From miriam.friedel at gmail.com Mon Aug 4 14:48:27 2014 From: miriam.friedel at gmail.com (Miriam Friedel) Date: Mon, 4 Aug 2014 14:48:27 -0400 Subject: [MINC-users] Pydpiper: a pipelining toolkit for MINC Message-ID: Hello all, At the Mouse Imaging Centre, we've been working for the last few years on developing a new toolkit for running image registration pipelines. While improvements are ongoing, the core applications and underlying framework are stable, so we wanted to share it with all of you. Our goal with Pydpiper was to create a toolbox of classes and modules that could be combined in different ways to create novel registration pipelines. We've created four applications to begin (described in more detail in the paper linked below), but we hope that others will contribute additional applications as time goes on. In some sense, this is a toolkit for non-developers. While we welcome contributions from seasoned programmers, we hope that scientists with less coding experience will be able to put together their own pipelines without much difficulty. The github repository for Pydpiper is here. Fork it and have fun! https://github.com/mfriedel/pydpiper The paper we've written, which describes Pydpiper in more detail, is here: http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00067/abstract Our wiki, with more information about how to use the toolkit and run it on a virtual machine, is here: https://wiki.mouseimaging.ca/display/MICePub/Pydpiper We welcome your comments and feedback! Miriam From thomas.funck at mail.mcgill.ca Wed Aug 20 15:52:08 2014 From: thomas.funck at mail.mcgill.ca (Thomas Funck) Date: Wed, 20 Aug 2014 19:52:08 +0000 Subject: [MINC-users] Issues installing minc-tools-master Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065317F1425@EXMBX2010-3.campus.MCGILL.CA> Hi, I'm trying to install the "minc-tools-master" package on my computer (Ubuntu 14.04 - Trusty) but have come across the following problem. I successfully ran $LIBMINC_DIR=/home/t/neuro/src2/lib/ $cmake -DCMAKE_INSTALL_PREFIX=/home/t/neuro/src2/ CMakeLists.txt but running "$make" failed: "[ 1%] Built target invert_raw_image [ 2%] Building C object progs/CMakeFiles/minc_modify_header.dir/minc_modify_header/minc_modify_header.c.o /home/t/neuro/quarantines/08-14-minc/tgz/minc-tools-master/progs/minc_modify_header/minc_modify_header.c:98:18: fatal error: minc.h: No such file or directory #include ^ compilation terminated. make[2]: *** [progs/CMakeFiles/minc_modify_header.dir/minc_modify_header/minc_modify_header.c.o] Error 1 make[1]: *** [progs/CMakeFiles/minc_modify_header.dir/all] Error 2 make: *** [all] Error 2" The problem seems very simple, I just don't know how to tell make where "minc.h" is located. I tried setting "LIBMINC_DIR=/home/t/neuro/src2/" but then cmake can't find "libminc2.a". Thanks, Thomas From vladimir.fonov at gmail.com Wed Aug 20 15:55:18 2014 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 20 Aug 2014 15:55:18 -0400 Subject: [MINC-users] Issues installing minc-tools-master In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065317F1425@EXMBX2010-3.campus.MCGILL.CA> References: <53F3FD0032C9CC4BA836E8F0FC289065317F1425@EXMBX2010-3.campus.MCGILL.CA> Message-ID: Hello, I think you actually need minc-toolkit ( https://github.com/BIC-MNI/minc-toolkit ) minc-tools is a collection of basic minc tools which needs libminc to be compiled minc-toolkit is a metaproject which includes everything minc-related (including libminc and minc-tools) On Wed, Aug 20, 2014 at 3:52 PM, Thomas Funck wrote: > Hi, > > I'm trying to install the "minc-tools-master" package on my computer (Ubuntu 14.04 - Trusty) but have come across the following problem. I successfully ran > > $LIBMINC_DIR=/home/t/neuro/src2/lib/ > $cmake -DCMAKE_INSTALL_PREFIX=/home/t/neuro/src2/ CMakeLists.txt > > but running "$make" failed: > > "[ 1%] Built target invert_raw_image > [ 2%] Building C object progs/CMakeFiles/minc_modify_header.dir/minc_modify_header/minc_modify_header.c.o > /home/t/neuro/quarantines/08-14-minc/tgz/minc-tools-master/progs/minc_modify_header/minc_modify_header.c:98:18: fatal error: minc.h: No such file or directory > #include > ^ > compilation terminated. > make[2]: *** [progs/CMakeFiles/minc_modify_header.dir/minc_modify_header/minc_modify_header.c.o] Error 1 > make[1]: *** [progs/CMakeFiles/minc_modify_header.dir/all] Error 2 > make: *** [all] Error 2" > > The problem seems very simple, I just don't know how to tell make where "minc.h" is located. I tried setting "LIBMINC_DIR=/home/t/neuro/src2/" but then cmake can't find "libminc2.a". > > Thanks, > > Thomas > > > > > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com