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Comment: cifti-matlab beta release, reorder and relabel options

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2. How do you get CIFTI files into MATLAB?

HCP has developed 2 3 ways to read and write CIFTI files in MATLAB:

BETA TESTING, FOR MEG MRI USERS (This tool pads the matrix with NaNsis mostly stable, and will become our primary recommendation soon):

A. PLEASE DON'T USE THIS OPTION WITH HCP MRI DATA AT THIS TIME. Using the code developed for the HCP megconnectome data analysis pipelines that are implemented using the FieldTrip toolbox. The code is available in stand-alone format from https://github.com/Washington-University/cifti-matlab, in the ft_cifti folder.  This approach loads the complete CIFTI XML header information into a MATLAB structure, including information on what each CIFTI index represents. Where possible it will also load gifti surface files.

FOR MRI USERS (This tool does not introduce NaNs):

B. Using Workbench v1.0 or newer + GIFTI toolbox I (formerly option C). A new CIFTI library has been written for matlab, which is backwards compatible with ciftiopen, etc from option II, but provides information about what each CIFTI index represents.  There are no external dependencies when reading CIFTI-2 files, which should cover all HCP CIFTI files in virtually all data releases.  To read CIFTI-1 files with this code, install Connectome Workbench v1.0 or newer, available here.  If you you feel comfortable trying this library that we have been using for internal processing for a short time, it is available at https://github.com/Washington-University/cifti-matlab.

STABLE:

II (formerly option B). Using Workbench v1.0 or newer + GIFTI toolbox code (descriptions below). This method has the limitation of not telling you what the CIFTI indices represent (what vertex or voxel, etc) and it creates intermediate files (that are deleted as part of the provided code). For this approach you need a couple of prerequisites:

1) Connectome Workbench (available here) needs to be installed on the system.

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ciftisavereset(newcii,'path/to/newfile','path/to/wb_command');


ALPHA TESTING, FOR MRI MEG USERS (This tool is not yet ready for production usepads the matrix with NaNs):C. A new CIFTI library has been written for matlab, which is intended to be backwards compatible with ciftiopen, etc from option B, but provides information about

what each CIFTI index represents.  There are no external dependencies when reading CIFTI-2 files, which should cover all HCP CIFTI files in recent data releases.  To read CIFTI-1 files with this code, install Connectome Workbench v1.0 or newer, available here.  If you can accept the risk of a very new library generating incorrect output files, the library is available at III (formerly option A). PLEASE DON'T USE THIS OPTION WITH HCP MRI DATA AT THIS TIME. Using the code developed for the HCP megconnectome data analysis pipelines that are implemented using the FieldTrip toolbox. The code is available in stand-alone format from https://github.com/Washington-University/cifti-matlab/releases/tag/v1-final.  This approach loads the complete CIFTI XML header information into a MATLAB structure, including information on what each CIFTI index represents. Where possible it will also load gifti surface files.

3. I see that HCP distributes group average dense connectome files. Do you also provide connectivity matrices for individual subjects?

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