig.de> Hello again, I am looking to download win32 versions of register and Display, for some clinical collaborators of mine, but I cannot find them in the http://www.bic.mni.mcgill.ca/software/ , http://www.bic.mni.mcgill.ca/software/distribution/ , or http://packages.bic.mni.mcgill.ca/win32/ directories. Can anyone give me an idea where to look? Best wishes, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 From sridar at mrs.mni.mcgill.ca Wed Jun 25 12:28:02 2008 From: sridar at mrs.mni.mcgill.ca (Dr. Sridar Narayanan) Date: Wed, 25 Jun 2008 12:28:02 -0400 Subject: [MINC-users] MINC-users Digest, Vol 35, Issue 10 In-Reply-To: Message-ID: Hi Michel, This is not a direct answer to your question, but just to alert you to a potential gotcha with CT data. Assuming you are creating MINC volumes from DICOM, check whether a gantry head angle was used during acquisition (DICOM field 0018,1120). If so, then you cannot simply stack the slices into a volume. You'll need to convert each slice to an individual .mnc file and regrid the data using volregrid. Otherwise, you'll get a lovely shear distortion in the volume. Cheers, Sridar > Hi all, > > after registering inner ear data, I'm now playing with cardiac data. I have > preop CT and DynaCT data to register. Can anyone comment about the > appropriateness of the default w_translations w_rotations and step parameters > appropriate for this anatomy? > > One of the two data sets spans a good part of the chest, but the registration > can probably be determined by the heart and aorta alone, and perhaps > incrementally improved with masks based on the coronary arteries and aorta. > > Cheers, > > Michel From stinson at bic.mni.mcgill.ca Wed Jun 25 21:01:28 2008 From: stinson at bic.mni.mcgill.ca (Eric STINSON - B. Pike Lab) Date: Wed, 25 Jun 2008 21:01:28 -0400 (EDT) Subject: [MINC-users] mincbundle and minc on ubuntu hardy heron Message-ID: <200806260101.m5Q11SmZ014136@yorick.bic.mni.mcgill.ca> Hi everyone, Has there been any progress on the mincbundle errors reported by Alex in the libppm.so.9 thread? I'm running into the same types of errors when trying to install minc (on a i386 machine running xubuntu Hardy Heron. I also tried on an AMD64 running Ubuntu Hardy Heron with the same results.) using the instructions here: http://wiki.bic.mni.mcgill.ca/index.php/MincDebian I get the following errors: Err http://packages.bic.mni.mcgill.ca ./ libmni-perllib-perl 0.08-1 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ minc 2.0.15 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ bicpl 1.4.5 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ ebtks 1.6.1 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ classify 1.0.08 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ display 1.4.2 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ mincblob 1.2.1 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ mincmorph 1.4 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ mni-autoreg 0.99.3 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ n3 1.10.1 404 Not Found Err http://packages.bic.mni.mcgill.ca ./ register 1.3.6 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//libmni-perllib-perl_0.08-1_all.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//minc-2.0.15-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//bicpl-1.4.5-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//ebtks-1.6.1-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//classify-1.0.08-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//display-1.4.2-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mincblob-1.2.1-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mincmorph-1.4-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mni-autoreg-0.99.3-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//n3-1.10.1-linux-2.6-i386.deb 404 Not Found Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//register-1.3.6-linux-2.6-i386.deb 404 Not Found E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing? Any thoughts? I'm anxious to get minc working! Thanks! Eric From a.janke at gmail.com Wed Jun 25 21:07:43 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 26 Jun 2008 11:07:43 +1000 Subject: [MINC-users] mincbundle and minc on ubuntu hardy heron In-Reply-To: <200806260101.m5Q11SmZ014136@yorick.bic.mni.mcgill.ca> References: <200806260101.m5Q11SmZ014136@yorick.bic.mni.mcgill.ca> Message-ID: Hi all, I made a new "mincbundle" package last night and hope to finish testing it today so that i can upload