Release 1.8.5

From VoxBoWiki

Jump to: navigation, search

Note: VoxBo 1.8.5 is currently available just as a "preview" release (version 1.8.5pre8), including separate distributions for Linux, OSX/Intel, and Cygwin. Note that the Cygwin release includes only command line utilities, no graphical programs. Most of the code is quite stable, but there are many rough edges we hope to iron out before the final 1.8.5 release. This page will be revised as the final release evolves.

If you use VoxBo, please consider filling out the usage survey.

Contents

Downloading this release

Here are links to the downloads for release 1.8.5pre8:

You can also download VoxBo from NITRC.org:

If for whatever reason you want older stuff, or just want to surf what's available, here's a convenient link to the archive of downloads:

What's New

This release features a new "desktop mode," allowing you to use VoxBo without elaborate installation, without a cluster, and without root access. I.e., the way most software runs.

This release includes the following general improvements:

  • minor bug fixes and improvements too numerous to iterate
  • Lesion analysis is a major new focus of development
  • the codebase is 64-bit compatible now (although the official releases are still 32-bit), and the build is greatly improved


This release also includes the following more specifically noted improvements:

  • 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 NIfTI, cub, and tes formats
    • individual volumes from 4D files can be read as 3D data using syntax like this: foo.tes:17 (18th volume from foo.tes)
    • the inclusion mask for a 4D file can be read as a 3D volume using syntax like this: foo.tes:mask
    • MRIcro roi files now supported (transparently if hdr file available), as well as voi (which are really .nii.gz)
    • 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 (for now)
    • VoxBo file formats should be more compatible across operating systems
  • vbview2 (a completely new version of vbview), featuring:
    • layering, with user-settable transparency, layer hiding, and other per-layer settings
    • smarter automatic windowing (contrast/brightness)
    • more capable file loading dialog (supports loading multiple files, provides info on image files)
    • nice color scale widget that you can copy and paste into your figures
    • some missing features, including mask drawing and loading stat maps from GLM directories (use vbstatmap to generate the maps) — it's not a bad idea to keep the old version around
  • an improved scheduler
    • general improvements to performance, reliability, and scalability
    • killing and halting jobs should be much more reliable
    • much better at handling dead and revived servers
    • smarter prioritizing of hosts
    • benchmark feature implemented, see sample defaults file
    • voxq queue option can be used to turn queueing on and off without shutting down the scheduler completely
  • vbbatch improvements
    • 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:
    • 0 — don't run
    • 1 — run at night only
    • 2 — low priority
    • 3 — normal priority
    • 4/5 — high priority
  • vbconv has been overhauled:
    • argument structure is new, see help
    • removing NaNs/Infs is an option that's off by default
    • you can pass a range for 4D files
  • vb2tes now includes input filenames in header if the output is really a tes file, has some new arguments, and is more helpful when things go wrong. however, the program is also deprecated in favor of vbconv and vbim
  • glminfo has new features that replace the old auditglm job
  • 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. It's also now much smarter about memory usage, and should be faster. The -d and -dr options let you get an exact p value for a stat value of interest.
  • Two new contrast scales are available: hyp and phase. If you don't know what these are, then you don't need them.
  • plotscreen widget improvements
  • glm and gdw have been re-organized a bit, and glm now provides some useful canned models
  • vbview and vbdumpstats now let you extract principal components
  • vbi now handles VoxBo matrix files
  • handling of slope and intercept in image files is handled more consistently
  • using foobar[imgdir] now correctly writes 4D output using the imgdir format (directory full of img/hdr pairs)
  • vbpermmat now accepts either a 4D or vector file as an argument, to specify the number of permuted elements
  • vbperminfo -u creates a special 4D volume with a p map, stat map, and z map, by carrying out a permutation test separately in each voxel. this volume can be used as input to vbfdr
  • parsing of numeric ranges is smarter (i.e., 7345-52 is parsed as 7345-7352)

New lesion analysis stuff

  • vbtmap is a new executable for calculating t maps for lesion analysis
  • makevlsm is a script for carrying out vbtmap-based VLSM analyses either on a single machine or using the queue

New executables

  • vbim is an all-purpose image munger — if it doesn't have the features you need, get your requests in now
  • vboverlap hack could be useful in calculating overlap between masks
  • vbvolregress is available for a variety of simple regressions, including typical group GLMs, lesion analysis, analyses with image covariates, etc.
  • vbfilter will do frequency domain filtering of 1D or 4D files (e.g., for functional connectivity studies)
  • vbmaskinfo provides useful information about 4D files containing series of masks (e.g., series of lesion maps)
  • vbscale is an ugly little program for creating color scales for figures
  • makevlsm is a new shell script for running VLSM analyses
  • vbregion provides information on regions matching criteria in a 3D file
  • dcmsplit can be used to anonymize DICOM data. Please verify that it does what you need before relying on it.

Deprecated and/or removed

We recommend you avoid using the following programs, which are either deprecated or removed:

Usage notes

VoxBo now supports gzip-compressed NIfTI and VoxBo files (i.e., nii, cub, and tes). Although (un)compression introduces some overhead, in many cases it can greatly reduce the amount of disk i/o, resulting in both space savings and improved speed of file reads/writes.

Installation

For general information on installation, see the release 1.8 installation instructions.

Building

If you'd like to build this release, here are notes on how to go about it:

  • Build_1.8.5 (this page will be created when the official 1.8.5 release is done)
Retrieved from "http://www.voxbo.org/index.php/Release_1.8.5"
Personal tools