From elef at indiana.edu Fri Jun 2 16:32:39 2023 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Fri, 2 Jun 2023 16:32:39 -0400 Subject: [Neuroimaging] Are you attending ISMRM this week June 3rd to June 8th? Message-ID: Hello imagers!, I am attending ISMRM with some of the DIPY folks this year. If you are in Toronto this week and want to learn more about DIPY or Python in medical imaging send us an email to meet. In addition, if any of the core devs of nibabel, nilearn, nipype, heudiconv or other py-imaging projects are in Toronto let me know. I would love to catch up. Kindest 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 matthew.brett at gmail.com Mon Jun 5 06:54:06 2023 From: matthew.brett at gmail.com (Matthew Brett) Date: Mon, 5 Jun 2023 11:54:06 +0100 Subject: [Neuroimaging] Practice and theory of brain imaging course: July 31 - September 22 2023 Message-ID: Dear all, This is just to let you know that we are now accepting requests to join our second full version of the Neuroimaging Practice and Theory Course, running over 8 weeks, from the week beginning 31 July through the week ending 22nd September, 2023 The course teaches reproducible brain imaging analysis, and is for anyone with sound basic knowledge of Python and the Numpy array library. The course is free in terms of money, but we ask for a substantial commitment in terms of your time : https://nipraxis.org/summer-2023/#how-much-time-will-it-take See https://nipraxis.org for more on the course in general, and https://nipraxis.org/summer-2023 for more on this iteration. To apply, please read the introduction in https://nipraxis.org/summer-2023/ and then fill out this form: https://forms.gle/fz2E6q6HvqnyCmSp9 Cheers, Matthew (for the Nipraxis team) From pestilli at utexas.edu Mon Jun 12 15:30:07 2023 From: pestilli at utexas.edu (Franco Pestilli) Date: Mon, 12 Jun 2023 15:30:07 -0400 Subject: [Neuroimaging] 2023 Big Data Neuroscience Ohio State University Message-ID: Dear Friends and Colleagues, *We would appreciate spreding the word about the event below.* The ACNN 2023 workshop registration is open! *Fill out registration form here* The *Advanced Computational Neuroscience Network (ACNN) Big Data Workshop for 2023 will be taking place September 14 and 15* at the Ohio State University. This conference will feature national and international experts in neuroimaging, biomedical research, neuroscience, and data science, with a focus on highly dense behavioral and physiological data integration. The speakers will address challenges and successes in the integration of multimodal, multidimensional, multiscale data, regarding data standards, representation, and sharing. A workshop on the second day will focus on reproducible methods in neuroimaging. Students and trainees are encouraged to register and present a poster in the datablitz and poster sessions, and to interact with the speakers! Posters and presentations on neuroimaging, deep phenotyping analyses, heterogenous dataset analyses with relevance to human neuroscience, and neuroinformatics, for example, are all welcome. The schedule of speakers and topics is in the attached flier, and on our website!! *To be eligible for partial travel awards or to present your research (as poster and/or lightning talk), please submit an abstract by July 14, 2023 *(as part of registration). *Fill out registration form here* Detailed information can also be found here: https://neurosciencenetwork.org/ACNN_Workshop_2023.html On behalf of the ACNN 2023 organizing committee, Lei Wang, The Ohio State University Jessica Turner, The Ohio State University Ruchika Prakash, The Ohio State University Xia Ning, The Ohio State University Dhabaleswar Panda, The Ohio State University Chelsea Kane, The Ohio State University Tim Lucas, The Ohio State University Satya Sahoo, Case Western Reserve University Franco Pestilli, University of Texas at Austin Ivo Dinov, University of Michigan at Ann Arbor *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 | Founder and Director brainlife.io Co-Chair Data Working Group internationalbraininitiative.org Director Wellcome-Kavli International Governance for Neurodata Director Brain Imaging Data Structure (BIDS) Connectivity Project Program Committee Association for Psychological Science (outgoing) 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 elodie.savary at outlook.com Wed Jun 14 05:24:38 2023 From: elodie.savary at outlook.com (Elodie Savary) Date: Wed, 14 Jun 2023 09:24:38 +0000 Subject: [Neuroimaging] Register for the NiPreps hackathon with the OHBM'23 Brainhack! Message-ID: Hello Everyone, We are thrilled to invite you to the NiPreps Hackathon's second edition at OHBM'23 Brainhack in Montreal, Canada (July 19-21) - Find all the details here: https://github.com/orgs/nipreps/discussions/39! [https://opengraph.githubassets.com/91f53b1fef108b733635a15fc2d3a725327e54bba6717ba967b8115a2010dd39/orgs/nipreps/discussions/39] Register for the NiPreps hackathon with the OHBM'23 Brainhack! ? nipreps ? Discussion #39 We are thrilled to announce that the NiPreps Hackathon's second edition will be part of the upcoming OHBM'23 Brainhack (July 19-21, Maison Notman House, Montreal, Canada). Registration To join us f... github.com See you in Montreal! -------------- next part -------------- An HTML attachment was scrubbed... URL: From info at incf.org Thu Jun 15 06:15:03 2023 From: info at incf.org (INCF) Date: Thu, 15 Jun 2023 12:15:03 +0200 Subject: [Neuroimaging] Please share: Call for investigator-led session abstracts! Message-ID: Hello! INCF is looking for applications to investigator-led sessions at INCF Assembly 2023! Please forward this email or share the following posts with your community through your social media channels, newsletters, or other communication streams: *1. Retweet this post! * *2. Share this post on Twitter!* *?Call to present at INCF Neuroinformatics Assembly 2023!?* *Want to speak in investigator-led talks on FAIR neuroscience? INCF is calling for abstracts! ?* *? Abstract deadline: Jun 23Submit y* *our abstract today: bit.ly/INCFAssembly2023ILPA * *#FAIR #neuroscience #OpenScience* *3. Share this post on your social media channel of choice!* *?Call to present at INCF Neuroinformatics Assembly 2023!?* *Want to speak in investigator-led talks on FAIR neuroscience? INCF is calling for abstracts!* *INCF's annual Assembly is a unique venue where neuroscience researchers, tool developers, standards developers, and infrastructure providers can meet with potential collaborators and hear about the latest advancements in neuroinformatics and FAIR neuroscience.* *Abstract deadline: Jun 23* *Submit your abstract today: bit.ly/INCFAssembly2023ILPA * Thanks for your help, and see you at Assembly! /The INCF Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From amir.saleh at uni-oldenburg.de Mon Jun 26 07:16:53 2023 From: amir.saleh at uni-oldenburg.de (Amirhussein Abdolalizadeh Saleh) Date: Mon, 26 Jun 2023 11:16:53 +0000 Subject: [Neuroimaging] [fmriprep] Weird SDC Message-ID: <0fc6914551f747c58b458bb426f4ab73@uni-oldenburg.de> Hi all, I am using fmriprep 23.0.2 for resting-state fMRI analysis. I tried it on two subjects and whatever the option I use, I get a really weird susceptibility distortion correction (see attached). For example: * In "local_withFieldmap_AP.svg" data was acquired using a multi-band sequence (PE-dir = AP) with fieldmap (phase and magnitude) data available. * In "online_fieldmapless_LR.svg" data is from a single-band sequence (PE-dir = LR) with fieldmap-less method. * In "local_fieldmapless_AP.svg" data is from a multi-band sequence (PE-dir = AP) with fieldmap-less method. Interestingly, the last subject was analyzed without the issues above using the older versions of fmriprep (21.x). The analysis is being done on a high-performance cluster using Singularity fmriprep package. Looking forward to your comments. Best, Amir ------------------------------ AmirHussein Abdolalizadeh Saleh, MD Postdoc, Research Training Group 'Neuromodulation' Department of Psychology School of Medicine and Health Sciences Carl von Ossietzky University Oldenburg Ammerl?nder Heer Str. 114-118 - A07 0-053 26111 Oldenburg, Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: local_withFieldmap_AP.svg Type: image/svg+xml Size: 843851 bytes Desc: local_withFieldmap_AP.svg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: online_fieldmapless_LR.svg Type: image/svg+xml Size: 744039 bytes Desc: online_fieldmapless_LR.svg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: local_fieldmapless_AP.svg Type: image/svg+xml Size: 883220 bytes Desc: local_fieldmapless_AP.svg URL: From chenwang1 at link.cuhk.edu.cn Thu Jun 29 09:03:45 2023 From: chenwang1 at link.cuhk.edu.cn (Chen Wang (SDS, 120090637)) Date: Thu, 29 Jun 2023 13:03:45 +0000 Subject: [Neuroimaging] Reconstruction issues using MAP-MRI model Message-ID: Dear Developers, We are a medical lab from Shenzhen Research Institute of Big Data, China. We are doing an urgent and important research about Intermittent Exotropia, which is a common progressive disease in children. We need to reconstruct the brain parameters using MAP-MRI model from dipy. However, we met a problem with the reconstruction of the whole brain. We have searched our problem in the forum on github but there isn't any valuable solution. Therefore, we are writing this email to ask for help. The details are shown below. When we run the example code reconst_mapmri.ipynb (https://dipy.org/documentation/1.7.0/examples_built/07_reconstruction/reconst_mapmri/#sphx-glr-examples-built-07-reconstruction-reconst-mapmri-py), it is good when we use the image fragment data_small [40:65, 50:51]. However, when we run the code on the whole brain, the images of RTOP, RTAP, and RTPP parameters will be wrong, which contain no signals. We have also tried the preprocessing step to add a mask by Brain segmentation with median_otsu.ipynb (https://dipy.org/documentation/1.7.0/examples_built/04_preprocessing/brain_extraction_dwi/), but it does not work. The correct and wrong outputs are shown below. Wrong output: [cid:f70f8de6-953a-4336-ae46-c7a16ce692fe] Correct output: [cid:72682e07-4f6c-4d32-a688-f6b484447e53] We'd highly appreciated it if you could help us solve this problem. Thanks a lot! Looking forward to your reply! Best wishes, Chen Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 45970 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 36902 bytes Desc: image.png URL: From jevillalonr at gmail.com Fri Jun 30 19:45:49 2023 From: jevillalonr at gmail.com (=?UTF-8?Q?Julio_Villal=C3=B3n?=) Date: Fri, 30 Jun 2023 16:45:49 -0700 Subject: [Neuroimaging] Reconstruction issues using MAP-MRI model In-Reply-To: References: Message-ID: Hi Chen, >From the MSD map that you are showing it looks like the fitting of MAP-MRI ran successfully. The order of magnitude of RTOP, RTAP and RTPP is very small: 10e-7 to 10e-9. Maybe if you try adjusting the display range of values (the "window") you'll see maps similar to the ones in the lower row. Best, Julio Villal?n El vie, 30 jun 2023 a las 7:08, Chen Wang (SDS, 120090637) (< chenwang1 at link.cuhk.edu.cn>) escribi?: > Dear Developers, > > We are a medical lab from Shenzhen Research Institute of Big Data, China. We > are doing an urgent and important research about Intermittent Exotropia, > which is a common progressive disease in children. We need to reconstruct > the brain parameters using MAP-MRI model from dipy. However, we met a > problem with the reconstruction of the whole brain. We have searched our > problem in the forum on github but there isn't any valuable solution. > Therefore, we are writing this email to ask for help. The details are shown > below. > > When we run the example code reconst_mapmri.ipynb ( > https://dipy.org/documentation/1.7.0/examples_built/07_reconstruction/reconst_mapmri/#sphx-glr-examples-built-07-reconstruction-reconst-mapmri-py > ), it is good when we use the image fragment data_small [40:65, 50:51]. > However, when we run the code on the whole brain, the images of RTOP, RTAP, > and RTPP parameters will be wrong, which contain no signals. We have also > tried the preprocessing step to add a mask by Brain segmentation with > median_otsu > .ipynb > ( > https://dipy.org/documentation/1.7.0/examples_built/04_preprocessing/brain_extraction_dwi/ > ), but it does not work. The correct and wrong outputs are shown below. > > Wrong output: > > Correct output: > > We'd highly appreciated it if you could help us solve this problem. Thanks > a lot! Looking forward to your reply! > Best wishes, > Chen Wang > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 45970 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 36902 bytes Desc: not available URL: