Release 1.8.5
From VoxBoWiki
Please note that 1.8.5 is currently available just as a "preview" release (version 1.8.5pre), consisting just of binaries for Linux, OSX/Intel, and OSX/PPC. The code is quite stable, but there are many rough edges we hope to iron out before the final 1.8.5 release.
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[edit] Introduction
We are excited to announce the release of VoxBo 1.8.5 for Linux, OSX, and Cygwin (Windows). If you have a previous 1.8 series installation, you can just unpack it to a separate location and copy over the binaries. Please note that this is likely to be the last Cygwin-based distribution for Windows. Future Windows releases will probably not be Cygwin-dependent, although the Cygwin environment remains a viable working environment.
- for installation instructions, see below
- to get it, see Getting VoxBo
- please consider filling out the usage survey
- if you would like a copy of the virtual machine we use to build the Linux distribution, please drop us a line
Here's what's new as of 1.8.5:
[edit] What's New
- improved file format support
- greatly improved DICOM support, including images not previously handled
- some older ACR/NEMA format images now supported as DICOM
- gzipped file support in nii, cub, and tes formats
- MRIcro roi files now supported (transparently if hdr file available)
- an old GE MR file format is restored, even though i know nothing about this format
- file format plug-ins and associated issues are a thing of the past
- vbimagemunge is the future of image munging in voxbo; if it doesn't have the features you need, get your requests in now
- numerous vbview changes:
- crashing bugs fixed
- more capable file loading dialog (supports loading multiple files, provides info on image files)
- fitted responses now just include covariates of interest
- windowing (brightness and contrast) now much smarter
- for stat overlays, now provides a little scale widget that you can copy and paste into your figures
- general performance improvements
- note this is an interim version of vbview, the major overhaul is still not done
- the scheduler
- major performance improvements
- killing and halting jobs should be much more reliable
- much better at handling dead and revived servers
- now sorts hosts on rank and then random
- benchmark feature implemented, see sample defaults file
- voxq --queue option can be used to turn queueing on and off without shutting down the scheduler
- elapsed time for running jobs should be more accurate
- some improvement in email notifiation code (more coming soon)
- vbbatch
- now allows you to build a sequence with successive calls, and then submit it all at once (-a, -f, and -s flags)
- broken IND mechanism fixed
- -e flag for setting email address (or suppressing email)
- -sn and -jn flags for more informative display in queue
- maxjobs now defaults to 10
- the new default priority is 3; new semantics are 1(night) 2(low) 3(normal) 4/5(jump)
- vboverlap hack could be useful in calculating overlap between masks
- vb2tes now includes input filenames in header if the output is really a tes file.
- vb2tes has some new arguments, and is more helpful when things go wrong
- vbmaskinfo provides useful information about 4D files containing series of masks (e.g., series of lesion maps)
- vbconv has been overhauled
- glminfo has new features that replace the old auditglm job
- new executable vbfilter will do frequency domain filtering of 1D or 4D files
- vbi now handles mat files and is generally more reliable
- vbperminfo now understands 4D files, making it easy to compact an iterations directory into a single 4D file
- new contrasts: hyp and phase
- plotscreen widget improvements
- glm and gdw have been re-organized a bit, and glm now provides some useful canned models
- vbstatmap wasn't honoring masks, now it does
- vbview and vbdumpstats now let you extract principal components
- many build improvements
- vbvolregress is available for a variety of simple regressions, including typical group GLMs, lesion analysis, analyses with image covariates, etc.
[edit] Installation
Please note that 1.8.5pre is a preview release of 1.8.5, including just binaries. You can copy some or all of them into your existing VoxBo binary directory, or wherever else you like. If you would like to try out the new scheduler (which has been very stable here at the CfN), you will need to create a world-writable directory called "drop" within your main VoxBo directory. This will be eliminated at some point, but it's necessary for now.
For general information, see the release 1.8 installation instructions.
[edit] Building
If you'd like to build this release, here are notes on how to go about it for our supported architectures:
