brainhackorg / brainhack_cloud Goto Github PK

Title

Ressource request MLOPsZoomCamp

Is this a new project?

yes

People involved

@likeajumprope

Project Description

Both for the purpose of checking out the platform and because I am participating in the MlOpsZoomCamp, (https://github.com/DataTalksClub/mlops-zoomcamp) I'd like to request some ressources (see below). Also trying to figure out whether this might be a good way to teach people the usage of the cloud

Link to project repository/sources

https://github.com/likeajumprope/mlops-zoomcamp

What resources do you require?

Virtual Machines, Object Storage

Anything else?

I guess I COULD just create this project myself as admin, but thought I'd better go the traditional way..

Title

watts_up_compute

Is this a new project?

no

People involved

Nikhil Bhagwat, nikhil153, [email protected]
Johanna Bayer, likeajumprope, https://www.linkedin.com/in/johanna-bayer
Sebastian Urchs, surchs, [email protected]

Project Description

Integration of compute-tracker tools into neuroimaging pipelines to estimate carbon footprint of image processing

This is an ongoing project by the Sustainability and Environmental Action group (SEA-SIG) at the Organisation for Human Brain Mapping (OHBM). In this project we aim at better understanding the environmental costs of commonly used research pipelines and develop tools to help reduce them.

Recently there have been several projects that track cpu/gpu "power draws" incurred during a compute task. These statistics can then be translated into carbon-footprint based on your location and time of processing.

Link to project repository/sources

https://github.com/nikhil153/fmriprep/blob/carbon-trackers/singularity/carbon_trackers_readme.md

What resources do you require?

HPC

Anything else?

No response

Title

Benchmark denoising strategies on fMRIPrep output

Is this a new project?

yes

People involved and contact details (including email address!)

Hao-Ting Wang @htwangtw [email protected]

Project Description

The project is a continuation of load_confounds. The aim is to evaluate the impact of denoising strategy on functional connectivity data, using output processed by fMRIPrep LTS.

The main tool is now a part of nilearn.

Link to project repository/sources

https://github.com/SIMEXP/fmriprep-denoise-benchmark

What resources do you require?

HPC

Anything else?

No response

Title

tunel: apps for high performance computing

Is this a new project?

no

People involved and contact details (including email address!)

@vsoch (email provided to sbollmann_MRI on Twitter

Project Description

• What are you doing, for whom, and why?
  Tunel is a "bring your own apps" framework for HPC. It makes it easy to launch (typically locally developed and constrained) applications via unix sockets, either to a cluster node or jobs nodes via this method. I am seeking minimal access to resources (likely an infrequent access to a login node + single job node) to continue the development of the slurm launcher. I no longer have access to a SLURM cluster and have been testing with the open science grid (htcondor without node access).

Link to project repository/sources

• Main GitHub Organization: https://github.com/tunel-apps
• Tunel Software: https://github.com/tunel-apps/tunel
• Documentation: https://tunel-apps.github.io/tunel/
• Apps: https://tunel-apps.github.io/tunel/_static/apps/

What resources do you require?

HPC

Anything else?

I only require access to a login node and a worker node, not even anything substantially impressive in terms of memory or compute!

The Oracle team would like to know which resources we need for the brainhack in which geo-regions (GPUs need to be requested in advance so they are available in the right data centres)

• How can we get an estimate on this?
• We need to request the resources in the region where it's available: https://www.oracle.com/cloud/data-regions/#northamerica
• We need to subscribe to the regions where users need resources

HPC Module Maintenance / Update

This is a test during the maintenance/update of the HPC module. This module currently reflects computeCA exclusively and will be supplemented by information about the Brainhack Cloud. In order to document the procedure properly I need to apply the process a student would have to run and access to the Brainhack Cloud to test what parameters need changing, if any. Maybe you Brainhack Cloud admins can pitch in? In the best case the only thing that's different is the ssh connection?

Is this a new project?

yes

People involved and contact details (including email address!)

Thomas S. Hartmann
[email protected]
@thecyclingcyclopse on GH

Project Description

• What are you doing, for whom, and why?
  Updating Brainhack HPC module for Brainhack School 2023 because it's fun!

