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  1. The Virtual Brain
  2. TVB-428

Status of : CIFTI format for Import/Export

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    • Type: Task
    • Status: Closed
    • Priority: Major
    • Resolution: Won't Fix
    • Affects Version/s: None
    • Fix Version/s: None
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      Description

      CIFTI file is a file format that stores data from surfaces (vertices)
      and volumes (voxels) concurrently in a single file comprising a listed
      set of brainordinates (brain coordinates). The volume component of a
      CIFTI file can be any selected list of voxels (e.g., only subcortical
      gray-matter voxels) that need not conform to cuboidal or ‘N x M x O’
      volumetric dimensions.

      The Connectome Workbench currently supports CIFTI files for dense time
      series (.dtseries.nii), dense connectomes (.dconn.nii), dense labels (*.dlabel.nii)

      • dense conectomes CIFTI (connectivity matrix) refers to connectivity
        matrix CIFTI files that contain correlations between every surface or
        volume brainordinate and every other surface or volume ordinate in our
        model of the brain. For example, a grayordinates × grayordinates dense
        connectome file contains a connectivity value between every
        grayordinate and every other grayordinate. Dense connectomes can also
        be asymmetric, such as a structural connectivity matrix between
        grayordinates (all gray matter structures) and whiteordinates (all
        white matter structures).
        brainordinates x brainordinates
      • dense connectome labels CIFTI files (grayordinates × label maps)
        contain a name and/or color label for every brainordinate. These files
        will be useful for mapping combined cortical and subcortical
        parcellations. dense scalar CIFTI files contain real-valued data for
        every brainordinate mapped to a color palette. A dense scalar file can
        contain one map or frame (such as a single cortical myelin map) or a
        series of spatial maps (e.g. tfMRI contrast maps or ICA component
        spatial maps) that can have distinct labels for each frame.
      • dense time-series is a type of dense scalar CIFTI file
        (grayordinates × time) that can be viewed as a series of maps (or
        animated movie) displayed on cortical surfaces and subcortical
        volume slices or as a timecourse graph for a selected grayordinate,
        using the timecourse graph window (and as an average timecourse for
        all grayordinates within a selected ROI). This type of file is
        particularly useful for viewing resting state fMRI time series.
        (brain oridnates x time points)

      What we ultimately want is a dense connectome matrix based
      on/resulting from a tractography method from diffusion data. What is
      the relationship between the coordinates of diffusion voxels and the
      node indices of the surfaces of structural images?

      The CIFTI standard space is in MNI space (subcortical voxels). The
      correspondgin surface is also in MNI space. From some discussion I
      read that the cifti files do not contain surface coordinates.

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            • Assignee:
              lia.domide Lia Domide
              Reporter:
              lia.domide Lia Domide
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