Mailman 3 March 2022 - DIPY

Kurtosis Tensor Rotation
by Ana Fouto 28 Mar '22

28 Mar '22

Hi, I am doing single-voxel simulations and I want to apply tensor rotation to the following theoretical tensor: DT[0][0] = 0.1783e-3; DT[0][1] = 0.0011e-3; DT[0][2] = 0.0125e-3; DT[1][0] = 0.0011e-3, DT[1][1] = 0.1459e-3; DT[1][2] = 0.0034e-3; DT[2][0] = 0.0125e-3; DT[2][1] = 0.0034e-3; DT[2][2] = 0.4028e-3 kt[0] = 0.5698; kt[1] = 0.3208; kt[2] = 2.6049; kt[3] = -0.1142; kt[4] = -1.1531, kt[5] = 0.3944; kt[6] = -0.5409; kt[7] = 0.7220; kt[8] = 0.777; kt[9] = 0.2865; kt[10] = 0.4700; kt[11] = 0.2065; kt[12] = -0.0005; kt[13] = 0.1655; kt[14] = -0.4157 This is how I am generating rotation directions: # Simulate tensor rotations: theta = np.pi * np.random.rand(nDTdirs) phi = 2 * np.pi * np.random.rand(nDTdirs) hsph_initial = HemiSphere(theta=theta, phi=phi) hsph_updated, potential = disperse_charges(hsph_initial, 5000) DTdirs = hsph_updated.vertices This is how I am applying tensor rotation: for d_i in tqdm(np.arange(nDTdirs)): time.sleep(0.3) # for current simulated tensor direction angles = DTdirs[d_i] sticks = _check_directions(angles) R = all_tensor_evecs(sticks) DT = np.dot(np.dot(R, DT), R.T) eigvals, eigvects = decompose_tensor(DT) dt_rot = np.array([DT[0][0], DT[0][1], DT[1][1], DT[0][2], DT[1][2], DT[2][2]]) kt_rot = Wrotate(kt, R) I think DT tensor rotation is working well because my estimations are converging to the correct ground truth. However, DKI estimates are not converging, which makes me wonder if the *Wrotate* function is well applied. Thank you for your attention! Ana

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[DIPY Workshop 2022] The workshop is over, get ready for next steps.
by Eleftherios Garyfallidis 27 Mar '22

27 Mar '22

Thank you all for attending the DIPY Workshop 2022. It was a pleasure meeting all of you. DIPY Workshop 2022 in numbers The workshop was a great success! Thanks a lot to everyone who contributed and participated in every way possible. We had a record-breaking 560 registered attendees. We answered 250+ questions at the live Q&A sessions and presented 20+ demos at the live demo sessions. [image: image.png] What is next? Follow us on twitter: @dipymri <https://twitter.com/dipymri> Star our repository on GitHub: @ dipy <https://github.com/dipy/dipy> Use our software and *cite* DIPY <https://doi.org/10.3389/fninf.2014.00008> and FURY <https://doi.org/10.21105/joss.03384>! [DIPY] Garyfallidis, Eleftherios, et al. "Dipy, a library for the analysis of diffusion MRI data." Frontiers in neuroinformatics 8 (2014): 8. DOI: https://doi.org/10.3389/fninf.2014.00008 [FURY] Garyfallidis, Eleftherios, et al. "FURY: advanced scientific visualization." Journal of Open Source Software 6.64 (2021): 3384. DOI: https://doi.org/10.21105/joss.03384 *Weekly office hours* to continue providing one-to-one support will be available for the rest of the month. Schedule for that is on the way ... Finally, make sure you attend our bi-weekly *open meetings*. Have a great weekend! Eleftherios

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Thank you!
by Ale Stella 27 Mar '22

27 Mar '22

Good morning, I am Alessandra Caporale, a postdoctoral researcher in neuro and vascular imaging. I wish to thank you for the extremely useful workshop you organized. The sessions were very interesting, the talks were to the point, and I learnt a lot! I am now using DIPY for tractography, and the tutorials on the website are just amazing! Thank you so much for your daily emails to inform about the new videos available! I feel extremely lucky for this opportunity to participate to this fantastic workshop, and learn more about DIPY! Should you need any help in the organization of future workshops, please do not hesitate to contact me in the future, I will be very happy to help (it would be an opportunity to show my gratitude!). I wish you a nice day, Alessandra Caporale -- ----------------------------------------------------------------------- Alessandra, Stella Caporale ITAB, Institute for Advanced Biomedical Technologies Via Luigi Polacchi, 66100 Chieti CH, Italy Email: alessandra.c <silvia.capuani(a)roma1.infn.it>aporale(a)unich.it

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Registration
by yusuf oner 26 Mar '22

26 Mar '22

Hi I have just noticed about your meeting after the registration deadline. Is it possible to register now and to get access to your handout and recordings? Thank you Yusuf Oner MD Sent from my iPhone

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Thank you for organize the DIPY workshop
by Yusheng Wang 25 Mar '22

25 Mar '22

Dear Eleftherios and teams, This is Yusheng Wang. One of the attendees of the DIYP workshop. I am a first-year Ph.D. student of the SDSU/UCSD joint doctoral program in language and communicative disorders. I am working in the Laboratory for the Brain Dynamics of Language, supervised by Dr. Stephanie Riès. My first-year project is trying to use diffusion imaging to investigate the neural networks underlying language and cognition in individuals with post-stroke aphasia. Thanks to you and your team for hosting a great workshop! The contents were informative and intensive. It was nice to learn from you and your teams. I want to say I didn't talk too much because I am not very confident in my English speaking, but I enjoyed the workshop! It was amazing. Thank you for everything again. We had collected some data with a single shell and are currently planning to collect more data and add more sequences (still discussing). Etienne, thank you for answering my questions in the one-on-one session. Everything is new to me. Thanks to the workshop, I can better understand what I am doing. I hope I can learn more from you all in the future. :) Best, Yusheng

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[DIPY Workshop 2022] Day 5 videos are now available and keynote on recent Nat. Methods paper!
by Eleftherios Garyfallidis 25 Mar '22

25 Mar '22

Hello all, This is the last day of the workshop. We plan to end the workshop strongly with very important topics and talks. Some of the highlights include: a) *Image registration* in *DIPY* (affine and nonrigid) including *eddy current *and *motion* correction by DIPY's *Serge Koudoro!*. b) Removing *SoS noise* with *CNNs* by Prof. *Hu Cheng!* c) *Brain extraction* using *V-Nets* and *Conditional Random Fields* by *Jong Sung Park!* d) *Tissue classification* (using T1 or dMRI data) by Dr. *Julio Villalon* and *Prof. Cheng!* e) A *live keynote* by Dr. *Matthew Cieslak* talking about his recent Nature Methods paper on *QSIPrep!* f) A* live demo* session demonstrating *QSIPrep* and *pyAFQ* by Prof. *Ariel Rokem*. To watch the talks and obtain the live zoom links simply go to *go to dipy.org <http://dipy.org/> -> Login -> Workshop Space -> 2022 -> Schedule and click on Day 5.* [image: image.png] See you all online at the live session and the Q&As! Onwards and upwards, Eleftherios p.s. To get access to this content you need to register here <https://dipy.org/workshops/dipy-workshop-2022#Registration>.

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[DIPY Workshop 2022] Day 4 videos are available + big day of tractometry!
by Eleftherios Garyfallidis 24 Mar '22

24 Mar '22

Hello all, We released the fourth day of educational videos! Today you will hear about our statistical frameworks (*BUAN *and* AFQ*) to perform group studies on wm bundles. Some of the highlights include: a) *Tractometry and group statistics *videos by Bramsh Chandio and Prof. Jaroslaw Harezlak. b) *Population-specific bundle atlasing* by David Romero-Bascones. c) A novel non-rigid registration method of bundles called *BundleWarp*. d) Our *live keynote talk* at *2pm EDT* by *Dr. Kurt Schilling* on the *challenges of tractography *and how we can surpass them. e) A *live demo* of *BUAN* at the demo session at 4pm EDT. *Simply go to dipy.org <http://dipy.org/> -> Login -> Workshop Space -> 2022 -> Schedule and click on Day 4.* [image: image.png] See you online! Best regards, Eleftherios p.s. To get access to this content you need to register here <https://dipy.org/workshops/dipy-workshop-2022#Registration>.

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[DIPY Workshop 2022] Day 3 videos are ready for you + exciting live keynotes!
by Eleftherios Garyfallidis 23 Mar '22

23 Mar '22

Hello all, We released the third day of educational videos! Some of the *highlights *today include: a) A video by *Dr. Rheault* showing *how to correct tractography file formats and understand their spaces*. Example data sets and notebooks for this talk are available here. <https://drive.google.com/file/d/1sy1REAljO_ztHf358Rnhy3R_8jez9h4s/view?usp=…> b) A first live keynote at 11 am EDT with *Dr. Aydogan* explaining *parallel transport tractography*. This tracking approach has been successful across many challenges and you should know about it. c) A second live keynote at 2 pm EDT with *Prof. O'Donnell* who will speak about the super exciting work in performing *white matter parcellation using deep learning*. *Simply go to dipy.org <http://dipy.org/> -> Login -> Workshop Space -> 2022 -> Schedule and click on Day 3.* [image: image.png] See you online and at the integrated chatroom. On behalf of the DIPY team, Eleftherios p.s. If you have not registered yet please register here <https://dipy.org/workshops/dipy-workshop-2022#Registration>.

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[DIPY Workshop 2022] Day 2 educational videos are out of the oven!
by Eleftherios Garyfallidis 22 Mar '22

22 Mar '22

Hello all, We released the first day of educational videos!! *Simply go to dipy.org <http://dipy.org/> -> Login -> Workshop Space -> 2022 -> Schedule and click on Day 2.* [image: image.png] *Don't miss the live sessions. We have two live Keynote talks today one at 11 am EDT and one at 2pm EDT as well as live Q&A and Demo sessions later in the day!* See you online and at the integrated chatroom. On behalf of the DIPY team, Eleftherios p.s. If you have not registered yet please register here <https://dipy.org/workshops/dipy-workshop-2022#Registration>.

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[DIPY Workshop 2022] Individual (one-to-one) help sessions
by Eleftherios Garyfallidis 22 Mar '22

22 Mar '22

Hello all, From today we will start having a quick help session (for installation or other issues) at 11am or 5 pm EDT. Reserve a slot by adding your information here <https://docs.google.com/spreadsheets/d/1FOJ102nq9aR_LOc6kPRzCCj-VxNd61eKf2E…> . Cheers, Eleftherios

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