From pestilli at utexas.edu Wed Feb 2 18:21:18 2022 From: pestilli at utexas.edu (Franco Pestilli) Date: Wed, 2 Feb 2022 17:21:18 -0600 Subject: [Neuroimaging] Postdoc Position In Austin Texas Message-ID: Dear Friends and colleagues We are looking for an enthusiastic you fellow to join us on a 2-year project funded by an NIH R01 by the BRAIN initiative. The project focuses on open science and data sharing standards. We are set to extend the Brain Imaging Data Structure (BIDS) to cover brain connectivity data. Here you can find a full description of the project. BIDS has become an exciting standard and the community is growing large: https://bids.neuroimaging.io/ A few papers relevant to the project are below: https://www.nature.com/articles/sdata201644 https://www.nature.com/articles/s41597-019-0104-8 https://www.nature.com/articles/sdata2018110 https://www.nature.com/articles/s41597-019-0105-7 https://www.biorxiv.org/content/10.1101/2021.06.16.448390v1 https://www.medrxiv.org/content/10.1101/2021.10.22.21265382v3 We would appreciate it if you could share this email with your trainees and younger colleagues. The project has a broad reach and could be a great base for developing further projects related to human neuroscience, neuroinformatics, computer science and machine learning depending on the interest of the applicant. Best regards, Project Leader Franco Pestilli co-Investigators Russ Poldrack, Stanford University, California, USA Ariel Rokem, University of Washington Seattle, Washington USA Theodore Satterthwaite, University of Pennsylvania, Pennsylvania, USA Other Personnel. Franklin Feingold, Stanford University, California, USA Eugene Duff, Imperial College, London, UK Cyril Pernet, Neurobiology Research Unit, Denmark Robert Smith, Florey Institute, Australia Oscar Esteban, Lausanne, Switzerland Matt Cieslak, University of Pennsylvania, Pennsylvania, USA *FRANCO PESTILLI*, *Ph.D.* | *Associate Professor* Department of Psychology | College of Liberal Arts | The University of Texas at Austin he/him | pestilli at utexas.edu | web | GitHub | brainlife.io CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Wed Feb 9 08:06:41 2022 From: matthew.brett at gmail.com (Matthew Brett) Date: Wed, 9 Feb 2022 13:06:41 +0000 Subject: [Neuroimaging] Next meeting on data formats - planning Message-ID: Hi all, I've put up a message about planning the next meeting on neuroimaging data formats - here: https://nipy.discourse.group/t/data-formats-review/ If you're interested - please do have a look, and consider joining the discussion. I do apologize, my Zoom skills failed me for the last meeting, and I didn't record it; I will be careful to do that, for the next meeting. Cheers, Matthew From avesani at fbk.eu Wed Feb 9 10:52:01 2022 From: avesani at fbk.eu (Paolo Avesani) Date: Wed, 9 Feb 2022 16:52:01 +0100 Subject: [Neuroimaging] Postdoctoral Fellowship in Machine Learning for Brain Connectivity in Clinical Neuroscience Message-ID: A postdoctoral fellowship in Machine Learning for Brain Connectivity in Clinical Neuroscience We are pleased to announce the opening of one Postdoctoral Fellowship at the Neuroinformatics Lab, an interdisciplinary initiative between the Center for Mind/Brain Sciences (CIMeC) of the University of Trento, and the Center for Digital Health of Fondazione Bruno Kessler. The position is part of the ?Neusurplan? project, an integrated approach to neurosurgery planning based on multimodal and longitudinal data. The goal is to pursue an integrated approach to pre-operative neurosurgical planning, combining structural and functional characterization of brain connectivity. The data driven strategy will take advantage of a unique dataset of intra-operative points of directed electrical stimulation and the related functional responses. In this project, the candidate will pursue research on machine learning methods for neuroimaging data analysis to study and characterize brain connectivity, with applications to longitudinal studies and clinical practice. The ideal candidate should have a mixed background in neuroimaging techniques and numerate disciplines, like computer science, engineering, physics, or mathematics. This project is in collaboration with the Division of Neurosurgery, S. Chiara Hospital, Trento (IT). The position is for a 2 year Postdoc Fellowship (May, 2022 - April, 2024). We welcome expressions of interest for this position, please contact Paolo Avesani (paolo.avesani at unitn.it) and/or Emanuele Olivetti (olivetti at fbk.eu) with your CV and a statement of intent. The University of Trento ranks among top Italian Universities ( https://www.unitn.it/en/ateneo/1636/rankings). Fondazione Bruno Kessler ranks first among the Italian research centers in Engineering and Computer Science ( https://magazine.fbk.eu/en/news/fbk-ranks-1st-in-italy-for-scientific-excellence-in-three-areas ). To also consider a work/life balance, there is more than our passion for translational research. You can check these pointers for a flavor of life quality in Trentino: https://www.visittrentino.info/en; https://www.discovertrento.it/en A few papers related to the project are below: Bert? G,et al., (2021) Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation, Neuroimage, 224 https://doi.org/10.1016/j.neuroimage.2020.117402 Sarubbo S, et al., (2020) Mapping critical cortical hubs and white matter pathways by direct electrical stimulation: an original functional atlas of the human brain, Neuroimage, 205 https://doi.org/10.1016/j.neuroimage.2019.116237 Astolfi P, et al., (2020) Tractogram filtering of anatomically non-plausible fibers with geometric deep learning, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) LNCS, vol 12267. Springer https://doi.org/10.1007/978-3-030-59728-3_29 Sarubbo S, et al., (2021) Planning brain tumor resection using a probabilistic atlas of cortical and subcortical structures critical for functional processing: a proof of concept, Operative Neurosurgery, 20(3), 175-183 https://doi.org/10.1093/ons/opaa396 -- -- Le informazioni contenute nella presente comunicazione sono di natura? privata e come tali sono da considerarsi riservate ed indirizzate? esclusivamente ai destinatari indicati e per le finalit? strettamente? legate al relativo contenuto. Se avete ricevuto questo messaggio per? errore, vi preghiamo di eliminarlo e di inviare una comunicazione? all?indirizzo e-mail del mittente. -- The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. If you received this in error, please contact the sender and delete the material. -------------- next part -------------- An HTML attachment was scrubbed... URL: From alex.crimi at yahoo.com Mon Feb 14 09:36:55 2022 From: alex.crimi at yahoo.com (Alex Crimi) Date: Mon, 14 Feb 2022 14:36:55 +0000 (UTC) Subject: [Neuroimaging] International Neuro Summer School 2022 Lipari (Italy) References: <1421342632.1943734.1644849416370.ref@mail.yahoo.com> Message-ID: <1421342632.1943734.1644849416370@mail.yahoo.com> Dear Colleagues,?I would like to invite you to | | | | | | | ? | | | | | | | A first edition of the Neuro Summer School dedicated to bridging global neuroscience world?International Neuro Imaging Summer School 4th-9th July 2022? | | | ? | | | | ? | | | It?s time to put our brains together! After the pandemic of the last 2 years, we want to restart connecting people working on neuro-imaging, neuro-oncology, and neuroscience. N3S2 is calling! 4th-9th July 2022, the Lipari Island, the best opportunity to meet world-class scientists and discover?neuro-imaging, neuro-oncology, neuro-science. Meet great brains and participate in fruitful discussions, share the scientific passion in the idyllic background of the Aeolian Islands. Join N3S2 Summer School. The event will be held at the Aktea hotel of Lipari (ME) in Italy. | | | ? | | Apply now | | ? | | | | ? | | | Meet our speakers! | | | ? | | | | ? | | | | ? | | | The N3S2 idea and what to expect? | | | ? | | | - Theoretical lectures by well-known experts - Practical workshops - Networking (event around the Stromboli Volcano) - Poster session - Culinary experience guaranteed by the Mediterranean flavors - ? even dolphins? watching is possible! Sounds like a perfect beginning of summer? Si! Absolutely yes! Join us!!! | | | ? | | Apply | | ? | | | | | | | | | | | | | | | | | | | | | | ? | | ? | | | | | Sano ? Centre for Computational Personalised Medicine - International Research Foundation sano.science?|?info at sano.science Czarnowiejska 36 building C5 30-054 Krak?w, Poland | | | ? | | | | ? | | | This project has received funding from the European Union?s Horizon 2020 research and innovation programme under grant agreement No 857533 and from the International Research Agendas Programme of the Foundatin for Polish Science No MAB PLUS/2019/13. | | | ? | | | | ? | | | | | | | -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1644849171350blob.jpg Type: image/png Size: 275331 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1644849269647blob.jpg Type: image/png Size: 811969 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: 1644849358873blob.jpg Type: image/png Size: 61054 bytes Desc: not available URL: From markiewicz at stanford.edu Fri Feb 18 13:20:05 2022 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Fri, 18 Feb 2022 18:20:05 +0000 Subject: [Neuroimaging] [Nibabel] Intent to deprecate int64 NIfTI images Message-ID: Hi all, I want to bring everyone's attention to this issue:?https://github.com/nipy/nibabel/issues/1089 I will reproduce the reasoning here, but the issue includes the specific changes to the API and accompanying warnings: > 64 bit integer images are easy to generate in nibabel due to numpy semantics, but almost universally incompatible