From a.janke at gmail.com Thu Nov 6 06:02:58 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 6 Nov 2008 22:02:58 +1100 Subject: [MINC-users] mrisim (1.0.2) Message-ID: Hi all, I have just uploaded mrisim 1.0.2 here: http://packages.bic.mni.mcgill.ca/tgz/mrisim-1.0.2.tar.gz This is only a build fix (mainly from to ) as in its current state it would not build on intrepid and thus likely not in later debian releases also. Mind you it is in desperate need of a new maintainer as all I have been doing for the last while is just applying band-aids where needed. :) Let me know if this new package works for you (or not). -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From a.janke at gmail.com Thu Nov 6 08:17:47 2008 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 7 Nov 2008 00:17:47 +1100 Subject: [MINC-users] For the Ubuntu crash test dummies Message-ID: http://packages.bic.mni.mcgill.ca/ubuntu-intrepid/ Note that N3 and brain=-view are not there due to annoying C++ changes that have happened I think with namespaces, the problem itself is with EBTKS from what I can tell so far but have not had time to dig much deeper into the causes. Have fun. -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From a.janke at gmail.com Thu Nov 6 08:18:55 2008 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 7 Nov 2008 00:18:55 +1100 Subject: [MINC-users] For the Ubuntu crash test dummies In-Reply-To: References: Message-ID: On Fri, Nov 7, 2008 at 12:17 AM, Andrew Janke wrote: > http://packages.bic.mni.mcgill.ca/ubuntu-intrepid/ PS: Note that this is still uploading from a machine in oz, so they will all appear there over the next little while. a From se at hst.aau.dk Thu Nov 6 08:55:41 2008 From: se at hst.aau.dk (Simon Fristed Eskildsen) Date: Thu, 6 Nov 2008 14:55:41 +0100 (CET) Subject: [MINC-users] For the Ubuntu crash test dummies In-Reply-To: Message-ID: <1474816711.132841225979741293.JavaMail.root@zimbra-store01.hst.aau.dk> > Note that N3 and brain=-view are not there due to annoying C++ > changes > that have happened I think with namespaces, the problem itself is > with > EBTKS from what I can tell so far but have not had time to dig much > deeper into the causes. Is this related to the problems described in my previous posting "problem with nu_estimate_np_and_em" which were solved by reverting to an earlier minc version? Simon From a.janke at gmail.com Thu Nov 6 21:07:27 2008 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 7 Nov 2008 13:07:27 +1100 Subject: [MINC-users] For the Ubuntu crash test dummies In-Reply-To: <1474816711.132841225979741293.JavaMail.root@zimbra-store01.hst.aau.dk> References: <1474816711.132841225979741293.JavaMail.root@zimbra-store01.hst.aau.dk> Message-ID: > Is this related to the problems described in my previous posting "problem with nu_estimate_np_and_em" which were solved by reverting to an earlier minc version? Nope, 'fraid not. Unless you take "C++ code" as related.. :) a From mishkind at gmail.com Sat Nov 8 22:21:14 2008 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Sat, 8 Nov 2008 22:21:14 -0500 Subject: [MINC-users] mni.cortical.statistics help Message-ID: <9c5abb60811081921j6dd31c63qc27ef215b2bb6f25@mail.gmail.com> Hi, I am using a simple glim file which contains filename,group but my group has three categories (group1,group2,group3). After running y~group here: vs <- mni.vertex.statistics(gf, 'y ~ group', vertex.table=dt) I look at the vertstats file and I have the following tstatistics: tstatistic.group1 tstatistic.group2 tstatistic.intercept What do these mean though? ie Does tstatistic.group1 = group1 vs (group2+group3) ? group1 vs group2 ? group1 vs group3? Is there a way to control the comparisons, or do i have to make separate glim files with a max of two groups in them? Ideally I would like to see group1 vs group 2 group1 vs group 3 group 1 vs group2+group3 thanks, mishkin From nikelski at bic.mni.mcgill.ca Sat Nov 8 22:52:46 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Sat, 8 Nov 2008 22:52:46 -0500 Subject: [MINC-users] mni.cortical.statistics help In-Reply-To: <9c5abb60811081921j6dd31c63qc27ef215b2bb6f25@mail.gmail.com> References: <9c5abb60811081921j6dd31c63qc27ef215b2bb6f25@mail.gmail.com> Message-ID: Hi, Whenever you run a regression using a categorical predictor, one of the levels of that predictor is designated as the reference level; all other groups are compared against that reference. So, I would suggest: (1) use the "relevel" command to make sure that the reference group is the one that you want. (2) as we are using R and not a lesser stats package such as SPSS, I suggest that you explicitly label your levels. See the "levels" and "labels" arguments of the"factor" command. This will make is easier to see what your levels are on your output. (3) you can, of course, run an analysis using one level as the reference, relevel, and then run again using the new reference, if that's useful to you. Enjoy your weekend ;) -Jim On Sat, Nov 8, 2008 