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

Connectome Workbench 

One platform containing wb_view for surface and volume brain visualization and wb_command command line tools (particularly for CIFTI manipulation)

FSL

The FMRIB team has released FSL version 5.0.10, which includes beta versions of melodic, film, and flameo that are CIFTI-compliant. Additional CIFTI-compliant tools are planned for upcoming release of the FSL 6.0 major update.

PALM

PALM — Permutation Analysis of Linear Models — is a tool that allows inference using permutation methods. It runs in matlab, octave, or from the command-line, and is capable of some processing on CIFTI files.

FieldTrip

specific commands: ft_sourceparcellate, ft_sourceplot, ft_volumewrite, ft_read_cifti, ft_write_cift
FieldTrip allows MEG/EEG source reconstruction on source models that represent the full-brain as a volumetric grid, on the cortical sheet as a triangulated surface. After estimated the activity on the dense (volumetric or surface) source model, FieldTrip allows for averaging of the activity within parcels. Alternative to the dense source reconstruction followed by combining the estimate over the parcel, FieldTrip allows for specifying the parcels prior to source estimation. The parcellated representation of MEG/EEG source activity is represented in a similar format as channel-level data, i.e. each parcel is represented as channel in the MATLAB data structure. This allows all channel-level analysis tools to be applied on the parcellated source reconstruction.

 

Reading HCP data into MATLAB

Workbench v1.0 (or greater) + GIFTI toolbox code

specific commands: ciftiopen.m, ciftisave.m, ciftisavereset.m
These functions allow the use of CIFTI files and MATLAB by interfacing with the GIFTI toolbox matlab library. ciftiopen/ciftisave does not parse the XML file, meaning that extra steps are necessary to determine what the CIFTI indices represent (which vertex or voxel, etc).

CIFTI-matlab

specific commands: ft_read_cifti, ft_write_cifti
The CIFTI-matlab toolbox contains a subset of functions from the FieldTrip toolbox to facilitate the use of CIFTI files and MATLAB without having to know the details of high-level FieldTrip toolbox for MEG/EEG analysis. The CIFTI-matlab toolbox does not distinguish between between the data types, but focusses on the content of the CIFTI files.



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