with non-Python tools. We must balance breaking existing Python scripts, the Python library ecosystem, and the wider neuroimaging ecosystem that uses NIfTI as an interchange format. Recognizing that we are currently contributing to breakage in the wider ecosystem, we have decided to deprecate 64-bit integer image creation except via explicit override. There will be a series of PRs, probably in the first half of March to implement these changes. A couple have already started. Please let us know what we can do to help make the transition as smooth as possible for any downstream libraries and ultimately, users. Happy to discuss the decision further, but please also see the discussion that led to this decision: https://github.com/nipy/nibabel/issues/1046 Best, --? Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University From jbpoline at gmail.com Fri Feb 18 14:30:17 2022 From: jbpoline at gmail.com (JB Poline) Date: Fri, 18 Feb 2022 14:30:17 -0500 Subject: [Neuroimaging] [Nibabel] Intent to deprecate int64 NIfTI images In-Reply-To: References: Message-ID: Hi Chris, Do we have a sense of how much is broken in the wider community ? SPM is matlab based but doesn't have this issue ? Cheers JB On Fri, Feb 18, 2022 at 1:20 PM Christopher Markiewicz < markiewicz at stanford.edu> wrote: > Hi all, > > I want to bring everyone's attention to this issue: > https://github.com/nipy/nibabel/issues/1089 > > I will reproduce the reasoning here, but the issue includes the specific > changes to the API and accompanying warnings: > > > 64 bit integer images are easy to generate in nibabel due to numpy > semantics, but almost universally incompatible with non-Python tools. We > must balance breaking existing Python scripts, the Python library > ecosystem, and the wider neuroimaging ecosystem that uses NIfTI as an > interchange format. Recognizing that we are currently contributing to > breakage in the wider ecosystem, we have decided to deprecate 64-bit > integer image creation except via explicit override. > > There will be a series of PRs, probably in the first half of March to > implement these changes. A couple have already started. > > Please let us know what we can do to help make the transition as smooth as > possible for any downstream libraries and ultimately, users. > > Happy to discuss the decision further, but please also see the discussion > that led to this decision: https://github.com/nipy/nibabel/issues/1046 > > Best, > -- > Christopher J. Markiewicz, PhD > Center for Reproducible Neuroscience > Stanford University > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From markiewicz at stanford.edu Fri Feb 18 15:42:47 2022 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Fri, 18 Feb 2022 20:42:47 +0000 Subject: [Neuroimaging] [Nibabel] Intent to deprecate int64 NIfTI images In-Reply-To: References: Message-ID: Hi JB, I believe SPM also doesn't read or write INT64 images. Python (and at base nibabel) seems to be unique as a producer of these files. Best, Chris ________________________________ From: Neuroimaging on behalf of JB Poline Sent: Friday, February 18, 2022 14:30 To: Neuroimaging analysis in Python Subject: Re: [Neuroimaging] [Nibabel] Intent to deprecate int64 NIfTI images Hi Chris, Do we have a sense of how much is broken in the wider community ? SPM is matlab based but doesn't have this issue ? Cheers JB On Fri, Feb 18, 2022 at 1:20 PM Christopher Markiewicz > wrote: Hi all, I want to bring everyone's attention to this issue: https://github.com/nipy/nibabel/issues/1089 I will reproduce the reasoning here, but the issue includes the specific changes to the API and accompanying warnings: > 64 bit integer images are easy to generate in nibabel due to numpy semantics, but almost universally incompatible with non-Python tools. We must balance breaking existing Python scripts, the Python library ecosystem, and the wider neuroimaging ecosystem that uses NIfTI as an interchange format. Recognizing that we are currently contributing to breakage in the wider ecosystem, we have decided to deprecate 64-bit integer image creation except via explicit override. There will be a series of PRs, probably in the first half of March to implement these changes. A couple have already started. Please let us know what we can do to help make the transition as smooth as possible for any downstream libraries and ultimately, users. Happy to discuss the decision further, but please also see the discussion that led to this decision: https://github.com/nipy/nibabel/issues/1046 Best, -- Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbpoline at gmail.com Fri Feb 18 15:44:19 2022 From: jbpoline at gmail.com (JB Poline) Date: Fri, 18 Feb 2022 15:44:19 -0500 Subject: [Neuroimaging] [Nibabel] Intent to deprecate int64 NIfTI images In-Reply-To: References: Message-ID: I see - thanks ! JB On Fri, Feb 18, 