Differences between revisions 9 and 10

1. NextGenCode

Contents

NextGenCode

a grab-bag of notes on what we'd like to see in the ideal freesurfer source code environment, and runtime

1.0.1. Newer respository

evaluate DVCS like git. if not something relatively modern like SVN which lets you do admin operations easily unlike CVS.
source only checkout which excludes all distribution data. For faster and thinner local builds.

1.0.2. CMake building

cmake replacing autotools as the build enviro

1.0.3. Third-Party Packages

one-stop-shopping build of all 3rd party packages --> like neurodebian
evaluate necessity of 3rd-party packages, eg PetSc

1.0.4. Source Code cleanups

continued source code cleanup:
- remove all #if 0 code and duplicated stuff
source code documentation
more low-level unit tests

1.0.5. GPU Transition

memory structures changed to allow easier cpu (and gpu) parallelization (see rge notes)

1.0.6. recon-all

complete replacement of recon-all with ????

1.0.7. Installation details

eliminate clutter in $FREESURFER_HOME ( for the installation ).
- for instance, the distribution data after installation should be in $FREESURFER_HOME/data. GEMS, the newest FS package, already uses this. It's data is in $FREESURFER_HOME/data/GEMS

1.0.8. Scripting language support

First phase is to wrap IO and utils so that it's possible for everyone to write scripts (Python, Numpy) in FreeSurfer instead of adding binaries to the source distribution. evaluate Cython as possible means.

When done properly, instead of adding a directory ( by mimicking the dummy/ project we have ) and toying with the Autotools, one can simply write a Python script like following:

import fs.utils as u
import fs.io as io

im = io.MRIread('test.mgz')
m = u.MRImean(im, 5)

Deletions are marked like this.	Additions are marked like this.
Line 44:	Line 44:
When done properly, instead of adding a directory ( by mimicking the dummy/ project we have ) and toying with the Autotools. Once can simply write a Python script like following:	When done properly, instead of adding a directory ( by mimicking the dummy/ project we have ) and toying with the Autotools, one can simply write a Python script like following: