Release 1.8.5

From VoxBoWiki

Contents 1 Introduction 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

Introduction

We are excited to announce the release of VoxBo 1.8.5 for Linux and OSX. If you have a previous 1.8 series installation, we suggest you rename it and unpack this distribution in its place. Please note that there is no Cygwin or other Windows build for this release currently. I'm hoping to resolve this soon.

To get this release, see Getting VoxBo. Also, please consider filling out the usage survey

What's New

• bug fixes and minor feature improvements too numerous to iterate
• the codebase is 64-bit compatible now
• Lesion analysis is a major new focus of development

• 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)
  • 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

• Completely new version of vbview:
  • note that this is a major rewrite, so some features are missing. It's not a bad idea to keep the old version around.
  • vbview now has layering, with user-settable transparency, layer hiding, and other per-layer settings
  • automatic windowing (contrast/brightness) is smarter
  • 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
  • many general performance improvements

• the 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
  • elapsed time for running jobs should be more accurate
  • some improvement in email notifiation code

• 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:
  • 0 — don't run
  • 1 — run at night only
  • 2 — low priority
  • 3 — normal priority
  • 4/5 — high priority

• 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

• 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

• 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.
• 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)
• many build improvements, especially for OSX

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)
• dcmsplit is useful for anonymizing DICOM data
• 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:

• vb2tes, vb2cub, vb2img, vb2imgs, and vb2vmp are deprecated in favor of vbconv
• 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, are 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

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, 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.

Building

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

• Linux
• OSX