Right. Peace,
Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Sang-Yun Oh <[email protected]<mailto:[email protected]>> Date: Tuesday, May 16, 2017 at 11:25 AM To: Timothy Coalson <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Infinite values in Group average data This makes more sense! Sorry I missed your mention of fisher-z transform So I would apply tanh to each element to revert back to regular correlation coefficients Thank you for your help! Best, Sang On Mon, May 15, 2017 at 5:57 PM Timothy Coalson <[email protected]<mailto:[email protected]>> wrote: After the fisher-z transform, you can have values greater than 1, see the graph on the right: https://en.wikipedia.org/wiki/Fisher_transformation This is why the "correct" answer for the diagonal is infinity for the "zcorr" file. Tim On Mon, May 15, 2017 at 7:51 PM, Sang-Yun Oh <[email protected]<mailto:[email protected]>> wrote: I am also finding that some off-diagonal elements in this matrix are also greater than 1 indicating this matrix is not a correlation matrix. In [5]: img Out[5]: memmap([[ 8.66434002e+00, 1.96847185e-01, 1.66294336e-01, ..., 1.01449557e-01, 7.45474100e-02, 1.15624115e-01], [ 1.96847185e-01, inf, 3.36383432e-01, ..., -5.70017472e-03, -5.49946353e-02, 3.72834280e-02], [ 1.66294336e-01, 3.36383432e-01, inf, ..., -4.45242636e-02, -6.07097335e-02, -1.51601573e-02], ..., [ 1.01449557e-01, -5.70017472e-03, -4.45242636e-02, ..., inf, 1.91883039e+00, 9.20160294e-01], [ 7.45474100e-02, -5.49946353e-02, -6.07097335e-02, ..., 1.91883111e+00, 8.31776619e+00, 8.82132888e-01], [ 1.15624115e-01, 3.72833721e-02, -1.51601573e-02, ..., 9.20160294e-01, 8.82132888e-01, 8.66434002e+00]], dtype=float32) Any insight would be appreciated Thanks, Sang On Mon, May 15, 2017 at 1:13 PM Sang-Yun Oh <[email protected]<mailto:[email protected]>> wrote: Thank you for the response. I am, too, confused by some being non-zero finite values, and others being infinities. Before computing a correlation matrix, if standardized by subtracting the mean and scaling by variance, all diagonal elements should be exactly 1. What I am concerned about is how the whole matrix was computed, since a fundamental characteristic of correlation matrix is not satisfied Best, Sang On Mon, May 15, 2017 at 11:33 AM Timothy Coalson <[email protected]<mailto:[email protected]>> wrote: Per the name "zcorr", the correlation values have been z-transformed (fisher's small z transform). I am somewhat confused as to why some elements in the diagonal are not infinite. The "true" value of applying this transform would be infinite on the entire diagonal, as arctanh(1) is infinite. I am guessing this result was generated in matlab, as wb_command actually prevents infinities when using the z transform, putting a cap on the correlation (when not using z-transform, it shows correlations of 1 as expected). Whatever analysis you do with correlation matrices like this should ignore the diagonal anyway, since it is correlation to itself. Tim On Mon, May 15, 2017 at 3:57 AM, Sang-Yun Oh <[email protected]<mailto:[email protected]>> wrote: I downloaded group average functional correlation file: HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii Some diagonal elements of the square matrix (91282x91282) are infinite (Please see below). I want to use this matrix in ananalysis; however, I am not sure how to understand or deal with infinite diagonal values. I appreciate any insight Thanks, Sang ====================== In [1]: import nibabel In [2]: asdf = nibabel.load('HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii') In [3]: img = asdf.get_data() In [4]: img.shape Out[4]: (1, 1, 1, 1, 91282, 91282) In [5]: S = img[0,0,0,0,:,:] In [6]: S Out[6]: memmap([[ 8.66434002e+00, 1.96847185e-01, 1.66294336e-01, ..., 1.01449557e-01, 7.45474100e-02, 1.15624115e-01], [ 1.96847185e-01, inf, 3.36383432e-01, ..., -5.70017472e-03, -5.49946353e-02, 3.72834280e-02], [ 1.66294336e-01, 3.36383432e-01, inf, ..., -4.45242636e-02, -6.07097335e-02, -1.51601573e-02], ..., [ 1.01449557e-01, -5.70017472e-03, -4.45242636e-02, ..., inf, 1.91883039e+00, 9.20160294e-01], [ 7.45474100e-02, -5.49946353e-02, -6.07097335e-02, ..., 1.91883111e+00, 8.31776619e+00, 8.82132888e-01], [ 1.15624115e-01, 3.72833721e-02, -1.51601573e-02, ..., 9.20160294e-01, 8.82132888e-01, 8.66434002e+00]], dtype=float32) In [7]: S.diagonal() Out[7]: memmap([ 8.66434002, inf, inf, ..., inf, 8.31776619, 8.66434002], dtype=float32) _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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