at 10:21 PM, Mishkin Derakhshan wrote: > Hi, > I am using a simple glim file which contains > filename,group > but my group has three categories (group1,group2,group3). > > After running y~group here: > vs <- mni.vertex.statistics(gf, 'y ~ group', vertex.table=dt) > > I look at the vertstats file and I have the following tstatistics: > tstatistic.group1 > tstatistic.group2 > tstatistic.intercept > > What do these mean though? ie > Does tstatistic.group1 = > group1 vs (group2+group3) ? > group1 vs group2 ? > group1 vs group3? > > Is there a way to control the comparisons, or do i have to make > separate glim files with a max of two groups in them? > > Ideally I would like to see > group1 vs group 2 > group1 vs group 3 > group 1 vs group2+group3 > > thanks, > mishkin > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University Tel: (514) 340-8222 x 2298 Fax: (514) 340-8295 From mishkind at gmail.com Sun Nov 9 17:27:29 2008 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Sun, 9 Nov 2008 17:27:29 -0500 Subject: [MINC-users] mni.compute.FDR question Message-ID: <9c5abb60811091427o3015af39ib7582dee5d25ec39@mail.gmail.com> Hi, I'm receiving what I think is an error (but might actually be a result?) when I use the mni.compute.FDR function in R from the mni.cortical.statistics package, but I'm not sure. Here is my R code, and the warning messages: library(mni.cortical.statistics) gf <- mni.read.glim.file("input.glim",TRUE,FALSE,"csv") dt <- mni.build.data.table(gf) ms <- mni.mean.statistics(gf, 'y ~ group', vertex.table=dt) summary(ms) vs <- mni.vertex.statistics(gf, 'y ~ group', vertex.table=dt) mni.write.vertex.stats(vs, "output.vertstats", mean.stats=ms, glim.matrix=gf) q <- mni.compute.FDR(vs$tstatistic[,2], df=23, fdr=0.05) Warning messages: 1: In max(r$ix[r$x == TRUE]) : no non-missing arguments to max; returning -Inf 2: In qt((sorted.p.values$x[max(r$ix[r$x == TRUE])])/2, df) : NAs introduced by coercion 3: In return(fdr.threshold, q) : multi-argument returns are deprecated When I check the fdr threshold value it is NA. Does this mean that there are no significant differences between my two groups, or is there an error with my data? The reason I say this is because I ran this exact code three time but with different groups: 1. CONTROLS VS SPMS - i get an fdr threshold 2. CONTROLS VS RRMS - i get NA 3. CONTROLS VS RENAMED-CONTROLS - I also get NA which is how I reverse engineered my theory that there was no significant difference. Of course I want to know if this is the case for sure before I draw any conclusions about my data. thanks, mishkin From jason at bic.mni.mcgill.ca Sun Nov 9 19:02:14 2008 From: jason at bic.mni.mcgill.ca (Jason Lerch) Date: Sun, 9 Nov 2008 19:02:14 -0500 Subject: [MINC-users] mni.compute.FDR question In-Reply-To: <9c5abb60811091427o3015af39ib7582dee5d25ec39@mail.gmail.com> References: <9c5abb60811091427o3015af39ib7582dee5d25ec39@mail.gmail.com> Message-ID: <323299C4-8FD9-409A-A15A-DACBFC169CBD@bic.mni.mcgill.ca> Yup, that's exactly what it means: no results at that FDR - see min(q $q) for the best possible FDR threshold in that particular dataset. Jason On 9-Nov-08, at 5:27 PM, Mishkin Derakhshan wrote: > Hi, > I'm receiving what I think is an error (but might actually be a > result?) when I use the mni.compute.FDR function in R from the > mni.cortical.statistics package, but I'm not sure. > > Here is my R code, and the warning messages: > > library(mni.cortical.statistics) > gf <- mni.read.glim.file("input.glim",TRUE,FALSE,"csv") > dt <- mni.build.data.table(gf) > ms <- mni.mean.statistics(gf, 'y ~ group', vertex.table=dt) > summary(ms) > vs <- mni.vertex.statistics(gf, 'y ~ group', vertex.table=dt) > mni.write.vertex.stats(vs, "output.vertstats", mean.stats=ms, > glim.matrix=gf) > q <- mni.compute.FDR(vs$tstatistic[,2], df=23, fdr=0.05) > > Warning messages: > 1: In max(r$ix[r$x == TRUE]) : > no non-missing arguments to max; returning -Inf > 2: In qt((sorted.p.values$x[max(r$ix[r$x == TRUE])])/2, df) : > NAs introduced by coercion > 3: In return(fdr.threshold, q) : multi-argument returns are deprecated > > > When I check the fdr threshold value it is NA. Does this mean that > there are no significant differences between my two groups, or is > there an error with my data? The reason I say this is because I ran > this exact code three time but with different groups: > 1. CONTROLS VS SPMS - i get an fdr threshold > 2. CONTROLS VS RRMS - i get NA > 3. CONTROLS VS RENAMED-CONTROLS - I also get NA > > which is how I reverse engineered my theory that there was no > significant difference. Of course I want to know if this is the case > for sure before I draw any conclusions about my data. > > thanks, > mishkin > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users From kumakura at bic.mni.mcgill.ca Mon Nov 10 22:42:39 2008 From: kumakura at bic.mni.mcgill.ca (Yoshitaka KUMAKURA) Date: Mon, 10 Nov 2008 22:42:39 -0500 Subject: [MINC-users] VOI value extraction on Windows Message-ID: Dear all, Is there any free Windows software that displays .mnc or .nii 3D images, sets simple VOIs and calculates the mean values? Something easy for beginners would be better. Best regards, Yoshi From a.janke at gmail.com Mon Nov 10 23:17:52 2008 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 11 Nov 2008 15:17:52 +1100 Subject: [MINC-users] VOI value extraction on Windows In-Reply-To: References: Message-ID: Hi, There is at least mricron for .nii files. I think it does what you want. http://www.sph.sc.edu/comd/rorden/mricron/ You can make register/display work on windows via cygwin but it is not always for the faint hearted. a On Tue, Nov 11, 2008 at 2:42 PM, Yoshitaka KUMAKURA wrote: > Dear all, > > Is there any free Windows software that displays .mnc or .nii 3D images, > sets simple VOIs and calculates the mean values? Something easy for > beginners would be better. > > Best regards, > Yoshi > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From vladimir.fonov at gmail.com Mon Nov 10 23:27:57 2008 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Mon, 10 Nov 2008 23:27:57 -0500 Subject: [MINC-users] VOI value extraction on Windows In-Reply-To: References: Message-ID: <491909CD.3080802@gmail.com> Hello, Yoshitaka KUMAKURA wrote: > Is there any free Windows software that displays .mnc or .nii 3D images, > sets simple VOIs and calculates the mean values? Something easy for > beginners would be better. I think the most user-friendly way to do this right now is to install virtual machine with Ubuntu and then install minc packages. You can also try ITKsnap for VOI drawing and visualization ( http://www.itksnap.org/ ) it is very possible that it will have MINC support soon, especially if somebody will be willing to test it. -- Best regards, Vladimir S. Fonov ~ vladimir.fonov gmail.com From kumakura at bic.mni.mcgill.ca Wed Nov 12 01:12:23 2008 From: kumakura at bic.mni.mcgill.ca (Yoshitaka KUMAKURA) Date: Wed, 12 Nov 2008 01:12:23 -0500 Subject: [MINC-users] VOI value extraction on Windows In-Reply-To: <491909CD.3080802@gmail.com> References: <491909CD.3080802@gmail.com> Message-ID: Thank you, Andrew and Vladimir. Yoshi On Mon, 10 Nov 2008, Vladimir S. Fonov wrote: > Hello, > > Yoshitaka KUMAKURA wrote: > > Is there any free Windows software that displays .mnc or .nii 3D images, > > sets simple VOIs and calculates the mean values? Something easy for > > beginners would be better. > > I think the most user-friendly way to do this right now is to install > virtual machine with Ubuntu and then install minc packages. > > You can also try ITKsnap for VOI drawing and visualization ( > http://www.itksnap.org/ ) it is very possible that it will have MINC > support soon, especially if somebody will be willing to test it. > -- > Best regards, > Vladimir S. Fonov ~ vladimir.fonov gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From alex at bic.mni.mcgill.ca Wed Nov 12 16:19:20 2008 From: alex at bic.mni.mcgill.ca (Alex Zijdenbos) Date: Wed, 12 Nov 2008 16:19:20 -0500 Subject: [MINC-users] MINC virtual machine [was: VOI value extraction on Windows] Message-ID: Hello all, Given Vladimir's suggestion and that I was just building one of these, I made a Ubuntu virtual machine with Andrew's 'mincbundle' installed in it, available at: http://packages.bic.mni.mcgill.ca/virtual-machines/ I also added some rudimentary instructions; hopefully it will serve somebody :) -- Alex On Mon, Nov 10, 2008 at 11:27 PM, Vladimir S. Fonov wrote: > Hello, > > Yoshitaka KUMAKURA wrote: >> Is there any free Windows software that displays .mnc or .nii 3D images, >> sets simple VOIs and calculates the mean values? Something easy for >> beginners would be better. > > I think the most user-friendly way to do this right now is to install > virtual machine with Ubuntu and then install minc packages. > > You can also try ITKsnap for VOI drawing and visualization ( > http://www.itksnap.org/ ) it is very possible that it will have MINC > support soon, especially if somebody will be willing to test it. > -- > Best regards, > Vladimir S. Fonov ~ vladimir.fonov gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From a.janke at gmail.com Wed Nov 12 16:44:07 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 13 Nov 2008 08:44:07 +1100 Subject: [MINC-users] MINC virtual machine [was: VOI value extraction on Windows] In-Reply-To: References: Message-ID: Hi Alex, Looks like good fun.. ;) a 2008/11/13 Alex Zijdenbos : > Hello all, > > Given Vladimir's suggestion and that I was just building one of these, > I made a Ubuntu virtual machine with Andrew's 'mincbundle' installed > in it, available at: > > http://packages.bic.mni.mcgill.ca/virtual-machines/ > > I also added some rudimentary instructions; hopefully it will serve somebody :) > > -- Alex > > > On Mon, Nov 10, 2008 at 11:27 PM, Vladimir S. Fonov > wrote: >> Hello, >> >> Yoshitaka KUMAKURA wrote: >>> Is there any free Windows software that displays .mnc or .nii 3D images, >>> sets simple VOIs and