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| [[Navigation(children)]] | = FreeSurfer Dev Guide = |
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| '''Index''' | * Visit the BuildGuide for instructions on building and installing freesurfer manually. * Visit the GitHub page for an introduction to the github workflow. * Visit the GitAnnex page for detailed instructions on using git annex. |
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| [[TableOfContents]] | == Adding a New C Program == |
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| === Medical Image Format FAQ === [http://www.dclunie.com/medical-image-faq/html Medical Image Format FAQ] === CVS Checkout === You can checkout the FreeSurfer source code from the NMR center using local CVS access or remotely by using SSH as the CVS remote connection method. ==== Local CVS Access ==== The CVS repository is /space/repo/1/dev. Use this as your CVSROOT. You can either set it as an environment variable: {{{setenv CVSROOT /space/repo/1/dev}}} or specify it in the checkout command with the -d option. Note that the CVS root is cached in a CVS checkout directory, so if you choose to use the -d method, you will only have to do it once during your first checkout. Check out the code with the CVS checkout command. The archive name is dev. {{{cvs checkout dev}}} or {{{cvs -d /space/repo/1/dev checkout dev}}} This will copy the entire archive to your directory, creating a directory called dev/. Now set up your environment to use this dev directory by running the script in dev/: {{{cd dev source set_dev_env_to_here.csh}}} ==== Remote CVS Access ==== Tell CVS to use SSH to access the archive by setting the following environment variable: {{{setenv CVS_RSH ssh}}} Use the following string as your CVS root: {{{:ext:USER@MACHINE.nmr.mgh.harvard.edu:/space/repo/1/dev}}} Where USER is your username and MACHINE is one of the NMR machines visible to the outside, i.e. gate, entry, or door. Then use the CVS commands normally. Note that using this method makes an SSH connection for every CVS command, and you will be required to enter your password every time. You may want to look into a utility to automatically authenticate SSH connections, such as SSH agent. === Building === ==== Adding a new binary to the tree ==== Assuming that you have a source file {{{MYPROG.c}}} that compiles into MYPROG and want to add it to the FreeSurfer tree: 1) Make the directory in dev and copy the source file there. Name the directory MYPROG and the source file {{{MYPROG.c}}}. |
If you'd like to add a new program to the tree, you should create a new subdirectory with the title of your tool. As an example, let's create a new c++ program called `mri_process`. First, we'll create a top-level subdirectory that contains our new c++ file and an empty `CMakeLists.txt` file: |
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| mkdir dev/MYPROG cp MYPROG.c dev/MYPROG |
freesurfer/ mri_process/ CMakeLists.txt mri_process.cpp |
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| 2) Tell the autotools to build your program when you type {{{make}}} from the top dir. a) Modify {{{dev/configure.in}}} to add {{{MYPROG/Makefile}}} to the list at the end of the file in the definition of {{{AC_OUTPUT}}}. Be sure to add a backslash at the end of line: |
In order to configure our new code, we should add the following to the empty `CMakeLists.txt` file. |
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| AC_OUTPUT( \ ... other files ... MYPROG/Makefile \ ) |
project(mri_process) include_directories(${FS_INCLUDE_DIRS}) add_executable(mri_process mri_process.cpp) target_link_libraries(mri_process utils) install(TARGETS mri_process DESTINATION bin) |
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| b) Modify {{{dev/Makefile.am}}} to add {{{MYPROG}}} to the {{{SUBDIRS}}} definition. (You can also alternatively it to the end of {{{MRISUBDIRS}}} or {{{MRISSUBDIRS}}} if more appropriate.) {{{ SUBDIRS= ... other directories ... MYPROG }}} c) Copy {{{dev/dummy/Makefile.am}}} into {{{MYPROG/}}} and customize it, replacing 'dummy' with 'MYPROG'. Be sure to change: {{{ bin_PROGRAMS = MYPROG }}} d) Copy in the additional testing file {{{dev/dummy/myown.c}}}. You can customize it for your test program later. 3) Run {{{automake}}} from {{{dev/}}}. You should get no errors. If you do, make sure you followed the above instructions properly. Also try the AutoconfTroubleshooting page. Verify that this stepped work by checking if {{{MYPROG/Makefile.in}}} was created. 4) Run {{{autoconf}}} to generate a new {{{configure}}} script that now includes your new MYPROG directory. 5) Run {{{./configure}}} with the parameters you previously used. To check these out, run {{{head config.log}}} from {{{dev/}}}. The output should include the {{{./configure}}} line you used. Copy it, but leave out the {{{--no-create --no-recursion}}} options if present. {{{ [dev/]$ head config.log This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by Freesurfer configure 0.1, which was generated by GNU Autoconf 2.57. Invocation command line was $ ./configure --with-mni-dir=/usr/pubsw/packages/mni/current --prefix=/home/kteich/freesurfer/dev --no-create --no-recursion ## --------- ## ## Platform. ## [dev/]$ ./configure --with-mni-dir=/usr/pubsw/packages/mni/current --prefix=/home/kteich/freesurfer/dev }}} Note: Do not just copy this example, use what's in your own {{{config.log}}} file! 6) Run {{{make}}} and verify that your binary program {{{MYPROG/MYPROG}}} was created. 7) Check in your changes. {{{ [dev/] cvs ci -m "Added MYPROG" configure configure.in Makefile.am Makefile.in [dev/] cvs add MYPROG [dev/] cd MYPROG [MYPROG/] cvs add Makefile.am Makefile.in MYPROG.c myown.c [MYPROG/] cvs commit -m "First checkin." Makefile.am Makefile.in MYPROG.c myown.c }}} ==== autoconf Troubleshooting ==== [AutoconfTroubleshooting] === RPM === [RpmInfo] |
This will compile `mri_process.cpp`, link it against the `utils` freesurfer library, and copy the executable to the `$FREESURFER_HOME/bin` directory during install. To include this subdirectory in the main freesurfer build, make sure to modify the top-level `CMakeLists.txt` by adding `mri_process` to the long list of included directories at the bottom of the file. Now, after reconfiguring your build, you can run `make` in the `mri_process` directory of your build tree to successfully compile the new program. If you're having trouble configuring and building freesurfer, be sure to visit the BuildGuide for step-by-step instructions. |
FreeSurfer Dev Guide
Visit the BuildGuide for instructions on building and installing freesurfer manually.
Visit the GitHub page for an introduction to the github workflow.
Visit the GitAnnex page for detailed instructions on using git annex.
Adding a New C Program
If you'd like to add a new program to the tree, you should create a new subdirectory with the title of your tool. As an example, let's create a new c++ program called mri_process. First, we'll create a top-level subdirectory that contains our new c++ file and an empty CMakeLists.txt file:
freesurfer/
mri_process/
CMakeLists.txt
mri_process.cppIn order to configure our new code, we should add the following to the empty CMakeLists.txt file.
project(mri_process)
include_directories(${FS_INCLUDE_DIRS})
add_executable(mri_process mri_process.cpp)
target_link_libraries(mri_process utils)
install(TARGETS mri_process DESTINATION bin)This will compile mri_process.cpp, link it against the utils freesurfer library, and copy the executable to the $FREESURFER_HOME/bin directory during install. To include this subdirectory in the main freesurfer build, make sure to modify the top-level CMakeLists.txt by adding mri_process to the long list of included directories at the bottom of the file. Now, after reconfiguring your build, you can run make in the mri_process directory of your build tree to successfully compile the new program. If you're having trouble configuring and building freesurfer, be sure to visit the BuildGuide for step-by-step instructions.