WF UI

(1) Accept 3 files: diffusion_data.nii.gz, diffusion_data.bvecs, diffusion_data.bvals

> run validator (sca-product-neuro-diffusion)

(2) Accept an single anatomy file (T1w): anatomy.nii.gz

> run validator (sca-product-neuro-anatomy)

sca-service-freesurfer

(3) Run freesurfer on anatomy.nii.gz

sca-service-neuro-tracking

(4) create a white matter mask from the result of (3)

(5) run tracking (MRTRIX) using diffusion_data.niin.gz+.bvecs+.bvals and the output of (4)

sca-service-life

(6) Run life with the diffusion_data.nii.gz+.bvecs+.bvals and the output of (5) the .tck file

outputs "FE structure" in .mat

sca-service-connectome-data-comparison

(7) load the life results from the FE structure resulting from (6) into the graph in demo_connectome_data_comparison.m

TODO

brain-life.org/cortex (FreeSurfer) (just need t1 for input - validator should only validate dwi) brain-life.org/networkneuro (work with Brent)

dwParams = dtiInitParams dwParams = bvalue: [] gradDirsCode: [] clobber: 0 dt6BaseName: flipLrApFlag: 0 numBootStrapSamples: 500 fitMethod: 'ls' nStep: 50 eddyCorrect: 1 excludeVols: [] bsplineInterpFlag: 0 phaseEncodeDir: [] dwOutMm: [2 2 2] rotateBvecsWithRx: 0 rotateBvecsWithCanXform: 0