From markiewicz at stanford.edu Sun Feb 12 13:20:25 2023 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Sun, 12 Feb 2023 18:20:25 +0000 Subject: [Neuroimaging] ANN: NiBabel 5.0.1 Message-ID: Hi all, Quick announcement that I've published NiBabel 5.0.1. This bug-fix release includes a couple minor fixes as well as adds some metadata needed to allow downstream projects to type check their use of NiBabel objects and functions that we neglected in 5.0.0. Just to set some expectations around type-checking: This is a work in progress and we are (at least I am) new to Python typing. We might not get things right on the first try. Annotations that do not require breaking APIs may appear in minor releases, but we will not consider annotations part of the API for now. This means that, *if you type check your project based on our annotations, upgrading minor releases may require updating your annotations*. If you are not type checking your projects, this should have no impact on you. For the most part, we will not modify type annotations in bug-fix releases, though obviously a buggy annotation may need fixing, and we'll use our best judgment. As ever, thank you to everybody who reported issues, submitted patches and reviewed PRs. Please report any issues you have to https://github.com/nipy/nibabel/issues. The full changelog can be found at https://github.com/nipy/nibabel/releases/tag/5.0.1. Please cite the Zenodo archive, if you use NiBabel in your work: https://doi.org/10.5281/zenodo.7633628 Best, Chris From jbpoline at gmail.com Sun Feb 12 17:11:03 2023 From: jbpoline at gmail.com (JB Poline) Date: Sun, 12 Feb 2023 17:11:03 -0500 Subject: [Neuroimaging] ANN: NiBabel 5.0.1 In-Reply-To: References: Message-ID: Hi Chris, The lab is so grateful for the work congrats for the release ! JB On Sun, Feb 12, 2023 at 2:37 PM Christopher Markiewicz < markiewicz at stanford.edu> wrote: > Hi all, > > Quick announcement that I've published NiBabel 5.0.1. This bug-fix release > includes a couple minor fixes as well as adds some metadata needed to allow > downstream projects to type check their use of NiBabel objects and > functions that we neglected in 5.0.0. > > Just to set some expectations around type-checking: This is a work in > progress and we are (at least I am) new to Python typing. We might not get > things right on the first try. Annotations that do not require breaking > APIs may appear in minor releases, but we will not consider annotations > part of the API for now. This means that, *if you type check your project > based on our annotations, upgrading minor releases may require updating > your annotations*. If you are not type checking your projects, this should > have no impact on you. > > For the most part, we will not modify type annotations in bug-fix > releases, though obviously a buggy annotation may need fixing, and we'll > use our best judgment. > > As ever, thank you to everybody who reported issues, submitted patches and > reviewed PRs. > > Please report any issues you have to > https://github.com/nipy/nibabel/issues. > > The full changelog can be found at > https://github.com/nipy/nibabel/releases/tag/5.0.1. > > Please cite the Zenodo archive, if you use NiBabel in your work: > https://doi.org/10.5281/zenodo.7633628 > > Best, > Chris > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bertrand.thirion at inria.fr Sun Feb 12 17:14:46 2023 From: bertrand.thirion at inria.fr (Bertrand Thirion) Date: Sun, 12 Feb 2023 23:14:46 +0100 Subject: [Neuroimaging] ANN: NiBabel 5.0.1 In-Reply-To: References: Message-ID: Thx ! Bertrand Le 12/02/2023 ? 