my_sphere = Sphere(xyz=gtab.bvecs[~gtab.b0s_mask])
voxel2streamlineto see which streamlines pass through which voxels. I feed in the streamlines and the inverse of the DWI affine to map from streamline to voxel. I am having trouble interpreting the output, as I do not know how to map voxel index to location. Any guidance would be appreciated, thanks!
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data, affine, img = load_nifti(file2_path, return_img=True) bvals, bvecs = read_bvals_bvecs(fbval, fbvec) print(bvals) gtab = gradient_table(bvals, bvecs) print(gtab) tenmodel = TensorModel(gtab) print(len(bvals)) new_img = img.get_fdata() tenfit = tenmodel.fit(new_img)
dipy.align._public.SymmetricDiffeomorphicRegistration. Using the
.update()method, I have interpolated the displacement to a new 3D shape of (S,R,C,3). I would now like to split this 3D array into a list of 2D arrays and then apply each deformation field on a new 2D image. Is there a way of doing that?
# these are your original bvals and bvecs bvals = gtab.bvals bvecs = gtab.bvecs # here we select only 0 and 1000 bvals selelected_bvals = np.logical_or(bvals == 0, bvals == 1000) # here we pick only the 3D volumes from the 4D dMRI data pertaining to 0 and 1000 that we did above. data_selected = data[:, :, :, selelected_bvals] # now we also take only the bvals and bvecs of the same 0 and 1000 shells. gtab_selected = gradient_table(bvals[selelected_bvals], bvecs[selelected_bvals]) # now you can use these to fit the DTI model tenmodel = dti.TensorModel(gtab_selected) tenfit = tenmodel.fit(data_selected)
Is there a project outline for dipy such as a module connections graph?
Such as these I created for fmriprep and qsiprep: https://github.com/nipreps/fmriprep/discussions/2517 and https://github.com/PennLINC/qsiprep/discussions/289
nodesand therefore does not need a dataflow graph. However, I do know it is trivial to build these pipelines with DIPY and would like to know what exactly you need. Are you using vanilla DIPY to build pipelines?