2022 at 3:42 PM Christopher Markiewicz < markiewicz at stanford.edu> wrote: > Hi JB, > > I believe SPM also doesn't read or write INT64 images. Python (and at base > nibabel) seems to be unique as a producer of these files. > > Best, > Chris > ------------------------------ > *From:* Neuroimaging stanford.edu at python.org> on behalf of JB Poline > *Sent:* Friday, February 18, 2022 14:30 > *To:* Neuroimaging analysis in Python > *Subject:* Re: [Neuroimaging] [Nibabel] Intent to deprecate int64 NIfTI > images > > Hi Chris, > > Do we have a sense of how much is broken in the wider community ? SPM is > matlab based but doesn't have this issue ? > > Cheers > JB > > > > > On Fri, Feb 18, 2022 at 1:20 PM Christopher Markiewicz < > markiewicz at stanford.edu> wrote: > > Hi all, > > I want to bring everyone's attention to this issue: > https://github.com/nipy/nibabel/issues/1089 > > I will reproduce the reasoning here, but the issue includes the specific > changes to the API and accompanying warnings: > > > 64 bit integer images are easy to generate in nibabel due to numpy > semantics, but almost universally incompatible with non-Python tools. We > must balance breaking existing Python scripts, the Python library > ecosystem, and the wider neuroimaging ecosystem that uses NIfTI as an > interchange format. Recognizing that we are currently contributing to > breakage in the wider ecosystem, we have decided to deprecate 64-bit > integer image creation except via explicit override. > > There will be a series of PRs, probably in the first half of March to > implement these changes. A couple have already started. > > Please let us know what we can do to help make the transition as smooth as > possible for any downstream libraries and ultimately, users. > > Happy to discuss the decision further, but please also see the discussion > that led to this decision: https://github.com/nipy/nibabel/issues/1046 > > Best, > -- > Christopher J. Markiewicz, PhD > Center for Reproducible Neuroscience > Stanford University > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alex.crimi at yahoo.com Fri Feb 18 16:32:50 2022 From: alex.crimi at yahoo.com (Alex Crimi) Date: Fri, 18 Feb 2022 21:32:50 +0000 (UTC) Subject: [Neuroimaging] Post-doc positions at BAMlab In-Reply-To: References: Message-ID: <1626630163.386942.1645219970911@mail.yahoo.com> Dear all,? Sorry for cross-posting. We are looking for post-docs working in a brand new vibrant lab focused on neuroimaging? https://bam.sano.science/? More specifically, we are looking for talented ?graduated PHD (or close to graduation) working on functional and structural connectivity from MRI,EEG and fNIRS in daily use, as investigating changes in daily use allows to see neurological, psychiatric effects in a broader sense.? Apply even if the date on call is in the past, the positions will be filled when suitable candidates are found:https://sano.science/job-offers/eeg-fnirs-brain-analysis-in-real-world/? Required background and skills of the candidate:? - recent or pending PhD in relevant field of science (computer science/biomedical engineering or related fields);? - at least one first-author research publication in a peer-reviewed scientific journal, top conference or currently in press (e.g. Neuroimage, Nature Methods, Nature Communications, Nature Scientific Reports, PloS, IEEE TMI, ?);? - Python programming, medical imaging experience (preferably in 3D or 4D), statistics;? - knowledge of time series signal as fMRI, EEG or fNIRS;? - excellent written and oral English communication skills;? - additional assets: knowledge of brain anatomy and related tools (Dipy, FSL, etc), experince in circuit design or electronics DIY (Arduino, RaspberryPi, Jetson, etc).? ? We offer a fixed term contract for 40 hours per week for the duration of 2 years. This will be supported by an educational plan that includes attendance of courses and (international) meetings. The contract will include opportunities to participate in teaching and supervision of undergraduate and master students.? The salary, depending on relevant experience before the beginning of the employment contract, will be up to 12.000-14.000 PLN (2.6-3.1k EUR) gross per month, based on a full-time contract (40 hours a week) for the duration of 2 years with private medical care and a sports card.? Sano offers excellent opportunities for study and development, an access to many international conferences on computational medicine and a possibility to grow in a scientific society.? For scientific inquiries contacta.crimi at sanoscience.org? For organizational inquiries contacte.sokalska at sanoscience.org? ? -----------------------------------------------------------------------------------------I send emails at unusual times, I don't expect immediate response----------------------------------------------------------------------------------------- Dr. Alessandro Crimi Research Group Leader https://bam.sano.science ? ? Centre for Computational Medicine Czarnowiejska 36, building C5. 30-072 Krak?w, Poland? Phone: +48 575 455 016 www.sano.science ----------------------------------------------- Visiting Lecturer African Institute for Mathematical Sciences www.aims.edu.gh --------------------------------------------------------- https://twitter.com/Dr_Alex_Crimi -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Outlook-i4ajhvir.png Type: image/png Size: 12229 bytes Desc: not available URL: From matthew.brett at gmail.com Fri Feb 25 11:09:30 2022 From: matthew.brett at gmail.com (Matthew Brett) Date: Fri, 25 Feb 2022 16:09:30 +0000 Subject: [Neuroimaging] Next meeting on data formats - planning In-Reply-To: References: Message-ID: Hi, On Wed, Feb 9, 2022 at 1:06 PM Matthew Brett wrote: > > Hi all, > > I've put up a message about planning the next meeting on neuroimaging > data formats - here: > > https://nipy.discourse.group/t/data-formats-review/ > > If you're interested - please do have a look, and consider joining the > discussion. Just to say - and just in case you didn't join the Discourse forum - here is a WhenIsGood link for choosing a meeting time: https://whenisgood.net/k8i3z52 Please do forward to anyone who might be interested. Cheers, Matthew From garyfallidis at gmail.com Fri Feb 25 17:24:04 2022 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Fri, 25 Feb 2022 17:24:04 -0500 Subject: [Neuroimaging] DIPY Workshop 2022 - Online Edition Message-ID: Dear Neuroimaging Community, The Online DIPY Workshop is back with a great lineup of topics and speakers! Please forward this email to any interested parties. [image: image.png] For registration and more information please visit https://dipy.org/workshops/latest On behalf of the DIPY team, Eleftherios Garyfallidis, PhD Assistant 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 144580 bytes Desc: not available URL: From chuanjigao at gmail.com Mon Feb 28 11:36:19 2022 From: chuanjigao at gmail.com (Chuanji Gao) Date: Mon, 28 Feb 2022 17:36:19 +0100 Subject: [Neuroimaging] Python stuck when loading an overlay Message-ID: Hi, I'm running PySurfer using Spyder on my Mac Big Sur. Though I had no issue of loading one image, my Spyder would be not responding everytime I'm loading an overlay (see attached). Can someone give me some advice? Here is the code I used: import os from surfer import Brain subject_id = "fsaverage" hemi = "lh" surf = "inflated" print(subject_id) os.environ["SUBJECTS_DIR"] = "/Applications/freesurfer/7.1.1/subjects" brain = Brain(subject_id, hemi, surf, background="white") overlay_file = "/Volumes/T7/example/spmT_0008.nii" brain.add_overlay(overlay_file) Best, Chuanji -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pysurfer_issue.png Type: image/png Size: 780431 bytes Desc: not available URL: From arokem at uw.edu Mon Feb 28 13:45:24 2022 From: arokem at uw.edu (Ariel Rokem) Date: Mon, 28 Feb 2022 10:45:24 -0800 Subject: [Neuroimaging] Postdoctoral position: neuroinformatics and neuroscience of aging Message-ID: The Neuroinformatics Research & Development Group at the University of Washington Department of Psychology and eScience Institute conducts research on the biological basis of brain function using computational tools that we develop and maintain. We are seeking to fill an open position for a postdoctoral researcher. The successful candidate will have the opportunity to work together with a wide network of collaborators on data from the Adult Changes in Thought Study . The position is funded through a new 5-year NIH grant . The researcher will have an opportunity to ask a range of questions and study unique datasets of multi-modal imaging data that include longitudinal measurements of functional MRI, diffusion MRI, ante- and post-mortem measurements of structural MRI, as well as histological measurements conducted in the same individuals. These measurements are done in the context of a wealth of measurements of cognition, health, lifestyle, and environment. The position provides an opportunity to develop novel analysis pipelines and statistical methods to process, merge, and interpret these datasets in light of scientific questions about the brain basis of cognitive aging, with a particular focus on Alzheimer?s disease. *Required qualifications:*- PhD in Psychology, Neuroscience, or related fields. - Strong programming skills (preferably in the Python programming language) - (Experience analyzing large, complex, and heterogeneous datasets is preferred) Interested applicants should send a cover letter detailing their research interests, CV and the names of three references to arokem at uw.edu or apply through: https://apply.interfolio.com/94186 -------------- next part -------------- An HTML attachment was scrubbed... URL: