brain-life / workflow_ui Goto Github PK

(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)

(3) Run freesurfer on anatomy.nii.gz

(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)

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

outputs "FE structure" in .mat

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

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