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
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Dear All
I am new to DIPY. I am using dipy's tensor fit command used by Marc Golub in his free water estimation using Beltrami fit code (as I have only six directional clinical scans).
I would like to save the eigen vector files in nifti format which I would like to use for tractography using another software especially eigen vector 1.
I followed the documentation given in webpage https://workshop.dipy.org/documentation/1.6.0./examples_built/reconst_dti/
and used the command
save_nifti('…
[View More]tensor_evecs.nii.gz', tenfit.evecs.astype(np.float32), affine)
but it looks like the above command saves the Diffusion tensor matrix Dxx, Dxy etc and is of 3*3
How to get only the eigenvector 1, 2 and 3 separately and save them separately
I spent quite some time searching the DIPY documentation and email archives but was not able to find it. Can some in the email list kindly help me with the command to save the eigenvector 1 as a nifti file
Thanks
Venkat
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Dear All
I am new to DIPY. I am using dipy's tensor fit command used by Marc Golub
in his free water estimation using Beltrami fit code (as I have only six
directional clinical scans).
I would like to save the eigen vector files in nifti format which I would
like to use for tractography using another software especially eigen vector
1.
I followed the documentation given in webpage
https://workshop.dipy.org/documentation/1.6.0./examples_built/reconst_dti/
and used the command
save_nifti('…
[View More]tensor_evecs.nii.gz', tenfit.evecs.astype(np.float32), affine)
but it looks like the above command saves the Diffusion tensor matrix Dxx,
Dxy etc and is of 3*3
How to get only the eigenvector 1, 2 and 3 separately and save them
separately
I spent quite some time searching the DIPY documentation and email
archives but was not able to find it. Can some in the email list kindly
help me with the command to save the eigenvector 1 as a nifti file
Thanks
Venkat
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Hi dipy developers,
I hope you are doing well. I’m interested in separating the fornix .trk file from the HCP-842 atlas in MNI space ICBM 2009a, which is distributed with dipy. I noticed this in the associated README:
“For the Fornix (F) both left and right sides are included in one file. It is possible to easily separate them. Send an e-mail to dipy(a)python.org<mailto:dipy@python.org> to learn how.”
Could you give me guidance on this? I’m analyzing diffusion MRI data collected from …
[View More]epilepsy patients. The fornix is of particular interest to us, and it would be great to have separate models for the left and right fornices. Thank you so much.
Best,
Marc Jaskir
Neuroscience PhD candidate
University of Pennsylvania
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