calculates the mean values? Something easy for >>> beginners would be better. >> >> I think the most user-friendly way to do this right now is to install >> virtual machine with Ubuntu and then install minc packages. >> >> You can also try ITKsnap for VOI drawing and visualization ( >> http://www.itksnap.org/ ) it is very possible that it will have MINC >> support soon, especially if somebody will be willing to test it. >> -- >> Best regards, >> Vladimir S. Fonov ~ vladimir.fonov gmail.com >> _______________________________________________ >> 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 > -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From ljoh06 at hst.aau.dk Thu Nov 20 08:34:06 2008 From: ljoh06 at hst.aau.dk (Lars Johannesen) Date: Thu, 20 Nov 2008 14:34:06 +0100 Subject: [MINC-users] Regarding Ubuntu packages Message-ID: <4925674E.9030804@hst.aau.dk> Hello, I tried to compile emma 0.9.9 (newest version from: http://packages.bic.mni.mcgill.ca/tgz/), I am running Ubuntu Feisty AMD64 with the minc package from: http://packages.bic.mni.mcgill.ca/ubuntu-feisty-amd64/. And when compiling the mex-part, I got a error about lacking -fPIC, so I downloaded the newest minc2 tarball from same place as emma, configured with: ./configure --with-pic Normal build, and re-compiled emma and it worked fine - allthough there are some directories in the source directory of emma which seems to be made for minc1 ? Could it be that the minc2 ubuntu package lacks -fPIC ? and is it possible to get the ubuntu-source package ? Thanks in advance Best regards Lars Johannesen From nikelski at bic.mni.mcgill.ca Thu Nov 20 11:11:17 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Thu, 20 Nov 2008 11:11:17 -0500 Subject: [MINC-users] Intracranial Volume? Message-ID: Hi All, I'm currently doing some cortical thickness regressions, and would like to include a measure of intracranial volume as a covariate. Now, I know that I can get a measure of brain volume using either the Civet (native) brain mask, or by summing the tissue classification components (CSF,GM,WM), however, brain volume does not include the volume of CSF located between the cortical surface and the inner aspect of the skull. For a normal, young population, these measures may be effectively the same, but for elderly and demented, they are not. Any ideas? Cheers, -Jim -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University From sridar at mrs.mni.mcgill.ca Thu Nov 20 12:37:06 2008 From: sridar at mrs.mni.mcgill.ca (Dr. Sridar Narayanan) Date: Thu, 20 Nov 2008 12:37:06 -0500 Subject: [MINC-users] Intracranial Volume In-Reply-To: Message-ID: Hi Jim, Speak to Louis. He has the code to compute intracranial capacity (ICC) as part of his BICCR (Brain to ICC Ratio) measure of normalized brain volume. If you have a PD-weighted scan as part of your acquisition, you should be in business. Sridar > > Message: 2 > Date: Thu, 20 Nov 2008 11:11:17 -0500 > From: "EJ Nikelski" > Subject: [MINC-users] Intracranial Volume? > To: "minc users" > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi All, > > I'm currently doing some cortical thickness regressions, and would > like to include a measure of intracranial volume as a covariate. Now, > I know that I can get a measure of brain volume using either the Civet > (native) brain mask, or by summing the tissue classification > components (CSF,GM,WM), however, brain volume does not include the > volume of CSF located between the cortical surface and the inner > aspect of the skull. For a normal, young population, these measures > may be effectively the same, but for elderly and demented, they are > not. Any ideas? > > Cheers, > > -Jim > From a.janke at gmail.com Mon Nov 24 01:21:20 2008 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 24 Nov 2008 17:21:20 +1100 Subject: [MINC-users] Regarding Ubuntu packages In-Reply-To: <4925674E.9030804@hst.aau.dk> References: <4925674E.9030804@hst.aau.dk> Message-ID: Hi Lars, On Fri, Nov 21, 2008 at 12:34 AM, Lars Johannesen wrote: > I tried to compile emma 0.9.9 (newest version from: > http://packages.bic.mni.mcgill.ca/tgz/), I am running Ubuntu Feisty > AMD64 with the minc package from: > http://packages.bic.mni.mcgill.ca/ubuntu-feisty-amd64/. > > And when compiling the mex-part, I got a error about lacking -fPIC, so I > downloaded the newest minc2 tarball from same place as emma, configured > with: > ./configure --with-pic > > Normal build, and re-compiled emma and it worked fine > > Could it be that the minc2 ubuntu package lacks -fPIC ? Well I can say that it does. Given that I dont specify it. What I think is going on here though is that before packaging I strip out all the libtool .la files. There are many reasons for this but the predominant one is that the current build system I use to do this gets the build paths wrong and thus would give more pain than it is worth. The better answer to this is that I am currently working on getting my own PPA up and going here: https://launchpad.net/~a.janke/+archive For all the MINC tools that will build (finally) upon Steve Robins minc-tools build for Debian/Ubuntu. > and is it > possible to get the ubuntu-source package ? Certainly: http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.16.tar.gz Is what I build from. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From ljoh06 at hst.aau.dk Mon Nov 24 04:11:12 2008 From: ljoh06 at hst.aau.dk (Lars Johannesen) Date: Mon, 24 Nov 2008 10:11:12 +0100 Subject: [MINC-users] Regarding Ubuntu packages In-Reply-To: References: <4925674E.9030804@hst.aau.dk> Message-ID: <492A6FB0.6070009@hst.aau.dk> Andrew Janke skrev: > Hi Lars, > > On Fri, Nov 21, 2008 at 12:34 AM, Lars Johannesen wrote: > >> I tried to compile emma 0.9.9 (newest version from: >> http://packages.bic.mni.mcgill.ca/tgz/), I am running Ubuntu Feisty >> AMD64 with the minc package from: >> http://packages.bic.mni.mcgill.ca/ubuntu-feisty-amd64/. >> >> And when compiling the mex-part, I got a error about lacking -fPIC, so I >> downloaded the newest minc2 tarball from same place as emma, configured >> with: >> ./configure --with-pic >> >> Normal build, and re-compiled emma and it worked fine >> >> Could it be that the minc2 ubuntu package lacks -fPIC ? >> > > Well I can say that it does. Given that I dont specify it. What I > think is going on here though is that before packaging I strip out all > the libtool .la files. There are many reasons for this but the > predominant one is that the current build system I use to do this gets > the build paths wrong and thus would give more pain than it is worth. > Ok just had to confirm, not that strong in packaging, just thought I'd mention linkage problems. > The better answer to this is that I am currently working on getting my > own PPA up and going here: > > https://launchpad.net/~a.janke/+archive > > For all the MINC tools that will build (finally) upon Steve Robins > minc-tools build for Debian/Ubuntu. > Nice :) looking forward to it, will the emma toolbox be included in this ? > >> and is it >> possible to get the ubuntu-source package ? >> > > Certainly: > > http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.16.tar.gz > > Is what I build from. > Ok I mentioned the tarballs just to state, that it is not a version problem. best regards Lars > > From kumakura at bic.mni.mcgill.ca Wed Nov 26 08:35:04 2008 From: kumakura at bic.mni.mcgill.ca (Yoshitaka KUMAKURA) Date: Wed, 26 Nov 2008 08:35:04 -0500 Subject: [MINC-users] mnc2nii dumps core In-Reply-To: <492A6FB0.6070009@hst.aau.dk> References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> Message-ID: Dear minc-users, I have encountered a mnc file that can't be converted to nii. The clue seems to be nvox = '0', where I usually get '33554432'. How can I get this done properly? yoshi at ubuntu-vm:~$ mnc2nii -nii DRPLA_FDG_Feb1308_Q129ms1.mnc MINC type 5 signed 1 Segmentation fault (core dumped) Best regards, Yoshi From claude at bic.mni.mcgill.ca Wed Nov 26 11:02:14 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Wed, 26 Nov 2008 11:02:14 -0500 (EST) Subject: [MINC-users] mnc2nii dumps core References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> Message-ID: <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> Hi, For starters, what version are you using? Please post the result of this command: mnc2nii -version If you have an old version, I will recommend to use the latest version. If that does not work, I can investigate the problem if you can give me access to the mnc file. Usually mnc2nii works. Yours, Claude > I have encountered a mnc file that can't be converted to nii. The clue > seems to be nvox = '0', where I usually get '33554432'. How can I get this > done properly? > > yoshi at ubuntu-vm:~$ mnc2nii -nii DRPLA_FDG_Feb1308_Q129ms1.mnc > nifti_type = 'NIFTI-1+' > header_filename = 'DRPLA_FDG_Feb1308_Q129ms1.nii' > image_filename = 'DRPLA_FDG_Feb1308_Q129ms1.nii' > image_offset = '0' > ndim = '3' > nx = '256' > ny = '256' > nz = '512' > dx = '0.047' > dy = '0.047' > dz = '0.047' > datatype = '16' > datatype_name = 'FLOAT32' > nvox = '0' > nbyper = '4' > byteorder = 'LSB_FIRST' > scl_slope = '1' > scl_inter = '0' > xyz_units = '2' > xyz_units_name = 'mm' > time_units = '8' > time_units_name = 's' > descrip = 'mnc2nii DRPLA_FDG_Feb1308_Q129ms1.mnc' > sform_code = '1' > sform_code_name = 'Scanner Anat' > sto_xyz_matrix = '0.047 0 0 -6.016 0 0.047 0 -6.016 0 0 0.047 -12.032 0 > 0 0 1' > sto_ijk matrix = '21.2766 0 0 128 0 21.2766 0 128 0 0 21.2766 256 0 0 0 > 1' > sform_i_orientation = 'Left-to-Right' > sform_j_orientation = 'Posterior-to-Anterior' > sform_k_orientation = 'Inferior-to-Superior' > /> > MINC type 5 signed 1 > Segmentation fault (core dumped) > > > Best regards, > Yoshi > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From nikelski at bic.mni.mcgill.ca Wed Nov 26 23:56:38 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Wed, 26 Nov 2008 23:56:38 -0500 Subject: [MINC-users] ubuntu-intrepid packages available? Message-ID: Hi All, In order to see how the other half lives, I decided to do a full minc-bic install on my newly installed Ubuntu 8.10 machine using the pre-built packages (thanks, Andrew!). At any rate, I modified my sources.list to point at the BIC Intrepid packages, did the obligatory "sudo apt-get update", and then tried "sudo apt-get install mincbundle". Sadly, I get "Couldn't find package mincbundle". Ideas? I've noticed that the "Packages" file is empty ... don't know whether this is significant. Any help would be appreciated. Cheers, -Jim From a.janke at gmail.com Thu Nov 27 01:09:44 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 27 Nov 2008 17:09:44 +1100 Subject: [MINC-users] ubuntu-intrepid packages available? In-Reply-To: References: Message-ID: Hi Jim, On Thu, Nov 27, 2008 at 3:56 PM, EJ Nikelski wrote: > In order to see how the other half lives, I decided to do a full > minc-bic install on my newly installed Ubuntu 8.10 machine using the > pre-built packages (thanks, Andrew!). At any rate, I modified my > sources.list to point at the BIC Intrepid packages, did the obligatory > "sudo apt-get update", and then tried "sudo apt-get install > mincbundle". Sadly, I get "Couldn't find package mincbundle". Ideas? At the moment I am still in the throes of fixing a show stopper bug with EBTKS + N3. However to keep the early adopters satiated I have just started to upload what I do have built for Intrepid now. (with a Packages file!) Give it a few minutes to synch from Oz and you should be good on amd64 platforms. There is also a show-stopper bug in ParseArgv that I am in the process of figuring out the best fix for. This means that some options for minc commands will not be set correctly (like -verbose and -clobber) in some cases. Buyer beware! :) -- Andrew Janke - andrew.janke at anu.edu.au Department of Geriatric Medicine, ANU (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From kumakura at bic.mni.mcgill.ca Thu Nov 27 03:37:40 2008 From: kumakura at bic.mni.mcgill.ca (Yoshitaka KUMAKURA) Date: Thu, 27 Nov 2008 03:37:40 -0500 Subject: [MINC-users] mnc2nii dumps core In-Reply-To: <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> Message-ID: Dear Claude, Thank you for your reply. mnc2nii -version returns: program: 1.4 libminc: 1.4 netcdf : 3.6.1 of Mar 5 2007 07:16:16 $ I tried to install minc 1.51, but no success. Is minc 1.4 too old? I am ready to send you the minc file with a normal file from the same scanner. Best regards, Yoshi Kumakura On Wed, 26 Nov 2008, Claude LEPAGE wrote: > Hi, > > For starters, what version are you using? Please post the result of this command: > > mnc2nii -version > > If you have an old version, I will recommend to use the latest version. If > that does not work, I can investigate the problem if you can give me access > to the mnc file. Usually mnc2nii works. > > Yours, > > Claude > > > I have encountered a mnc file that can't be converted to nii. The clue > > seems to be nvox = '0', where I usually get '33554432'. How can I get this > > done properly? > > > > yoshi at ubuntu-vm:~$ mnc2nii -nii DRPLA_FDG_Feb1308_Q129ms1.mnc > > > nifti_type = 'NIFTI-1+' > > header_filename = 'DRPLA_FDG_Feb1308_Q129ms1.nii' > > image_filename = 'DRPLA_FDG_Feb1308_Q129ms1.nii' > > image_offset = '0' > > ndim = '3' > > nx = '256' > > ny = '256' > > nz = '512' > > dx = '0.047' > > dy = '0.047' > > dz = '0.047' > > datatype = '16' > > datatype_name = 'FLOAT32' > > nvox = '0' > > nbyper = '4' > > byteorder = 'LSB_FIRST' > > scl_slope = '1' > > scl_inter = '0' > > xyz_units = '2' > > xyz_units_name = 'mm' > > time_units = '8' > > time_units_name = 's' > > descrip = 'mnc2nii DRPLA_FDG_Feb1308_Q129ms1.mnc' > > sform_code = '1' > > sform_code_name = 'Scanner Anat' > > sto_xyz_matrix = '0.047 0 0 -6.016 0 0.047 0 -6.016 0 0 0.047 -12.032 0 > > 0 0 1' > > sto_ijk matrix = '21.2766 0 0 128 0 21.2766 0 128 0 0 21.2766 256 0 0 0 > > 1' > > sform_i_orientation = 'Left-to-Right' > > sform_j_orientation = 'Posterior-to-Anterior' > > sform_k_orientation = 'Inferior-to-Superior' > > /> > > MINC type 5 signed 1 > > Segmentation fault (core dumped) > > > > > > Best regards, > > Yoshi > > > > _______________________________________________ > > 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 a.janke at gmail.com Thu Nov 27 07:03:55 2008 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 27 Nov 2008 23:03:55 +1100 Subject: [MINC-users] mnc2nii dumps core In-Reply-To: References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> Message-ID: > mnc2nii -version returns: > > program: 1.4 > libminc: 1.4 > netcdf : 3.6.1 of Mar 5 2007 07:16:16 $ Hi, Not much work has gone into MINC 1.X for quite some time now. I would recommend you go with MINC 2.0.16 from here: http://packages.bic.mni.mcgill.ca/tgz What platform as you running on? There may be pre-built binaries to suit. -- Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/) Canberra->Australia +61 (402) 700 883 From sean at rogue-research.com Thu