Mailman 3 December 2021 - DIPY

Optimal b-values scheme for dipy.reconst.dti.TensorModel
by jan.valosek＠upol.cz Dec. 30, 2021

Dec. 30, 2021

Dear DIPY experts, I am considering how to design DWI protocol in sense of b0 images. Generally, I am thinking about two options: 1. Five b0 images at the beginning, then 32 uniformly distributed directions with b-value = 800 s/mm2 2. Interspersion of b0 images among DWI volumes in ration 1:8. My bval file would then look like: “0 800 800 800 800 800 800 800 800 0 800 800 800 800 800 800 800 800 0 800 800 800 800 800 800 800 800 0 800 800 800 800 800 800 800 800 0” Is dipy.reconst.dti.TensorModel able to take into account the second option (with interspersed b0) and benefit from it? Thank you in advance. Best, Jan

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BrainHack-bloomington, online edition starts tomorrow!
by Koudoro, Serge Dec. 15, 2021

Dec. 15, 2021

Hello all, It is not too late to register for the event! Feel free to join this hacking event and share a moment with us! https://brainhack.luddy.indiana.edu/ Cheers, Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro(a)iu.edu<mailto:skoudoro@indiana.edu>

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Re: Rototranslating the Bvecs
by Eleftherios Garyfallidis Dec. 13, 2021

Dec. 13, 2021

Thank you for your question Alex. Yes we do provide a function that does exactly that. The name of the function is *reorient_bvecs* (dipy.core.gradients.reorient_bvecs). If there is no tutorial about this online it would be great if you can provide one. On Mon, Dec 13, 2021 at 9:24 AM Alex Crimi via DIPY <dipy(a)python.org> wrote: > Hi there, > > not sure this is specific to Dipy but maybe it is. > As someone pointed out to me, if we register DWI to something else before > running the tractography the values in the bvec files should also be > rotated. There is even a paper explaining that this is critical: The > B-matrix must be rotated when correcting for subject motion in DTI data - > PubMed (nih.gov) <https://pubmed.ncbi.nlm.nih.gov/19319973/> > > What is your experience with this? Do you know any easy transformation for > this? > We need to do this as to carry out the diffusion harmonization (see my > previous mail) we need to register all volumes to each other. > > Best, > Alex >

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Rototranslating the Bvecs
by Alex Crimi Dec. 13, 2021

Dec. 13, 2021

Hi there, not sure this is specific to Dipy but maybe it is. As someone pointed out to me, if we register DWI to something else before running the tractography the values in the bvec files should also be rotated. There is even a paper explaining that this is critical: The B-matrix must be rotated when correcting for subject motion in DTI data - PubMed (nih.gov) What is your experience with this? Do you know any easy transformation for this?We need to do this as to carry out the diffusion harmonization (see my previous mail) we need to register all volumes to each other. Best,Alex

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Brainhack Global - Bloomington, Indiana (online edition) - December 16th-17th
by Koudoro, Serge Dec. 7, 2021

Dec. 7, 2021

Dear DIPY Community, Do you need help to add a new feature on DIPY? Do you want to share ideas or a moment with DIPY users and developers? or Do you have any questions about your DIPY code? Feel free to join us on December 16th-17th during our Brainhack event! (https://brainhack.luddy.indiana.edu/) Whatever your background or level of expertise is, you are encouraged to join us and participate: propose and discuss ideas, showcase demos, or contribute to activities initiated by others. This free online event will be a good opportunity to connect with each other (registration is mandatory). . Some users already have proposed projects that you might be interested in: * Add new features to image registration * Sphinx Gallery Integration in DIPY * Improve Patch2self * Sprint to fix issues on DIPY * Implementation of the generalized volumetric atlas-based method for tractogram segmentation * Convert python 2 dipy script to python 3 * Your project! You will find all the information (schedule, registration, ...) at https://brainhack.luddy.indiana.edu/ Please let me know if you have any questions. Cheers, Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro(a)iu.edu<mailto:skoudoro@indiana.edu>

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Open Meeting Talk Now- Tractography dissection variability - Starts in 15 min
by Koudoro, Serge Dec. 2, 2021

Dec. 2, 2021

Hello all, Just a friendly reminder about the talk of this week: Tractography dissection variability. It starts in 15min! ( 1pm EST / 6pm CET / 10am PT) Speaker : Kurt Schilling Paper : https://www.sciencedirect.com/science/article/pii/S1053811921007758?via%3Di…) Duration: 35-45min + questions / discussions. Connect here: https://iu.zoom.us/j/84926066336 Schedule: https://github.com/dipy/dipy/discussions/2398 See you online, On Behalf of the DIPY Team Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro(a)iu.edu<mailto:skoudoro@indiana.edu>

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Open Meeting Talk - Tractography dissection variability
by Koudoro, Serge Dec. 1, 2021

Dec. 1, 2021

Hello all, This week (Thursday, November 2nd), at 1 pm Eastern Time (7pm CET / 10am PT), we will be hearing from Kurt Schilling Dr. Schilling is a Professor at Vanderbilt University. The title of his talk is "Tractography dissection variability”. To prepare your question, you can read the paper at the following link https://www.sciencedirect.com/science/article/pii/S1053811921007758?via%3Di…) You can find more information about our speaker here: https://www.vanderbilt.edu/vise/visepeople/kurt-schilling/ The zoom link for this talk is https://iu.zoom.us/j/84926066336 More information about the open meetings is available here: https://github.com/dipy/dipy/discussions/2398 See you tomorrow, On Behalf of the DIPY Team Serge K Serge Koudoro Software Developer Intelligent Systems Engineering Garyfallidis Research Group<https://grg.luddy.indiana.edu/> School of Informatics, Computing, and Engineering Luddy Hall 700 N Woodlawn Ave, 4056 Bloomington, IN 47408 skoudoro(a)iu.edu<mailto:skoudoro@indiana.edu>

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