tonight (Oz time!) The amusing thing is that when I test it on my machine (the one on which I made mincbundle) this error does not happen. wierd. I am sure I am missing something! In any case the current status is: give it another bash tomorrow or later today if I can make it work. a On Thu, Jun 26, 2008 at 11:01, Eric STINSON - B. Pike Lab wrote: > Hi everyone, > > > Has there been any progress on the mincbundle errors reported by Alex in the libppm.so.9 thread? I'm running into the same types of errors when trying to install minc (on a i386 machine running xubuntu Hardy Heron. I also tried on an AMD64 running Ubuntu Hardy Heron with the same results.) using the instructions here: http://wiki.bic.mni.mcgill.ca/index.php/MincDebian > > > I get the following errors: > > Err http://packages.bic.mni.mcgill.ca ./ libmni-perllib-perl 0.08-1 > > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ minc 2.0.15 > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ bicpl 1.4.5 > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ ebtks 1.6.1 > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ classify 1.0.08 > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ display 1.4.2 > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ mincblob 1.2.1 > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ mincmorph 1.4 > > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ mni-autoreg 0.99.3 > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ n3 1.10.1 > 404 Not Found > Err http://packages.bic.mni.mcgill.ca ./ register 1.3.6 > 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//libmni-perllib-perl_0.08-1_all.deb 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//minc-2.0.15-linux-2.6-i386.deb 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//bicpl-1.4.5-linux-2.6-i386.deb 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//ebtks-1.6.1-linux-2.6-i386.deb 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//classify-1.0.08-linux-2.6-i386.deb 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//display-1.4.2-linux-2.6-i386.deb 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mincblob-1.2.1-linux-2.6-i386.deb 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mincmorph-1.4-linux-2.6-i386.deb 404 Not Found > > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mni-autoreg-0.99.3-linux-2.6-i386.deb 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//n3-1.10.1-linux-2.6-i386.deb 404 Not Found > Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//register-1.3.6-linux-2.6-i386.deb 404 Not Found > E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing? > > Any thoughts? I'm anxious to get minc working! > > Thanks! > Eric > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From alex at bic.mni.mcgill.ca Thu Jun 26 01:49:33 2008 From: alex at bic.mni.mcgill.ca (Alex Zijdenbos) Date: Thu, 26 Jun 2008 07:49:33 +0200 Subject: [MINC-users] mincbundle and minc on ubuntu hardy heron In-Reply-To: References: <200806260101.m5Q11SmZ014136@yorick.bic.mni.mcgill.ca> Message-ID: Hi Andrew, I suspect the fact that it works on your box, is due to the fact that the hardcoded paths that seem to have ended up in these packages somehow (see my previous email), actually exist on your box, but are highly unlikely to exist on any other box ;) -- A On Thu, Jun 26, 2008 at 3:07 AM, Andrew Janke wrote: > Hi all, > > I made a new "mincbundle" package last night and hope to finish > testing it today so that i can upload tonight (Oz time!) > > The amusing thing is that when I test it on my machine (the one on > which I made mincbundle) this error does not happen. wierd. I am > sure I am missing something! > > In any case the current status is: give it another bash tomorrow or > later today if I can make it work. > > a > > > On Thu, Jun 26, 2008 at 11:01, Eric STINSON - B. Pike Lab > wrote: >> Hi everyone, >> >> >> Has there been any progress on the mincbundle errors reported by Alex in the libppm.so.9 thread? I'm running into the same types of errors when trying to install minc (on a i386 machine running xubuntu Hardy Heron. I also tried on an AMD64 running Ubuntu Hardy Heron with the same results.) using the instructions here: http://wiki.bic.mni.mcgill.ca/index.php/MincDebian >> >> >> I get the following errors: >> >> Err http://packages.bic.mni.mcgill.ca ./ libmni-perllib-perl 0.08-1 >> >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ minc 2.0.15 >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ bicpl 1.4.5 >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ ebtks 1.6.1 >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ classify 1.0.08 >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ display 1.4.2 >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ mincblob 1.2.1 >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ mincmorph 1.4 >> >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ mni-autoreg 0.99.3 >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ n3 1.10.1 >> 404 Not Found >> Err http://packages.bic.mni.mcgill.ca ./ register 1.3.6 >> 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//libmni-perllib-perl_0.08-1_all.deb 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//minc-2.0.15-linux-2.6-i386.deb 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//bicpl-1.4.5-linux-2.6-i386.deb 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//ebtks-1.6.1-linux-2.6-i386.deb 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//classify-1.0.08-linux-2.6-i386.deb 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//display-1.4.2-linux-2.6-i386.deb 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mincblob-1.2.1-linux-2.6-i386.deb 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mincmorph-1.4-linux-2.6-i386.deb 404 Not Found >> >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//mni-autoreg-0.99.3-linux-2.6-i386.deb 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//n3-1.10.1-linux-2.6-i386.deb 404 Not Found >> Failed to fetch http://packages.bic.mni.mcgill.ca/ubuntu-hardy//data/home/rotor/data/epm-build/packages/deb-hardy//register-1.3.6-linux-2.6-i386.deb 404 Not Found >> E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing? >> >> Any thoughts? I'm anxious to get minc working! >> >> Thanks! >> Eric >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > > > -- > 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 Michel.Audette at medizin.uni-leipzig.de Thu Jun 26 03:31:03 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 26 Jun 2008 09:31:03 +0200 Subject: [MINC-users] win32 versions of register and Display In-Reply-To: <160E3DD4FB702C4CB860C65186686E6902425014@MRZS152229.medizin.uni-leipzig.de> References: A<160E3DD4FB702C4CB860C65186686E6902886E23@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6902425013@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69029C1E9E@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E6902425014@MRZS152229.medizin.uni-leipzig.de> Message-ID: <160E3DD4FB702C4CB860C65186686E6902425018@MRZS152229.medizin.uni-leipzig.de> Hello again, I found windows binaries in Frank Morales' page, but they don't seem to run on Windows XP. [Typing register elicits a response "GLUT: Fatal Error in no_program_name: pixel format with necessary capabilities not found".] The Windows MINC 2.0 software does not build Display or register. If anyone can suggest where to look for win32 versions, that would be great. Cheers, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Audette, Michel Sent: June 25, 2008 4:43 PM To: MINC users mailing list Subject: [MINC-users] win32 versions of register and Display Hello again, I am looking to download win32 versions of register and Display, for some clinical collaborators of mine, but I cannot find them in the http://www.bic.mni.mcgill.ca/software/ , http://www.bic.mni.mcgill.ca/software/distribution/ , or http://packages.bic.mni.mcgill.ca/win32/ directories. Can anyone give me an idea where to look? Best wishes, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From claude at bic.mni.mcgill.ca Thu Jun 26 08:43:07 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Thu, 26 Jun 2008 08:43:07 -0400 (EDT) Subject: [MINC-users] win32 versions of register and Display References: A<160E3DD4FB702C4CB860C65186686E6902886E23@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6902425013@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69029C1E9E@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E6902425014@MRZS152229.medizin.uni-leipzig.de> Message-ID: <200806261243.m5QCh7VE020072@yorick.bic.mni.mcgill.ca> Hi Michel, > Hello again, > > I found windows binaries in Frank Morales' page, but they don't seem to run on Windows XP. [Typing register elicits a response "GLUT: Fatal Error in no_program_name: pixel format with necessary capabilities not found".] > > The Windows MINC 2.0 software does not build Display or register. > > If anyone can suggest where to look for win32 versions, that would be great. Well, I did build Display and register on my Windows XP machine at home (mostly for fun), but using cygwin 5.1. It works nicely, no problem. Would you like to try those? Claude From Michel.Audette at medizin.uni-leipzig.de Thu Jun 26 09:52:38 2008 From: Michel.Audette at medizin.uni-leipzig.de (Audette, Michel) Date: Thu, 26 Jun 2008 15:52:38 +0200 Subject: [MINC-users] win32 versions of register and Display In-Reply-To: <200806261243.m5QCh7VE020072@yorick.bic.mni.mcgill.ca> References: A<160E3DD4FB702C4CB860C65186686E6902886E23@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6902425013@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69029C1E9E@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6902425014@MRZS152229.medizin.uni-leipzig.de> <200806261243.m5QCh7VE020072@yorick.bic.mni.mcgill.ca> Message-ID: <160E3DD4FB702C4CB860C65186686E690242501C@MRZS152229.medizin.uni-leipzig.de> Hi Claude, thanks for the kind reply. I guess I'll give it a try. Cheers, Michel Michel Audette, Ph.D. Innovation Center Computer Assisted Surgery (ICCAS) Semmelweisstra?e 14 Leipzig, Germany Phone: ++49 (0) 341 / 97 - 1 20 13 Fax: ++49 (0) 341 / 97 - 1 20 09 -----Original Message----- From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Claude LEPAGE Sent: June 26, 2008 2:43 PM To: MINC users mailing list Subject: Re: [MINC-users] win32 versions of register and Display Hi Michel, > Hello again, > > I found windows binaries in Frank Morales' page, but they don't seem to run on Windows XP. [Typing register elicits a response "GLUT: Fatal Error in no_program_name: pixel format with necessary capabilities not found".] > > The Windows MINC 2.0 software does not build Display or register. > > If anyone can suggest where to look for win32 versions, that would be great. Well, I did build Display and register on my Windows XP machine at home (mostly for fun), but using cygwin 5.1. It works nicely, no problem. Would you like to try those? Claude _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From laurence at bic.mni.mcgill.ca Thu Jun 26 09:59:48 2008 From: laurence at bic.mni.mcgill.ca (Laurence Mercier) Date: Thu, 26 Jun 2008 09:59:48 -0400 Subject: [MINC-users] win32 versions of register and Display In-Reply-To: <160E3DD4FB702C4CB860C65186686E690242501C@MRZS152229.medizin.uni-leipzig.de> References: A<160E3DD4FB702C4CB860C65186686E6902886E23@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6902425013@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69029C1E9E@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de><160E3DD4FB702C4CB860C65186686E6902425014@MRZS152229.medizin.uni-leipzig.de> <200806261243.m5QCh7VE020072@yorick.bic.mni.mcgill.ca> <160E3DD4FB702C4CB860C65186686E690242501C@MRZS152229.medizin.uni-leipzig.de> Message-ID: <4863A0D4.7090103@bic.mni.mcgill.ca> Hello Michel, I actually have register and Display running on my Windows XP machine... but I installed it while ago and am not sure from what source. I wonder if it is from the last package Andrew compiled for Windows (on top of cygwin)? Or maybe it is from Frank Morales page. For register I can call it directly from cygwin and for Display I first have to type startx and then call Display from the X window. Laurence Audette, Michel wrote: > Hi Claude, > > thanks for the kind reply. I guess I'll give it a try. > > Cheers, > > Michel > > Michel Audette, Ph.D. > Innovation Center Computer Assisted Surgery (ICCAS) > Semmelweisstra?e 14 > Leipzig, Germany > Phone: ++49 (0) 341 / 97 - 1 20 13 > Fax: ++49 (0) 341 / 97 - 1 20 09 > > > > > > -----Original Message----- > From: minc-users-bounces at bic.mni.mcgill.ca [mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Claude LEPAGE > Sent: June 26, 2008 2:43 PM > To: MINC users mailing list > Subject: Re: [MINC-users] win32 versions of register and Display > > Hi Michel, > >> Hello again, >> >> I found windows binaries in Frank Morales' page, but they don't seem to run on Windows XP. [Typing register elicits a response "GLUT: Fatal Error in no_program_name: pixel format with necessary capabilities not found".] >> >> The Windows MINC 2.0 software does not build Display or register. >> >> If anyone can suggest where to look for win32 versions, that would be great. > > Well, I did build Display and register on my Windows XP machine > at home (mostly for fun), but using cygwin 5.1. It works nicely, > no problem. Would you like to try those? > > Claude > _______________________________________________ > 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 penhunelab at gmail.com Thu Jun 26 15:32:47 2008 From: penhunelab at gmail.com (Penhune Lab) Date: Thu, 26 Jun 2008 15:32:47 -0400 Subject: [MINC-users] win32 versions of register and Display In-Reply-To: <4863A0D4.7090103@bic.mni.mcgill.ca> References: <160E3DD4FB702C4CB860C65186686E6902886E23@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E6902425013@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E69029C1E9E@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E6902425014@MRZS152229.medizin.uni-leipzig.de> <200806261243.m5QCh7VE020072@yorick.bic.mni.mcgill.ca> <160E3DD4FB702C4CB860C65186686E690242501C@MRZS152229.medizin.uni-leipzig.de> <4863A0D4.7090103@bic.mni.mcgill.ca> Message-ID: We have a copy that we got (i think) from Dr Jorge Armony. It runs natively on winXP. I don't know which version it is exactly, it reports: "register.exe: Version: 1.3 Aug 25, 1998" But i don't know if thats 1.3.0 or 1.3.x and just doesn't report the second decimal I also wrote a matlab script to call register from matlab that takes care of some path problems when calling register from a DOS shell (pretty much changing the directory delimiter \ to /) Let me know if you want a copy Alejandro On 6/26/08, Laurence Mercier wrote: > > Hello Michel, > > I actually have register and Display running on my Windows XP machine... > but I installed it while ago and am not sure from what source. I wonder > if it is from the last package Andrew compiled for Windows (on top of > cygwin)? Or maybe it is from Frank Morales page. For register I can call > it directly from cygwin and for Display I first have to type startx and > then call Display from the X window. > > > Laurence > > > > Audette, Michel wrote: > > Hi Claude, > > > > thanks for the kind reply. I guess I'll give it a try. > > > > Cheers, > > > > Michel > > > > Michel Audette, Ph.D. > > Innovation Center Computer Assisted Surgery (ICCAS) > > Semmelweisstra?e 14 > > Leipzig, Germany > > Phone: ++49 (0) 341 / 97 - 1 20 13 > > Fax: ++49 (0) 341 / 97 - 1 20 09 > > > > > > > > > > > > -----Original Message----- > > From: minc-users-bounces at bic.mni.mcgill.ca [mailto: > minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Claude LEPAGE > > Sent: June 26, 2008 2:43 PM > > To: MINC users mailing list > > Subject: Re: [MINC-users] win32 versions of register and Display > > > > Hi Michel, > > > >> Hello again, > >> > >> I found windows binaries in Frank Morales' page, but they don't seem to > run on Windows XP. [Typing register elicits a response "GLUT: Fatal Error in > no_program_name: pixel format with necessary capabilities not found".] > >> > >> The Windows MINC 2.0 software does not build Display or register. > >> > >> If anyone can suggest where to look for win32 versions, that would be > great. > > > > Well, I did build Display and register on my Windows XP machine > > at home (mostly for fun), but using cygwin 5.1. It works nicely, > > no problem. Would you like to try those? > > > > Claude > > _______________________________________________ > > 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 > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Laboratory for Motor Learning and Neural Plasticity Directed by Dr. Virginia Penhune Department of Psychology, Concordia University SP-A 244, 7141 Sherbrooke St. W Montreal, QC H4B 1R6 Canada (514)848-2424 ext. 7567 http://psychology.concordia.ca/fac/penhune/winindex.html From a.janke at gmail.com Fri Jun 27 09:07:09 2008 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 27 Jun 2008 23:07:09 +1000 Subject: [MINC-users] optizing minctracc parameters for heart data In-Reply-To: <160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de> References: <160E3DD4FB702C4CB860C65186686E6902886E23@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E6902425013@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E69029C1E9E@MRZS152229.medizin.uni-leipzig.de> <160E3DD4FB702C4CB860C65186686E69020202A4@MRZS152229.medizin.uni-leipzig.de> Message-ID: Hi Michel On Wed, Jun 25, 2008 at 21:07, Audette, Michel wrote: > after registering inner ear data, I'm now playing with cardiac data. I have preop CT and DynaCT data to register. Can anyone comment about the appropriateness of the default w_translations w_rotations and step parameters appropriate for this anatomy? Seems like you are a busy lad... I dont think there is any more magic beyond "just scale" to the organ size you are working with. In any case I usually just find it simpler to scale the organ and not the parameters. ie: make the heard the size of