Release 1.8.5

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Contents 1 Downloading this release 2 What's New 2.1 New lesion analysis stuff 2.2 New executables 2.3 Deprecated and/or removed 3 Usage notes 4 Installation 5 Building

Downloading this release

Here are links to the downloads for release 1.8.5. The individual tool downloads tend to be more recent than the full release downloads.

• Release 1.8.5 for Linux (about 117MB)
• Release 1.8.5 for OSX/Intel (about 191MB)
• Release 1.8.5 for Cygwin (about 46MB)
• Individual tool downloads for Linux
• Individual tool downloads for OSX
• Individual tool downloads for Cygwin

You can also download VoxBo from NITRC.org:

• VoxBo on NITRC.org

Or if you use a Debian-derived Linux distribution (e.g., Ubuntu), you should be able to get VoxBo (and many other useful packages) via NeuroDebian:

• NeuroDebian

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:

• VoxBo 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. Just download it, put it somewhere, and run it. In desktop mode, you can't take advantage of all the machines on your cluster, but you can take advantage of all the cores on your machine.

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
• many programs have new and useful flags, only some of which are highlighted below

This release includes the following two major bug fixes:

• a bug in the calculation of p values from F statistics has been fixed (see [1] and follow-ups)
• a long-standing bug in frequency filtering has been fixed (see [2] and follow-ups)

I have not heard that either of these bugs has caused any actual harm. Please let me know if you know otherwise.

This release also includes the following more specifically noted improvements:

• improved file format support
  • transparent support for gzipped files in NIfTI, cub, and tes formats
  • handling of files with scale information (slope/intercept) is greatly improved
  • greatly improved DICOM support, including some older ACR/NEMA format images that are now supported as DICOM
  • 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
  • matrix text files are now supported for input and output (for output, use the .mtx extension)

• vbview2 (a completely new version of vbview), featuring:
  • layering, with user-settable transparency, layer hiding, and other per-layer settings
  • time series browsing
  • 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
  • some command line arguments to make your life easier
  • integrated GLM loading and threshold calculation

• 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
  • the voxq queue option can be used to turn queueing on and off without shutting down the scheduler completely
  • you can use the "checkdir" flag in the defaults file to make sure all your servers can see the directories they need to
  • servers are now specified in the defaults file, the serverlist file is no longer used

• 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
  • -req flag allows specifying requirements

• the new default priority is 3; new semantics are:
  • 0 — don't run
  • 1 — run during off-hours only
  • 2 — low priority
  • 3 — normal priority
  • 4/5 — high priority

• vbconv has a new argument structure and some new arguments, see help.
• Batch jobs, whether in cluster mode or desktop mode, now store log files permanently in the analysis directories.
• glm/gdw now replace "Add Single Covariate" with "Add Covariate(s) from File," which accepts 1D or 2D files (using the columns in the latter case).
• vbpermgen and vbtcalc have improved graphical and command line interfaces.
• Programs that use random numbers (vbpermgen, vbsim, vbim) now allow seed-setting.
• voxq now by default doesn't show sequences that have been idle for a few days.
• vbrename now removes identifying DICOM elements by default.
• 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 replaces the old auditglm job.
• vbi now handles 2D files and is generally more reliable.
• vbi now takes the -f flag to dump header info for DICOM, NIfTI, and Analyyze files.
• 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.
• vbview2 and vbdumpstats now let you extract principal components
• 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).
• For programs that take a -q argument for FDR, if you specify 0, you'll get thresholds for a range of q values.

New lesion analysis stuff

• vbtmap is a new executable for calculating t maps for lesion analysis
• vbcmap is a new executable for calculating chi-squared maps for lesion analysis
• makevlsm is a script for carrying out vbtmap-based VLSM analyses either on a single machine or using the queue
• vbscoregen creates simulated behavioral data from lesion maps using your description of the lesion-behavior relationship

New executables

• vbtool is a little utility for little VoxBo-specific tasks. "vbtool tip" is fun.
• 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)
• 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 help de-identify DICOM meta-data. Please verify that it does what you need before relying on it.
• vbpermvec permutes a vector
• vbsim lets you create random (Gaussian) 1D, 3D, or 4D data (use vbmm2 for 2D)

Deprecated and/or removed

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

• vb2tes, vb2cub, vb2img, vb2imgs, and vb2vmp are deprecated in favor of vbconv
• analyzeinfo and dicominfo are deprecated in favor of vbi (using the -f flag)
• vbmaskmunge, vbimagemunge, and vbmunge, are deprecated in favor of vbim
• vbmakerfx is deprecated in favor of various vbprep scripts
• realign and norm in favor of recent realignment and warping programs from SPM, FSL, etc.
• merge3d, extractmask, fillmask, and vbthreshcalc are removed

Usage notes

gzipping your nii, cub, and tes files not only reduces your disk usage, it also helps with performance, since it reduces the amount of disk i/o required to read/write a file.

Installation

Most VoxBo programs are just simple binaries that you can run. Once you've downloaded them, the most you need to do is put them in your PATH, just to make your life easier.

A few of the binaries work better with support files that you can install in your home directory. If you've donwloaded the entire VoxBo distribution, unpack it and put it in a directory called VoxBo, voxbo, or .voxbo inside your home directory.

For more information about installing VoxBo on a single machine, see Desktop mode.

Installing of VoxBo on a cluster, so that jobs can parallelize across more than one machine, is a little trickier. See Cluster mode for more information.

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)