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added 19 commits
November 11, 2020 17:34
… note, pre changes
…rtosis coefficient (akc); modifications for multishell data - bookmark, not for release
… to LiFE forward model
…ensor model still - this is still locked on even when the kurtosis model isnt valid. Split one long print statement into 3 lines in feConnectomeEncoding. comments changed in feGet
…parently the original orientation of the data for linear indexing
…ned data, updated comments to match / describe
…he functions need to be updated to correctly parse inputs for these options - but that has to happen when the options work in the first place
…ed feConnectomeInit to pass warnings if a mismatch in file orientations is detected
… of offset / header info
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A working estimate for the LiFE model with multishell data. This pull request is to share a working development version.
This branch is still being actively tested. Forward model may not work. Single shell data will have problems being passed with the functions as they are. Change between tensor forward model and kurtosis forward model by commenting line 132/133 in feConnectomeBuildDictionaries.m
This is for testing changes required for multishell analysis / forward model.
% this will work for a test
fg = fgRead('cc_crop.tck');
nv = [ 0.0017 0.0003 0.0003; 0.0014 0.0002 0.0002 ];
k = [ 88.2725 -129.2530 -159.8982 -24.8088 32.5064 -0.3677 3.9417 -5.1648 2.4475 -32.0594 -24.1665 -45.5590 -12.9820 9.5266 -12.6976 ];
fe = feConnectomeInit('dwi.nii.gz', fg, [], [], [], 't1.nii.gz', 720, nv, k);
fit = feFitModel(feGet(fe, 'model'), feGet(fe, 'dsigdemeaned'), 'bbnnls', 500, 'preconditioner');
THIS IS A DEV BRANCH - NOT FULLY FUNCTIONAL