Here we keep a current list o= f software packages/tools that are CIFTI file format compliant:

One pl=
atform containing **wb_view** for surface and volume brain vis=
ualization and **wb_command** command line tools (particularly=
for CIFTI manipulation)

The FM= RIB team has released FSL version 5.0.10, which includes beta versions of m= elodic, film, and flameo that are CIFTI-compliant. Additional CIFTI-complia= nt tools are planned for upcoming release of the FSL 6.0 major update.=

PALM = =E2=80=94 Permutation Analysis of Linear Models =E2=80=94 is a tool that al= lows inference using permutation methods. It runs in matlab, octave, or fro= m the command-line, and is capable of some processing on CIFTI files.

specif= ic commands: ft_sourceparcellate, ft_sourceplot, ft_volumewrite, ft_read_ci= fti, ft_write_cifti

FieldT= rip allows MEG/EEG source reconstruction on source models that represent th= e full brain as a volumetric grid, and/or on the cortical sheet as a triang= ulated surface. After estimating the activity on the dense (volumetric or s= urface) source model, FieldTrip allows for averaging of the activity within= parcels. Alternatively, FieldTrip allows for specifying the parcels prior = to source estimation. The parcellated representation of MEG/EEG source acti= vity is represented in a format similar to channel-level data, i.e. each pa= rcel is represented as channel in the MATLAB data structure. This allows al= l channel-level analysis tools to be applied on the parcellated source reco= nstruction.

specif= ic commands: suma, cifti_tool

SUMA s= upports displaying cifti data.

specif= ic commands: cifti_read, cifti_write (plus drop-in compatibility for ciftio= pen, ciftisave, ciftisavereset)

Versio=
n 2 of the cifti-matlab toolbox was mostly rewritten, with a new design tha=
t more closely represents the internals of the file format, exposing nearly=
all of the information in the XML, and providing some helper functions to =
simplify some common operations. This is the recommended option for M=
RI-derived data, as it provides drop-in compatibility with ciftiopen and re=
lated functions, and should be faster, with less disk IO.

**Workbe=
nch v1.0 (or greater) + GIFTI toolbox code**

specif= ic commands: ciftiopen, ciftisave, ciftisavereset

These = functions allow the use of CIFTI files in MATLAB by using wb_command to con= vert to pseudo-GIFTI format and the GIFTI toolbox matlab library to read th= em. ciftiopen does not parse the XML within the file, meaning that addition= al external commands are necessary to determine what the CIFTI indices repr= esent (which vertex or voxel, etc).

**cifti-matlab v1=
(previous version)**

specif= ic commands: ft_read_cifti, ft_write_cifti

The ci= fti-matlab toolbox contains a subset of functions from the FieldTrip toolbo= x to facilitate the use of CIFTI files and MATLAB without having to install= the entire FieldTrip toolbox. The FieldTrip-based cifti-matlab toolbox doe= s some translation of the CIFTI file to match what FieldTrip can take as in= put, resulting in some changes to the indices of the data matrix.