Link to project repository/sources

school-brainhack/school-brainhack.github.io#167 (comment)

What resources do you require?

HPC

Anything else?

Actually I don't really require HPC, nor will the students require extensive compute power, but for the exercise it would be nice to have them access a cluster as intended by the exercise's creator.

edit:
minor typo

Hi all.

In the Policies doc under the Admins subpage of the Brainhack Cloud website, we have a mention of Policy for Cloud Shell Acess that gives rights to the user to access the Cloud shell. However such group is missing from the lists under Identity> Groups.

I understand from the Oracle's Cloud Shell documents that we do not need to create a specific group but when we create the group it is enough to give them the cloud shell access rights with

allow group <GROUP-NAME> to use cloud-shell in tenancy

is just enough.

I wonder if this is the recommended way of doing for us too? If so I will append the document and delete the group indication instead will indicate to type that line of rule for the shell access policy.

Title

Finding a way to plot weight maps from the outputs of non-linear decoder

Is this a new project?

yes

People involved

Shima Rastegarni

Project Description

• What are you doing, for whom, and why?

Link to project repository/sources

https://github.com/user_name/my_awesome_project

What resources do you require?

GPU resources

Anything else?

No response

Title

This project aims at testing things

Is this a new project?

yes

People involved

Steffen Bollmann, @stebo85, [email protected]

Project Description

• What are you doing, for whom, and why?
  Testing to apply for a project and provision resources

Link to project repository/sources

https://github.com/stebo85

What resources do you require?

Virtual Machines, Object Storage, other

Anything else?

no

The Oracle logo on the github Readme.md is made for dark mode and almost not visible in light mode.
Potential solutions:

1. Logo that is visible in both dark and light mode
2. Conditional logo (as that possible?)

Title

Easily accessible seed to voxel correlation and machine learning program in Python with high performance computer (HPC) and Docker.

Is this a new project?

yes

People involved

Claudéric DeRoy (Github user : neurok8050)

Project Description

• What are you doing, for whom, and why?
  I want to do the exercise from the HPC module. I also want to use the resource for my project.

Link to project repository/sources

https://github.com/brainhack-school2022/deroy_project

What resources do you require?

HPC

Anything else?

No response

The Oracle team would like to provide help by a cloud architect for the brainhack event and they asked if that person should be on-site in glasgow, virtual or both and how many support people we could need?

• when can we get an estimate on which projects we have and what these projects need?

Add bug or feature or design

• bug report

Current behavior

No response

Bug report information

No response

Expected behavior

No response

If the current behavior is a bug, please tell us about your environment

• all

Other information

No response

Title

NeuroCausal: an open source platform for the storage, sharing, synthesis and meta-analysis of neuropsychological data.

Is this a new project?

No response

People involved and contact details (including email address!)

Project leads
@vborghe Valentina Borghesani
@Sladja13 Sladjana Lukic
@pinheirochagas Pedro PINHEIRO-CHAGAS
@complexbrains Isil Bilgin

will send the emails separately.

Project Description

We are working with clinicians, neuroimagers, and software developers to develop an open source platform for the storage, sharing, synthesis and meta-analysis of human clinical data to the service of the clinical and cognitive neuroscience community so that the future of neuropsychology can be transdiagnostic, open, and FAIR.

Link to project repository/sources

https://github.com/neurocausal

What resources do you require?

HPC

Anything else?

We require access to a login & worker node and ~500 GB memory with internet access that will allow us to download/scrap papers using PubMed API and process/analyze the metadata

It might be nice to have a tutorial for folks on how to run NeuroDesk on the cloud

Title

Deep learning for fMRI

Is this a new project?

yes

People involved

[email protected]

Project Description

• What are you doing, for whom, and why?

Link to project repository/sources

https://github.com/user_name/my_awesome_project

What resources do you require?

GPU resources

Anything else?

No response

For certain devices the layout will not be optimal.

Title

Real-time shared data visualisation on the web with NiiVue

Is this a new project?

yes

People involved

• Taylor Hanayik @hanayik
• Chris Rorden @neurolabusc
• Chris Drake @cdrake

I'm not listing emails of collaborators without their consent, but I have linked to their public GitHub profiles.

