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Comment: wording

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1. What are *dtseries.nii, *.dconn.nii, *dlabel.nii, *.dscalar.nii files?

These are CiftiCIFTI-2 format files (see http://www.nitrc.org/projects/cifti/ for specs) that are output from the HCP Pipelines (pipeline code released on GitHub). The extension for CIFTI files is .[type].nii, where type is dconn, dtseries, dscalar, dlabel, pconn, or another such specifier. It ends in .nii because CIFTI uses the NIFTI-2 format, which specifies that the extension must be .nii.  The files include a specialized XML header extension to describe the indices, leaving most of the NIFTI-2 header blank/unused (spacing info, etc). Note that CIFTI files are not (and must not be) gzip'ed, as on-disk random access is used for access due to large file sizes.  However, we usually gzip our volume files, so the volume files we distribute will generally end in .nii.gz.

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ALPHA TESTING, FOR MRI USERS (This tool is not yet ready for production use):

C. A new cifti CIFTI library has been written for matlab, which is intended to be backwards compatible with ciftiopen, etc from option B, but provides the information of about what each CIFTI index represents.  Unless you are There are no external dependencies when reading CIFTI-1 files (the currently released HCP files should be exclusively CIFTI-2), there are no external dependencies (to 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 https://github.com/Washington-University/cifti-matlab.

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