Nov 27 10:55:20 2008 From: sean at rogue-research.com (Sean McBride) Date: Thu, 27 Nov 2008 10:55:20 -0500 Subject: [MINC-users] mnc2nii dumps core In-Reply-To: References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> Message-ID: <20081127155520.1709833785@kingu.local> On 11/27/08 11:03 PM, Andrew Janke said: >Not much work has gone into MINC 1.X for quite some time now. I would >recommend you go with MINC 2.0.16 from here: > > http://packages.bic.mni.mcgill.ca/tgz Nice to see a new release! What is the state of CMake support? I notice that the CMakeLists.txt contains: SET(CPACK_PACKAGE_VERSION_MAJOR 2) SET(CPACK_PACKAGE_VERSION_MINOR 0) SET(CPACK_PACKAGE_VERSION_PATCH 14) Perhaps there have been no recent changes in that department? Also, the 'ChangeLog' file is helpful, and having dates in there is great, but it's hard to figure out what changed between 2.0.15 and 2.0.16. Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From kumakura at bic.mni.mcgill.ca Fri Nov 28 12:52:35 2008 From: kumakura at bic.mni.mcgill.ca (Yoshitaka KUMAKURA) Date: Fri, 28 Nov 2008 12:52:35 -0500 Subject: [MINC-users] mnc2nii dumps core In-Reply-To: References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> Message-ID: Hello, mnc2nii of version 1.5 that I've just installed returns nvox = '1073741824'. Could this nvox depend on the versions of mnc2nii? I have no idea what this means. I tried installing minc2, which I am not familiar with, but I could not find how to convert a file in minc to nii, though I did not spend much time. So, I will now try to circumvent this problem, but leave my strange mnc file in /scratch2/yoshi just for possible improvement of minc. I appreciate all the suggestions posted. Have a nice weekend. Yoshi On Thu, 27 Nov 2008, Andrew Janke wrote: > > mnc2nii -version returns: > > > > program: 1.4 > > libminc: 1.4 > > netcdf : 3.6.1 of Mar 5 2007 07:16:16 $ > > Hi, > > Not much work has gone into MINC 1.X for quite some time now. I would > recommend you go with MINC 2.0.16 from here: > > http://packages.bic.mni.mcgill.ca/tgz > > What platform as you running on? There may be pre-built binaries to suit. > > > -- > 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 claude at bic.mni.mcgill.ca Fri Nov 28 13:38:07 2008 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Fri, 28 Nov 2008 13:38:07 -0500 (EST) Subject: [MINC-users] mnc2nii dumps core References: <4925674E.9030804@hst.aau.dk> <492A6FB0.6070009@hst.aau.dk> <200811261602.mAQG2EQZ4769144@yorick.bic.mni.mcgill.ca> Message-ID: <200811281838.mASIc7ep4894315@yorick.bic.mni.mcgill.ca> Hi Yoshi, I was able to reproduce the error with the latest version of mnc2nii. The program reports the following description: Hello, Can anyone help me with solving the following error please? I am trying to average the hemispheric object files of 50 subjects. (I am using matlab 6.1 on a local linux box.) Many thanks, Najma >> avsurf = SurfStatAvSurf( filesboth ); 50 x 2 files to read, % remaining: 100 ??? Error using ==> + Function '+' not defined for variables of class 'int32'. Error in ==> /export01/local/matlab7a/toolbox/surfstat/SurfStatReadSurf.m On line 66 ==> surf.tri=[surf.tri; int32(s.tri)+size(c,2)]; Error in ==> /export01/local/matlab7a/toolbox/surfstat/SurfStatAvSurf.m On line 29 ==> [s,ab]=SurfStatReadSurf(filenames(i,:),ab,2); From nikelski at bic.mni.mcgill.ca Fri Nov 28 18:36:00 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Fri, 28 Nov 2008 18:36:00 -0500 Subject: [MINC-users] [avsurf error]: Function '+' not defined for variables of class 'int32' In-Reply-To: References: Message-ID: Hi Najma, Are you using Surfstat to do this because you really want to ... or would you be willing to create the average surface with another (easier) method? Personally, I would use "average_objects" from the bicpl package. Just do ... >average_objects out.obj in1.obj in2.obj in3.obj ... (note that the output obj is the *first* argument.) Cheers, -Jim On Fri, Nov 28, 2008 at 4:41 PM, Najmeh Khalili M. wrote: > > Hello, > > Can anyone help me with solving the following error please? > I am trying to average the hemispheric object files of 50 > subjects. (I am using matlab 6.1 on a local linux box.) > > Many thanks, > Najma > >>> avsurf = SurfStatAvSurf( filesboth ); > 50 x 2 files to read, % remaining: 100 ??? Error using ==> + > Function '+' not defined for variables of class 'int32'. > > Error in ==> > /export01/local/matlab7a/toolbox/surfstat/SurfStatReadSurf.m > On line 66 ==> surf.tri=[surf.tri; > int32(s.tri)+size(c,2)]; > > Error in ==> > /export01/local/matlab7a/toolbox/surfstat/SurfStatAvSurf.m > On line 29 ==> > [s,ab]=SurfStatReadSurf(filenames(i,:),ab,2); > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University Tel: (514) 340-8222 x 2298 Fax: (514) 340-8295 From najma at bic.mni.mcgill.ca Sat Nov 29 00:47:48 2008 From: najma at bic.mni.mcgill.ca (Najmeh Khalili M.) Date: Sat, 29 Nov 2008 00:47:48 -0500 Subject: [MINC-users] [avsurf error]: Function '+' not defined for variables of class 'int32' In-Reply-To: References: Message-ID: Hi Jon & Jim; thanks for responding. In fact the matlab problem was because the matlab's int32 function worked only with matlab7 (and not matlab6.1 which I was using). HT to Pierre Bellec! Cheers Naj On Fri, 28 Nov 2008, EJ Nikelski wrote: > Hi Najma, > > Are you using Surfstat to do this because you really want to ... or > would you be willing to create the average surface with another > (easier) method? Personally, I would use "average_objects" from the > bicpl package. Just do ... > >average_objects out.obj in1.obj in2.obj in3.obj ... (note that the output obj is the *first* argument.) > > Cheers, > > -Jim > > > On Fri, Nov 28, 2008 at 4:41 PM, Najmeh Khalili M. > wrote: > > > > Hello, > > > > Can anyone help me with solving the following error please? > > I am trying to average the hemispheric object files of 50 > > subjects. (I am using matlab 6.1 on a local linux box.) > > > > Many thanks, > > Najma > > > >>> avsurf = SurfStatAvSurf( filesboth ); > > 50 x 2 files to read, % remaining: 100 ??? Error using ==> + > > Function '+' not defined for variables of class 'int32'. > > > > Error in ==> > > /export01/local/matlab7a/toolbox/surfstat/SurfStatReadSurf.m > > On line 66 ==> surf.tri=[surf.tri; > > int32(s.tri)+size(c,2)]; > > > > Error in ==> > > /export01/local/matlab7a/toolbox/surfstat/SurfStatAvSurf.m > > On line 29 ==> > > [s,ab]=SurfStatReadSurf(filenames(i,:),ab,2); > > > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > -- > ================================= > Jim Nikelski, Ph.D. > Postdoctoral Research Fellow > Bloomfield Centre for Research in Aging > Lady Davis Institute for Medical Research > Sir Mortimer B. Davis - Jewish General Hospital > McGill University > Tel: (514) 340-8222 x 2298 > Fax: (514) 340-8295 > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From nikelski at bic.mni.mcgill.ca Sun Nov 30 13:58:36 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Sun, 30 Nov 2008 13:58:36 -0500 Subject: [MINC-users] Intrepid I386 packages Message-ID: Hi All (and Andrew!), I've noticed that the Intrepid Packages file has been updated for amd64, however, Packages does *not* include the i386 packages ... although they do seem to be built. Sadly, as I am using an older amd-32 bit machine, the i386 packages would be awfully handy. Any reason why they were not included in Packages? Just curious. Thanks for all the work Andrew. -Jim -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University From a.janke at gmail.com Sun Nov 30 18:35:19 2008 From: a.janke at gmail.com (Andrew Janke) Date: Mon, 1 Dec 2008 10:35:19 +1100 Subject: [MINC-users] Intrepid I386 packages In-Reply-To: References: Message-ID: Hi Jim, On Mon, Dec 1, 2008 at 5:58 AM, EJ Nikelski wrote: > I've noticed that the Intrepid Packages file has been updated for > amd64, however, Packages does *not* include the i386 packages ... > although they do seem to be built. Sadly, as I am using an older > amd-32 bit machine, the i386 packages would be awfully handy. Any > reason why they were not included in Packages? Just curious. Try now. (well in about 20 minutes from now -- they are uploading). Unfortunately the machine that I build the 32 bit versions on is not that speedy.. meaning that they often don't build in time for the rsync thing that makes the Packages file. Time to adjust a cron entry I think. a From nikelski at bic.mni.mcgill.ca Sun Nov 30 21:27:44 2008 From: nikelski at bic.mni.mcgill.ca (EJ Nikelski) Date: Sun, 30 Nov 2008 21:27:44 -0500 Subject: [MINC-users] Intrepid I386 packages In-Reply-To: References: Message-ID: Hi Andrew, Yup, "apt-get mincbundle" now does its magic for the i386 packages. An initial brief examination looks good, with the exception that the various model files (305, 152, etc) do not appear to be apt-get-able. Thanks again for your help. Cheers, -Jim On Sun, Nov 30, 2008 at 6:35 PM, Andrew Janke wrote: > Hi Jim, > > On Mon, Dec 1, 2008 at 5:58 AM, EJ Nikelski wrote: >> I've noticed that the Intrepid Packages file has been updated for >> amd64, however, Packages does *not* include the i386 packages ... >> although they do seem to be built. Sadly, as I am using an older >> amd-32 bit machine, the i386 packages would be awfully handy. Any >> reason why they were not included in Packages? Just curious. > > Try now. (well in about 20 minutes from now -- they are uploading). > > Unfortunately the machine that I build the 32 bit versions on is not > that speedy.. meaning that they often don't build in time for the > rsync thing that makes the Packages file. Time to adjust a cron entry > I think. > > > a > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- ================================= Jim Nikelski, Ph.D. Postdoctoral Research Fellow Bloomfield Centre for Research in Aging Lady Davis Institute for Medical Research Sir Mortimer B. Davis - Jewish General Hospital McGill University Tel: (514) 340-8222 x 2298 Fax: (514) 340-8295