Dear all,
I am working on some generative model for tractography (either GAN or VAE).Originally I thought to encode from each voxel the tensor, then I have been readingthe Yixue Fenga and Bramsh Q. Chandio paper with VAE generting synthetic tractography. e.g. https://www.biorxiv.org/content/10.1101/2023.02.24.529954v3.full.pdf
I also tried to decompose the FINTA, GESTA... though their library has become quite complex to study.
What is still unclear to me. Is what kind of data you …
[View More]pass in the first layer (not what you have in the latent space). Independently whether it is a tract or a bundle, it seems you pass entire streamline (I assume as a series of x,y,z points) not individual tensors from individual voxels. Am I right?
Can someone clarify this aspect? Thanks
Best,Alex
[View Less]
Hi all,
We face this issue commonly where the tensor image doesn't look as expected
and the MD image is empty. For the same data, FSL creates perfect tensors
and MD images.
May I know if we are doing something wrong?
data, affine = load_nifti(os.path.join(os.getcwd(),
'_AXIAL_DTI_MDDW_20230421090830_32.nii'))
bvals, bvecs = read_bvals_bvecs(os.path.join(os.getcwd(),
'_AXIAL_DTI_MDDW_20230421090830_32.bval'), os.path.join(os.getcwd(),
'_AXIAL_DTI_MDDW_20230421090830_32.bvec'))
gtab = …
[View More]gradient_table(bvals, bvecs)
image_mask, mask_affine = load_nifti(os.path.join(os.getcwd(),
'brain_mask_warped.nii.gz'))
tensor_model = dti.TensorModel(gtab)
tensor=tensor_model.fit(data, mask=image_mask)
FA = fractional_anisotropy(tensor.evals)
FA[np.isnan(FA)] = 0
tensor_vals = dti.lower_triangular(tensor.quadratic_form)
save_nifti( os.path.join(os.getcwd(), 'tensor.nii.gz'), tensor_vals,
affine)
save_nifti( os.path.join(os.getcwd(), 'FA.nii.gz'), FA, affine)
[image: image.png][image: image.png]
Madhura
[View Less]
To whom it may concern,
I recently saw a video regarding bundle warp and I had a few questions:
1) Are we able to use this on whole brain streamlines or only smaller bundles?
2) If we are only able to do smaller bundles, is there an MNI atlas you are currently using to warp to MNI space? If so are you just taken segment at a time and getting individual warp fields?
3)Are the deformations in a format that we can convert to be ANTS compatible for other applications (such as improving T1 …
[View More]warping to an atlas by incorporating streamline warp calculations)?
Thanks,
Ajay
[View Less]