19:20, Christopher Markiewicz a ?crit?: > Hi all, > > Quick announcement that I've published NiBabel 5.0.1. This bug-fix release includes a couple minor fixes as well as adds some metadata needed to allow downstream projects to type check their use of NiBabel objects and functions that we neglected in 5.0.0. > > Just to set some expectations around type-checking: This is a work in progress and we are (at least I am) new to Python typing. We might not get things right on the first try. Annotations that do not require breaking APIs may appear in minor releases, but we will not consider annotations part of the API for now. This means that, *if you type check your project based on our annotations, upgrading minor releases may require updating your annotations*. If you are not type checking your projects, this should have no impact on you. > > For the most part, we will not modify type annotations in bug-fix releases, though obviously a buggy annotation may need fixing, and we'll use our best judgment. > > As ever, thank you to everybody who reported issues, submitted patches and reviewed PRs. > > Please report any issues you have to https://github.com/nipy/nibabel/issues. > > The full changelog can be found at https://github.com/nipy/nibabel/releases/tag/5.0.1. > > Please cite the Zenodo archive, if you use NiBabel in your work: https://doi.org/10.5281/zenodo.7633628 > > Best, > Chris > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging From elef at indiana.edu Mon Feb 13 12:27:28 2023 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Mon, 13 Feb 2023 12:27:28 -0500 Subject: [Neuroimaging] Registration for DIPY Workshop 2023 is now open! April 24-28, Santa Monica, CA Message-ID: Hello all, We are excited to announce that the registration for the DIPY Workshop 2023 is now open! Registration, program and more information is available at https://dipy.org/workshops/latest. This is an in person event. This year we are introducing a full day of Preprocessing (a challenging problem) and discussing new topics in Reconstruction, Microstructure Modeling, Denoising, Tractography, Tractometry and Visualization! In addition, Matthew Brett will talk about Nibabel which is an important project that has been developed in parallel with DIPY from the early days of the creation of Neuroimaging in Python. Other guest speakers include Jason Yeatman from Stanford and Sarah Heilbronner from UMN. The DIPY Workshop 2023 will take place on April 24-28 (Monday to Friday, 9 AM to 6 PM) by the ocean in beautiful Santa Monica (Los Angeles, California). The conference will be held at Le Merigot Hotel. Unlimited coffee, breakfast and snacks will be provided. In addition, - Sessions for guided practice (hands-on) will be available every day. - Attendees can present their work or problems of interest. - Certificates of attendance will be provided. Finally, a limited number of seats are provided. Register today! On behalf of the DIPY team, Eleftherios Garyfallidis, PhD Associate Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG | DIPY | FURY -------------- next part -------------- An HTML attachment was scrubbed... URL: From jacob.bunyamin at monash.edu Mon Feb 13 19:50:48 2023 From: jacob.bunyamin at monash.edu (Jacob Bunyamin) Date: Tue, 14 Feb 2023 11:50:48 +1100 Subject: [Neuroimaging] Combining binary mask to 3D volume Message-ID: Good afternoon, I am trying to overlay a binary mask to 3D volume and combine them into a single file. Is there any way to do this? Thank you, Kind regards, Jacob -- *Jacob Bunyamin* PhD Student *Department of Neuroscience* Central Clinical School, Monash University 99 Commercial Road Melbourne VIC 3004 *E:* jacob.bunyamin at monash.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From markiewicz at stanford.edu Mon Feb 13 20:52:46 2023 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Tue, 14 Feb 2023 01:52:46 +0000 Subject: [Neuroimaging] Combining binary mask to 3D volume In-Reply-To: References: Message-ID: Hi Jacob, If I'm understanding the problem correctly, you mean you have a 3D image (maybe T1-weighted or similar) and a 3D binary mask, and what you would like is the original image values where the mask is 1 and 0s where the mask is 0. Assuming that's correct, I might take this approach: import nibabel as nib import numpy as np img = nib.load(img_fname) mask_img = nib.load(mask_fname) data = img.get_fdata() mask = np.asanyarray(mask_img.dataobj) != 0 # Remove data outside the mask data[~mask] = 0 masked_img = img.