7.1.132. 3dReHoΒΆ

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REHO/Kendall W code, written by PA Taylor (July, 2012), part of FATCAT (Taylor & Saad, 2013) in AFNI.

ReHo (regional homogeneity) is just a renaming of the Kendall’s W (or Kendall’s coefficient of concordance, KCC, (Kendall & Babington Smith, 1939)) for set of time series. Application to fMRI data was described in paper: <<Regional homogeneity approach to fMRI data analysis>> by Zang, Jiang, Lu, He, and Tiana (2004, NeuroImage), where it was applied to the study of both task and resting state functional connectivity (RSFC).

    • USAGE: This program is made to read in data from 4D time series data set

      and to calculate Kendall’s W per voxel using neighborhood voxels. Instead of the time series values themselves, Kendall’s W uses the relative rank ordering of a ‘hood over all time points to evaluate a parameter W in range 0-1, with 0 reflecting no trend of agreement between time series and 1 reflecting perfect agreement. From W, one can simply get Friedman’s chi-square value (with degrees of freedom equal to `the length of the time series minus one’), so this can also be calculated here and returned in the second sub-brick: chi-sq = (N_n)*(N_t - 1)*W, with N_dof = N_t - 1, where N_n is the size of neighborhood; N_t is the number of time points; W is the ReHo or concordance value; and N_dof is the number of degrees of freedom. A switch is included to have the chi-sq value output as a subbrick of the ReHo/W. (In estimating W, tied values are taken into account by averaging appropriate rankings and adjusting other factors in W appropriately, which only makes a small difference in value, but the computational time still isn’t that bad).

  • COMMAND: 3dReHo -prefix PREFIX -inset FILE {-nneigh 7|19|27}
{-chi_sq} {-mask MASK} {-in_rois INROIS}
    • RUNNING, need to provide: -prefix PREFIX :output file name part. -inset FILE :time series file.
-chi_sq :switch to output Friedman chi-sq value per voxel
as a subbrick.
-mask MASK :can include a whole brain mask within which to calculate ReHo. Otherwise, data should be masked already.
-nneigh NUMBER :number of voxels in neighborhood, inclusive; can be:
7 (for facewise neighbors, only), 19 (for face- and edge-wise neighbors), 27 (for face-, edge-, and node-wise neighbors). The default is: 27.
-neigh_RAD R :for additional voxelwise neighborhood control, the

radius R of a desired neighborhood can be put in; R is a floating point number, and must be >1. Examples of the numbers of voxels in a given radius are as follows (you can roughly approximate with the ol’ 4*PI*(R^3)/3 thing):

R=2.0 -> V=33, R=2.3 -> V=57, R=2.9 -> V=93, R=3.1 -> V=123, R=3.9 -> V=251, R=4.5 -> V=389, R=6.1 -> V=949,

but you can choose most any value.

-neigh_X A
-neigh_Y B :as if that weren’t enough freedom, you can even have
-neigh_Z C ellipsoidal volumes of voxelwise neighbors. This is

done by inputing the set of semi-radius lengths you want, again as floats/decimals. The ‘hood is then made according to the following relation:

(i/A)^2 + (j/B)^2 + (k/C)^2 <=1.

which will have approx. V=4*PI*A*B*C/3. The impetus for this freedom was for use with data having anisotropic voxel edge lengths.

-in_rois INROIS :can input a set of ROIs, each labelled with distinct
integers. ReHo will be calculated per ROI. The output will be similar to the format of 3dROIstats: one row of numbers per INROIS subbrick, and the number of columns determined by the number of ROIs per subbrick (but only numbers are output). The output of this is in a file called PREFIX_ROI_reho.vals, and if `-chi_sq’ values are being output, then those for the ROI values will be output in an analogously formatted file called PREFIX_ROI_reho.chi. Voxelwise ReHo will still be calculated and output.
  • OUTPUT:
    [A] single file with name, e.g., PREFIX+orig.BRIK, which may have

    two subbricks (2nd subbrick if `-chi_sq’ switch is used): [0] contains the ReHo (Kendall W) value per voxel; [1] contains Friedman chi-square of ReHo per voxel (optional);

    note that the number of degrees of freedom of this value is the length of time series minus 1.

    [B] can get list of ROI ReHo values, as well (optional).

    • EXAMPLE:
      3dReHo
      -mask MASK+orig.

      -inset REST+orig -prefix REST_REHO -neigh_RAD 2.9 -chi_sq

    If you use this program, please reference the introductory/description paper for the FATCAT toolbox:

    Taylor PA, Saad ZS (2013). FATCAT: (An Efficient) Functional And Tractographic Connectivity Analysis Toolbox. Brain Connectivity 3(5):523-535.


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