a brain. > One of the two data sets spans a good part of the chest, but the registration can probably be determined by the heart and aorta alone, and perhaps incrementally improved with masks based on the coronary arteries and aorta. Sounds suspiciously like what happens with registration of mouse brain data. Here I was hoping they would comment on this but no luck so far! :) -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From jason at bic.mni.mcgill.ca Fri Jun 27 09:36:55 2008 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Fri, 27 Jun 2008 09:36:55 -0400 Subject: [MINC-users] optizing minctracc parameters for heart data In-Reply-To: References: <160E3DD4FB702C4CB860C65186686E6902886E23@MRZS152229.medizin.uni-leipzig.de> Message-ID: <4864ECF7.7040909@bic.mni.mcgill.ca> >> One of the two data sets spans a good part of the chest, but the registration can probably be determined by the heart and aorta alone, and perhaps incrementally improved with masks based on the coronary arteries and aorta. >> > > Sounds suspiciously like what happens with registration of mouse brain > data. Here I was hoping they would comment on this but no luck so far! > Allright, I'll bite. We never scale the organ, we change the parameters instead - and -w_translations is the one that you want. We've found it to be fairly insensitive to the exact values, i.e. -w_translations of 0.2 0.2 0.2 works as well as 0.06 for a 0.06 voxel size. Occasional very low values cause segfaults - which we've never gotten around to debugging as they don't happen very often, but be aware. We don't usually change -w_rotations. As for step size, we always use the a series of decreasing step sizes, ending up at either voxel size or, more commonly, twice the voxel size. We use a -sub_lattice of 6 and -lattice_diameter of 3 times the step size in each minctracc call. As for masking - that really depends on how variable the data outside the region of interest for you is. Low variability between source and target means that the mask won't have that great of an impact, high variability means that it could be essential. Similar answer with whether to use the gradients of the blur - for brains we always use them as that gives us better convergence (and mouse brains are very similar to each other), for something like mouse embryos the gradients makes the registration worse so we don't use it. Hope this helps, Jason > :) > > > > From Jean-Francois.Malouin at bic.mni.mcgill.ca Sat Jun 28 12:09:54 2008 From: Jean-Francois.Malouin at bic.mni.mcgill.ca (Jean-Francois Malouin) Date: Sat, 28 Jun 2008 12:09:54 -0400 Subject: [MINC-users] (forw) Display Message-ID: <20080628160954.GA167313@yorick.bic.mni.mcgill.ca> Someone help this soul. jf ----- Forwarded message from David Lee ----- From: David Lee To: Subject: Display Date: Fri, 27 Jun 2008 16:42:01 -0400 Message-ID: User-Agent: Microsoft-Entourage/11.4.0.080122 I was wondering how to fix this error when trying to run "Display" for the first time. I am running on Mac G5, OS 10.4.11. Installed 10.4 version of Display. Error: dyld: Library not loaded: /sw/lib/libglut.3.dylib Referenced from: /usr/local/mni/bin/./Display Reason: image not found Trace/BPT trap Thanks for your help. -David ----- End forwarded message ----- -- < From a.janke at gmail.com Sun Jun 29 03:21:23 2008 From: a.janke at gmail.com (Andrew Janke) Date: Sun, 29 Jun 2008 17:21:23 +1000 Subject: [MINC-users] (forw) Display In-Reply-To: <20080628160954.GA167313@yorick.bic.mni.mcgill.ca> References: <20080628160954.GA167313@yorick.bic.mni.mcgill.ca> Message-ID: Hi David, You will have to use fink to install GLUT. Once Fink is installed (pointy clicky thing) you do something like this in an X11 xterm/Terminal window: $ sudo fink install glut a On Sun, Jun 29, 2008 at 02:09, Jean-Francois Malouin wrote: > Someone help this soul. > jf > > ----- Forwarded message from David Lee ----- > > From: David Lee > To: > Subject: Display > Date: Fri, 27 Jun 2008 16:42:01 -0400 > Message-ID: > User-Agent: Microsoft-Entourage/11.4.0.080122 > > I was wondering how to fix this error when trying to run "Display" for the > first time. > > I am running on Mac G5, OS 10.4.11. Installed 10.4 version of Display. > > Error: > dyld: Library not loaded: /sw/lib/libglut.3.dylib > Referenced from: /usr/local/mni/bin/./Display > Reason: image not found > Trace/BPT trap > > Thanks for your help. > > -David > > ----- End forwarded message ----- > > -- > < > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883