__class__(data, img.affine, img.header) masked_img.to_filename(out_fname) I suspect nilearn has tools that would do this as well. And if your mask is aligned to your original image but not have the same shape and affine, you will need to resample your mask first before you can use the data arrays in this way. Best, Chris ________________________________________ From: Neuroimaging on behalf of Jacob Bunyamin via Neuroimaging Sent: Monday, February 13, 2023 19:50 To: neuroimaging at python.org Cc: Jacob Bunyamin Subject: [Neuroimaging] Combining binary mask to 3D volume Good afternoon, I am trying to overlay a binary mask to 3D volume and combine them into a single file. Is there any way to do this? Thank you, Kind regards, Jacob -- Jacob Bunyamin PhD Student Department of Neuroscience Central Clinical School, Monash University 99 Commercial Road Melbourne VIC 3004 E: jacob.bunyamin at monash.edu From jacob.bunyamin at monash.edu Mon Feb 13 21:06:25 2023 From: jacob.bunyamin at monash.edu (Jacob Bunyamin) Date: Tue, 14 Feb 2023 13:06:25 +1100 Subject: [Neuroimaging] Combining binary mask to 3D volume In-Reply-To: References: Message-ID: Thank you! On Tue, 14 Feb 2023 at 12:53, Christopher Markiewicz < markiewicz at stanford.edu> wrote: > Hi Jacob, > > If I'm understanding the problem correctly, you mean you have a 3D image > (maybe T1-weighted or similar) and a 3D binary mask, and what you would > like is the original image values where the mask is 1 and 0s where the mask > is 0. > > Assuming that's correct, I might take this approach: > > import nibabel as nib > import numpy as np > > img = nib.load(img_fname) > mask_img = nib.load(mask_fname) > > data = img.get_fdata() > mask = np.asanyarray(mask_img.dataobj) != 0 > > # Remove data outside the mask > data[~mask] = 0 > > masked_img = img.__class__(data, img.affine, img.header) > masked_img.to_filename(out_fname) > > I suspect nilearn has tools that would do this as well. And if your mask > is aligned to your original image but not have the same shape and affine, > you will need to resample your mask first before you can use the data > arrays in this way. > > Best, > Chris > > ________________________________________ > From: Neuroimaging stanford.edu at python.org> on behalf of Jacob Bunyamin via Neuroimaging < > neuroimaging at python.org> > Sent: Monday, February 13, 2023 19:50 > To: neuroimaging at python.org > Cc: Jacob Bunyamin > Subject: [Neuroimaging] Combining binary mask to 3D volume > > Good afternoon, > > I am trying to overlay a binary mask to 3D volume and combine them into a > single file. Is there any way to do this? > > Thank you, > > Kind regards, > > Jacob > > -- > Jacob Bunyamin > PhD Student > > Department of Neuroscience > Central Clinical School, Monash University > 99 Commercial Road > Melbourne VIC 3004 > E: jacob.bunyamin at monash.edu > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandra.badea at duke.edu Mon Feb 13 19:56:03 2023 From: alexandra.badea at duke.edu (Alexandra Badea, Ph.D.) Date: Tue, 14 Feb 2023 00:56:03 +0000 Subject: [Neuroimaging] Combining binary mask to 3D volume In-Reply-To: References: Message-ID: Do you mean as in multiplying the two volumes? Or perhaps you want to consider adding an alpha channel. Alexandra ________________________________ From: Neuroimaging on behalf of Jacob Bunyamin via Neuroimaging Sent: Monday, February 13, 2023 7:50 PM To: neuroimaging at python.org Cc: Jacob Bunyamin Subject: [Neuroimaging] Combining binary mask to 3D volume Good afternoon, I am trying to overlay a binary mask to 3D volume and combine them into a single file. Is there any way to do this? Thank you, Kind regards, Jacob -- Jacob Bunyamin PhD Student Department of Neuroscience Central Clinical School, Monash University 99 Commercial Road Melbourne VIC 3004 E: jacob.bunyamin at monash.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From z.baratz at gmail.com Tue Feb 14 05:25:38 2023 From: z.baratz at gmail.com (Zvi Baratz) Date: Tue, 14 Feb 2023 12:25:38 +0200 Subject: [Neuroimaging] pydicom Roadmap Request for Feedback Message-ID: Hi all, pydicom has recently opened a discussion thread to gain some feedback and help formulate a roadmap for future development. DICOM files are difficult to work with, but they are a fundamental part of neuroimaging research and will continue to be in the foreseeable future. I think this is a good opportunity to communicate our needs, propose ideas for improvement, and/or just say thanks and share with the maintainers how pydicom helped you in your research. All the best, Zvi -------------- next part -------------- An HTML attachment was scrubbed... URL: From jacob.bunyamin at monash.edu Tue Feb 14 18:53:43 2023 From: jacob.bunyamin at monash.edu (Jacob Bunyamin) Date: Wed, 15 Feb 2023 10:53:43 +1100 Subject: [Neuroimaging] Combining binary mask to 3D volume In-Reply-To: References: Message-ID: Good afternoon, Apologies for this basic question, If I wanted to create a new image from 3D volume and binary mask (combined with multiplication), is it better to use np.asanyarray or np.multiply? Thank you Kind regards, Jacob On Tue, 14 Feb 2023 at 13:06, Jacob Bunyamin wrote: > Thank you! > > On Tue, 14 Feb 2023 at 12:53, Christopher Markiewicz < > markiewicz at stanford.edu> wrote: > >> Hi Jacob, >> >> If I'm understanding the problem correctly, you mean you have a 3D image >> (maybe T1-weighted or similar) and a 3D binary mask, and what you would >> like is the original image values where the mask is 1 and 0s where the mask >> is 0. >> >> Assuming that's correct, I might take this approach: >> >> import nibabel as nib >> import numpy as np >> >> img = nib.load(img_fname) >> mask_img = nib.load(mask_fname) >> >> data = img.get_fdata() >> mask = np.asanyarray(mask_img.dataobj) != 0 >> >> # Remove data outside the mask >> data[~mask] = 0 >> >> masked_img = img.__class__(data, img.affine, img.header) >> masked_img.to_filename(out_fname) >> >> I suspect nilearn has tools that would do this as well. And if your mask >> is aligned to your original image but not have the same shape and affine, >> you will need to resample your mask first before you can use the data >> arrays in this way. >> >> Best, >> Chris >> >> ________________________________________ >> From: Neuroimaging > stanford.edu at python.org> on behalf of Jacob Bunyamin via Neuroimaging < >> neuroimaging at python.org> >> Sent: Monday, February 13, 2023 19:50 >> To: neuroimaging at python.org >> Cc: Jacob Bunyamin >> Subject: [Neuroimaging] Combining binary mask to 3D volume >> >> Good afternoon, >> >> I am trying to overlay a binary mask to 3D volume and combine them into a >> single file. Is there any way to do this? >> >> Thank you, >> >> Kind regards, >> >> Jacob >> >> -- >> Jacob Bunyamin >> PhD Student >> >> Department of Neuroscience >> Central Clinical School, Monash University >> 99 Commercial Road >> Melbourne VIC 3004 >> E: jacob.bunyamin at monash.edu >> _______________________________________________ >> Neuroimaging mailing list >> Neuroimaging at python.org >> https://mail.python.org/mailman/listinfo/neuroimaging >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.crimi at sanoscience.org Fri Feb 17 18:34:25 2023 From: a.crimi at sanoscience.org (Alex Crimi) Date: Fri, 17 Feb 2023 23:34:25 +0000 Subject: [Neuroimaging] AI for Neuro summer school in Sicily 2023 Message-ID: Dear all, we would like to invite you to the 2nd international Summer School on Neuroimaging, NeuroScience, Neuroncology. This year will focus mostly in AI for temporal patterns, and Glioblastoma 25th?29 June, 2023, Aktea Hotel, Lipari, Italy https://www.neuro.sano.science/ The event is also related to a special issue of Frontiers In Neuroimaging: https://www.frontiersin.org/research-topics/53517/brain-time-series-signals-and-machine-learning-from-spike-trains-to-dynamical-functional-connectivity We will have 2 sessions where participants can brainstorm and potentially prepare papers for the issue assisted. Scope: The school is aimed at providing lectures and workshops about Neuroimaging, NeuroScience, Neuroncology for PhD students, post-doctoral researchers, and faculty/company members. Program comprises lectures and workshops with * Gael Varoquaux (INRIA, ?cole normale sup?rieure, Scikit-learn) * Paul Thompson (UCLA, NIGMA consortium) * Luiz Pessoa (Maryland University) * Stephanie Forkel (Donders Institute) * Bozena Kaminska (Nencki Institute) * Giovanni Petri (CENTAI) * Daniel Margulies (CNRS) * Norbert Galldiks (Koeln University Hospital, Juelich Centrum) * Aly Abayazeed (Neosoma) * Lee Alex Donald Cooper (Northwestern University, Feinberg School of Medicine) * Susan Short (School of Medicine Leeds) * Andras Jakab (Children university hospital of Zurich) Organizing committee * Alessandro Crimi, Brian&More lab of Sano Science (Krakow, Poland) * Spyridon Bakas, Pereleman School of Medicine of University of Pennsylvania (Philadelphia, USA) We invite you to lectures by well-known worldwide speakers, workshops, and tutorials. Complete program will be posted. Climbing the sulphuric crater of Vulcano is planned, as well as a boat trip to Panarea lagoons and around the active volcano of Stromboli. The brainstorming sessions are planned at the Greek necropolis. We currently limit to 70 participants, with no particular pre-selection (First-Registered-First-Served). Further cases will be considered carefully according the CV. See you in Lipari. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Thu Feb 23 13:37:20 2023 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Thu, 23 Feb 2023 13:37:20 -0500 Subject: [Neuroimaging] Postdoctoral Position at DIPY HQ - Starting Summer/Fall 2023 Message-ID: Hello all, We are excited to announce a new Postdoctoral position here at Indiana University. The Postdoc will focus on improving DIPY' s statistical and machine learning capabilities. Professor Jaroslaw Harezlak (cc'ed) and myself will be supervising the work. Formal information about this position (and how to apply) is provided here https://indiana.peopleadmin.com/postings/16773 Happy to answer any questions you may have. Best regards, Eleftherios Garyfallidis, PhD Associate Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 GRG | DIPY | FURY -------------- next part -------------- An HTML attachment was scrubbed... URL: From garyfallidis at gmail.com Tue Feb 28 13:48:56 2023 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Tue, 28 Feb 2023 13:48:56 -0500 Subject: [Neuroimaging] ANN: DIPY 1.6.0 Message-ID: Hello all, We are excited to announce a new release of DIPY: DIPY 1.6.0 is out from the oven! In addition, registration for the oceanic DIPY workshop 2023 (April 24-28) is now open! Our comprehensive program is designed to equip you with the skills and knowledge needed to master the latest techniques and tools in structural and diffusion imaging. An intense hands-on experience in Santa Monica, Los Angeles! See the exquisite program here for this highly anticipated event . DIPY 1.6.0 (Monday, 16 January 2023) The release 1.6.0 received contributions from 22 developers (the full release notes are at: https://dipy.org/documentation/1.6.0./release_notes/release1.6/). Thank you all for your contributions and feedback! Please click here to check 1.6.0 API changes. Highlights of 1.6.0 release include: - NF: Unbiased groupwise linear bundle registration added. - NF: MAP+ constraints added. - Generalized PCA to less than 3 spatial dims. - Added positivity constraints to QTI. - New functionality to apply Symmetric Diffeomorphic Registration to points/streamlines. - New Human Connectome Project (HCP) data fetcher added. - New Healthy Brain Network (HBN) data fetcher added. - Multiple Workflows updated (DTIFlow, LPCAFlow, MPPCA) and added (RUMBAFlow). - Ability to handle VTP files. - Large codebase cleaning. - Large documentation update. - Closed 75 issues and merged 41 pull requests. To upgrade or install DIPY Run the following command in your terminal: pip install --upgrade dipy or conda install -c conda-forge dipy This version of DIPY depends on nibabel (3.0.0+). For visualization you need FURY (0.8.0+). Please support us by citing DIPY in your papers using the following DOI: 10.3389/fninf.2014.00008 Questions or suggestions? For any questions go to https://dipy.org, or send an e-mail to dipy at python.org We also have an instant messaging service and chat room available at https://gitter.im/dipy/dipy Finally, a new forum is available at https://github.com/dipy/dipy/discussions Have a wonderful time using the new version. On behalf of the DIPY developers, Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro https://dipy.org/contributors -------------- next part -------------- An HTML attachment was scrubbed... URL: