Mailman 3 March 2021 - DIPY

patch2self denoising attenuated b=0 images
by lmuftuler＠mcw.edu April 1, 2021

April 1, 2021

Hi, I was trying out the new patch2self denoising on a 4-shell (b=1k s/mm^2 up to 4k s/mm^2) diffusion data (total of 94 directions plus 4 b=0 images). First, I noticed that it attenuated the b=0 images (all four of them) with respect to the rest of the image series. This in turn reduced map-mri ZD maps by about 10% to 20%, which was expected b/c (E(q)) essentially got "smaller". Did anybody have any experience with this? Any suggestion why it happened and how to fix it? best, -Tugan

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DTI analysis for rats.
by Maurizio Bergamino March 25, 2021

March 25, 2021

Hello, I have a question: Is there any script/pipeline in Dipy that I can use for DTI in rats? Thanks, Maurizio Bergamino

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DIPY Website Down Tomorrow
by Serge K. March 22, 2021

March 22, 2021

Hello All, Due to an Electrical Outage on our server, the DIPY Website and the DIPY Workshop website *will NOT be reachable tomorrow (03/23/2021) from 8 am - 5 pm EST. * Sorry for the inconvenience Serge K ------------------------------ Simple is better than complex | http://pythonastuces.com

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DIPY Workshop 2021 - Day 5 videos released
by Eleftherios Garyfallidis March 19, 2021

March 19, 2021

Hello all, Thank you all 472 registered attendees for your interest in the DIPY workshop. If not a registered attendee please disregard this email. *Fifth day educational videos have been released! * Please go to dipy.org then *Login -> Workshop Space -> 2021 -> Schedule* That should bring you to the page below. Click on the fifth day. [image: image.png] This should bring you to the educational videos of the fifth day. On the left side you will see the different topics and on the right side you will be able to watch our videos. See below: [image: image.png] *Have in mind that the Coding Sprint starts at 11 am EST.* This is primarily for people who want to contribute new features to DIPY. Add your project here <https://docs.google.com/spreadsheets/d/1FOJ102nq9aR_LOc6kPRzCCj-VxNd61eKf2E…> . One-to-one online meetings, to get help with your data analysis, continue today; you can reserve a meeting using this spreadsheet <https://docs.google.com/spreadsheets/d/1eI_4J8qXmRhnFk-CRpNLVlm-cLWlN3ke5wL…> . The zoom link (and password) for the Coding Sprint, which allows you to work together with the DIPY team towards new developments, is available on the homepage of the workshop space. *After watching the videos please write down your questions and bring them forward in * *the Q&A session at 3 pm EST. * The zoom link (and password) of Q&A is also available on the homepage of the workshop space. The DIPY team is wishing you another wonderful day during this online experience. Thank you, Eleftherios Garyfallidis, PhD Assistant Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG <https://grg.sice.indiana.edu/> | DIPY <http://dipy.org/> | FURY <https://fury.gl/>

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DIPY Workshop 2021 - Day 4 videos released
by Eleftherios Garyfallidis March 18, 2021

March 18, 2021

Hello all, Thank you all 464 registered attendees for your interest in the DIPY workshop. If not a registered attendee please disregard this email. *Fourth day educational videos have been released! * Please go to dipy.org then *Login -> Workshop Space -> 2021 -> Schedule* That should bring you to the page below. Click on the fourth day. [image: image.png] This should bring you to the educational videos of the fourth day. On the left side you will see the different topics and on the right side you will be able to watch our videos. See below: [image: image.png] *Have in mind that the Coding Sprint starts earlier today at 11 am EST.* This is primarily for people who want to contribute new features to DIPY. Add your project here <https://docs.google.com/spreadsheets/d/1FOJ102nq9aR_LOc6kPRzCCj-VxNd61eKf2E…> . One-to-one online meetings, to get help with your data analysis, continue today; you can reserve a meeting using this spreadsheet <https://docs.google.com/spreadsheets/d/1eI_4J8qXmRhnFk-CRpNLVlm-cLWlN3ke5wL…> . The zoom link (and password) for the Coding Sprint, which allows you to work together with the DIPY team towards new developments, is available on the homepage of the workshop space. *After watching the videos please write down your questions and bring them forward in * *the Q&A session at 3 pm EST. * The zoom link (and password) of Q&A is available on the homepage of the workshop space. The DIPY team is wishing you another wonderful day during this online experience. *Have in mind that the day today has more topics than the previous days. So start watching!* Thank you, Eleftherios Garyfallidis, PhD Assistant Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG <https://grg.sice.indiana.edu/> | DIPY <http://dipy.org/> | FURY <https://fury.gl/> p.s. For people who registered today: How to Login After registration. Please go to https://dipy.org and Login (near top right corner of the website). See below: After logging in you go again at the top right where you see the black profile and select Workshop Space. Then you can navigate and see the schedule, integrated chat and courses. Be happy to say hi in the chat and ask questions.

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DIPY Workshop 2021 - Show your love
by Eleftherios Garyfallidis March 17, 2021

March 17, 2021

Hello all, If you have been enjoying the DIPY workshop please give us a star <https://github.com/dipy/dipy> in our GitHub Repository. [image: image.png] <https://github.com/dipy/dipy> If you use DIPY please cite this paper: Garyfallidis, E., Brett, M., Amirbekian, B., Rokem, A., Van Der Walt, S., Descoteaux, M. and Nimmo-Smith, I., 2014. Dipy, a library for the analysis of diffusion MRI data. *Frontiers in neuroinformatics*, *8*, p.8. Bibtex <https://scholar.googleusercontent.com/scholar.bib?q=info:INtSHPENHxAJ:schol…> EndNote <https://scholar.googleusercontent.com/scholar.enw?q=info:INtSHPENHxAJ:schol…> Thank you all and see you at 3pm EST for the live Q&A session. Today we discuss tractography, connectivity, multidimensional encoding and deep learning! Best, Eleftherios

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DIPY Workshop 2021 - Day 3 videos released
by Eleftherios Garyfallidis March 17, 2021

March 17, 2021

Hello all, Thank you all 455 registered attendees for your interest in the DIPY workshop. If not a registered attendee please disregard this email. *Third day educational videos have been released!* Please go to dipy.org then *Login -> Workshop Space -> 2021 -> Schedule* That should bring you to the page below. Click on the third day. [image: image.png] This should bring you to the educational videos of the third day. On the left side you will see the different topics and on the right side you will be able to watch our videos. See below: [image: image.png] *Have in mind that the data accelerator starts earlier at 11 am EST.* The DIPY team will be available to help you with your data. It would be great if you have a recent Python Distribution (such as Anaconda) and a recent DIPY version. To upgrade from Anaconda prompt (Windows) or Terminal (Linux, Mac) use: pip install -U dipy fury The zoom link (and password) for the Data Accelerator which allows you to meet with the DIPY team in person is available on the homepage of the workshop space. You can reserve a meeting using this spreadsheet <https://docs.google.com/spreadsheets/d/1eI_4J8qXmRhnFk-CRpNLVlm-cLWlN3ke5wL…> . *After watching the videos please write down your questions and bring them forward in the Q&A session at 3 pm EST. * The zoom link (and password) is available on the homepage of the workshop space. The DIPY team is wishing you a wonderful time during this online experience. Thank you, Eleftherios Garyfallidis, PhD Assistant Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG <https://grg.sice.indiana.edu/> | DIPY <http://dipy.org/> | FURY <https://fury.gl/> p.s. For people who registered today How to Login After registration. Please go to https://dipy.org and Login (near top right corner of the website). See below: After logging in you go again at the top right where you see the black profile and select Workshop Space. Then you can navigate and see the schedule, integrated chat and courses. Be happy to say hi in the chat and ask questions.

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DIPY Workshop 2021 - Day 2 videos released
by Eleftherios Garyfallidis March 16, 2021

March 16, 2021

Hello all, Thank you all 450 registered attendees for your interest in the DIPY workshop. If not a registered attendee please disregard this email. *Second day educational videos have been released!* Please go to dipy.org then *Login -> Workshop Space -> 2021 -> Schedule* That should bring you to the page below. Click on the second day. [image: image.png] This should bring you to the educational videos of the second day. On the left side you will see the different topics and on the right side you will be able to watch our videos. See below: [image: image.png] *Please write down your questions and bring them forward in the Q&A session at 3 pm EST. * The zoom link (and password) is available on the homepage of the workshop space. *Have in mind that the data accelerator starts earlier at 11 am EST.* The DIPY team will be available to help you with your data. It would be great if you have DIPY installed by then (pip install -U dipy fury). The zoom link (and password) for this event and spreadsheet to fill <https://docs.google.com/spreadsheets/d/1eI_4J8qXmRhnFk-CRpNLVlm-cLWlN3ke5wL…> are available on the homepage of the workshop space. Thank you, Eleftherios Garyfallidis, PhD Assistant Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG <https://grg.sice.indiana.edu/> | DIPY <http://dipy.org/> | FURY <https://fury.gl/> p.s. For people who registered today How to Login After registration. Please go to https://dipy.org and Login (near top right corner of the website). See below: After logging in you go again at the top right where you see the black profile and select Workshop Space. Then you can navigate and see the schedule, integrated chat and courses.

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How to upgrade to DIPY 1.4.0 - Installation instructions (Updated)
by Eleftherios Garyfallidis March 15, 2021

March 15, 2021

Hello all, To upgrade DIPY. Just go to the Anaconda prompt (Win) or Terminal (Mac or Linux) and do: *$ pip install -U dipy fury* In a previous email there were accidentally two -- rather than one -. One is correct. Thank you for pointing that out. Enjoy the new version! Best, Eleftherios

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DIPY Workshop 2021 - Day 1 videos released
by Eleftherios Garyfallidis March 15, 2021

March 15, 2021

Hello all, Thank you all 420 registered attendees for your interest in the DIPY workshop. If not a registered attendee please disregard this email. *First day educational videos have been released!* Please go to *Login -> Workshop Space -> 2021 -> Schedule* That should bring you to the page below. Click on the first day. [image: image.png] This should bring you to the educational videos of the first day. See below. [image: image.png] On the left side you will see the different topics and on the right side you will be able to watch our videos. *Please write down your questions and bring them forward in the Q&A session at 3 pm EST. * The zoom link (and password) is available on the homepage of the workshop space. *Have in mind that the data accelerator starts earlier at 11 am EST.* The DIPY team will be available to help you with your data. It would be great if you have DIPY installed by then. The zoom link (and password) for this event and spreadsheet to fill <https://docs.google.com/spreadsheets/d/1eI_4J8qXmRhnFk-CRpNLVlm-cLWlN3ke5wL…> are available on the homepage of the workshop space. Thank you, Eleftherios Garyfallidis, PhD Assistant Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG <https://grg.sice.indiana.edu/> | DIPY <http://dipy.org/> | FURY <https://fury.gl/>

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