Project Description

The primary aim of NiiVue is to translate the features of the widely used native desktop applications (MRIcroGL, Surfice) to their web-based equivalents. This will enable other researchers and developers to build cloud-based medical imaging tools with a powerful viewer that can operate on any device (desktop, tablet, mobile).

We are requesting resources to facilitate one of our goals: Real-time, shared visualisation in the browser. Specifically, a cloud VM will be used to host a WebSocket server that allows multiple NiiVue clients to share data with each other securely, and enable research collaboration and synchronisation in real-time across the globe.

Link to project repository/sources

https://github.com/niivue/niivue

What resources do you require?

Virtual Machines

Anything else?

No response

Title

A Uniform Environment for Cloud and HPC-based Neuroimaging Research Education for Novice Users

Is this a new project?

yes

People involved

John Absher, jrabsher, [email protected], [email protected]
Grigori Yourganov, grigori-yourganov, [email protected]
Taylor Hanayik, hanayik, [email protected]
Chris Rorden, neurolabusc, [email protected]

Project Description

Introduction
Neuroimaging research education for novice users typically requires a graphical user interface, because novice users lack familiarity with the command line. Meanwhile, the field of neuroimaging research increasingly utilizes cloud-based computing resources, data storage structures, and high performance computing environments. Along with these formidable technical challenges, there is increasing awareness of the need for reproducible data science, to assure that data, code, analysis and results are susceptible to peer review and scientific scrutiny. We believe that novice neuroimaging research students (from high school through professional levels of education) who utilize the same interface (e.g., NeuroDesk) in both a cloud-based learning/collaboration environment and an HPC production environment will be able to spend more time focusing on neuroscience/neuroimaging, and less time struggling with the technical complexities of these environments.
Background
For the past 5 years, the Structured Neuroimaging-Intensive Research Program (SNIRP) has introduced students to basic aspects of neuroimaging research. The program began with 2 undergraduate students and has grown to 21 students in the 2022 summer program. A seed grant has been obtained to study whether novice users benefit from a rudimentary graphical "front end" to neuroimaging tools such as MRIcroGL, FSL, SPM, Surfice, FSLeyes, and Matlab. By examining the user experience through the lens of "user-centered design" we hope to learn how to best enhance the learning experience for novice students. We begin this journey by observing students as they engage in tutorials designed to teach them neuroimaging research procedures, starting with FSL tutorials. Ultimately, we hope to engage the developers of open-source neuroimaging research tools (Freesurfer, SPM, AFNI, etc), related collaboration websites (e.g., github, NITRC), and data repositories (e.g., UK Biobank, ida.loni.usc.edu) in the curation of tutorials that novice users could easily access within a comprehensive cloud-based learning and collaboration environment housed on Oracle Cloud.
Methods

1. We propose to provide 21 SNIRP students and approximately 10 faculty advisors with access to NeuroDesk on Oracle Cloud.
2. NeuroDesk will be enhanced to include a simple graphical user interface for novice users to access tutorials.
3. This modified NeuroDesk (with GUI) will be cloned, and the clone will include monitoring capability that enables robust data collection to support user-centered design enhancements of the GUI. Only students who have signed an informed consent (for our approved seed grant project) will be subjected to data collection as they complete the tutorials.
4. The same NeuroDesk-GUI and NeuroDesk-GUI-for-research-subjects will be installed within transparent Singularity containers on the HPC Neuroimaging Research Core (HPCNIRC) environment located on the Palmetto Cluster at Clemson University. The transparent Singularity containers will allow students to access HPC resources and data on the HPCNIRC environment.
5. Students will gain critical "reproducibility" experience as they save and export their work on various tutorials from Oracle Cloud. Globus.org is utilized for large data transfers into and out of the Palmetto Cluster.
6. After demonstrating successful reproducibility using NeuroDesk on Oracle Cloud, and successful data transport into and out of the HPCNIRC, students will be able to save the products of their ongoing neuroimaging research using the same reproducible approaches they used for the tutorials.

Link to project repository/sources

This project relies on https://github.com/NeuroDesk
/
neurodesk.github.io

What resources do you require?

Virtual Machines, Object Storage, GPU resources, HPC, other

Anything else?

As a practicing neurologist, my expertise is primarily in neuroimaging and neuroscience, rather than HPC, coding/scripting, and these highly technical areas. In fact, a prime motivation for pursuing this project is my own experience, facing the challenges of learning these skills over the past 3+ decades.
Therefore, I humbly request the ability to add a few collaborators to this project, people who can do many of the things that are difficult or impossible for me to do, or that are too time consuming for my immediate colleagues to add to their considerable lists of priorities.

Thank you for considering this project request.

Sincerly,

John R. Absher, MD

Title

Github Actions runner for macapype package validation

Is this a new project?

yes

People involved

@davidmeunier79 @BastienCagna @oliviercoulon @kepkee

Project Description

Macapype is a python package for segmentation of non-human primate anatomical MRI images; It runs on github, with unittests and PEP8 check on PR; For pre-relsease / release, we would like to validate full pipeline runs with some example data. However, the github server are limited in memory size availble for Github Actions, and for some stedp of the validation (namely using FSL fnirt) requires up to 30 Gb of RAM. Hence my request to add brainhack_cloud ressources to run on release validation with github actions.

Link to project repository/sources

https://github.com/Macatools/macapype
https://macatools.github.io/macapype/

What resources do you require?

Virtual Machines

Anything else?

No response

Title

BrainHack School project to do some freesurfer analysis on 3D MRI structural images

Is this a new project?

yes

People involved and contact details (including email address!)

[email protected] (@Andjelaaaa)

Project Description

• What are you doing, for whom, and why?
  This project consists of running an automated script for freesurfer analysis on 3D brain data for the BrainHack School happening this summer 2022.

Link to project repository/sources

https://github.com/Andjelaaaa/dimitrijevic_project

What resources do you require?

Virtual Machines, Object Storage, GPU resources, HPC

Anything else?

If this could be approved quickly that would be great! Thanks in advance,

Andjela Dimitrijevic

Title

I'm working on the NARPS project at BrainHack. I'm on a M1 macbook and having a hard time downloading data and installing required packages so I'd very much appreciate access to the cloud.

Is this a new project?

No response

People involved

[email protected]
@Arshitha

Project Description

• What are you doing, for whom, and why?

Link to project repository/sources

https://github.com/Inria-Empenn/narps_open_pipelines

What resources do you require?

Virtual Machines, Object Storage, HPC

Anything else?

No response

Title

Participation in the ATLAS R2.0 - Anatomical Tracings of Lesions After Stroke Grand Challenge

Is this a new project?

No response

People involved

Sina Mansour L.
Niousha Dehestani

Project Description

We will be developing various machine learning models for stroke lesion segmentation which we started working on during the OHBM brainhack in this brainhack project.

We'd require remote Linux servers (preferably with GPUs) to train various ML models for the challenge.

Link to project repository/sources

We have not yet created a git repo, but will create one before completing the challenge and make it publicly available after the challenge here.

What resources do you require?

Virtual Machines, Object Storage, GPU resources

Anything else?

We would like to host a remote Linux server with ssh access. Here's a ballpark estimate of the required system specs:

• 16 CPU cores
• 128 GB memory
• 1TB storage
• GPU access for efficient training of deep learning models

We'll be able to configure the server to host a jupyter lab environment.

docker Oracle Linux 8

Title

Bayes on the brain in python

Is this a new project?

No response

People involved and contact details (including email address!)

Preethom Pal @Pregon [email protected]
Megan Campbell @meganEJcampbell [email protected]
Isabella Orlando @isabellaorlando [email protected]
Darin @dsleiter [email protected]
Adam @a-manoogian [email protected]
Kelly Garner @kel-github [email protected]

Project Description

• Running Bayesian mixture models on fmri data to test its viability as a computational approach

Link to project repository/sources

https://github.com/crnolan/pyrba

What resources do you require?

Virtual Machines, Object Storage, GPU resources, HPC

Anything else?

No response

Add bug or feature or design

• bug report
• feature request
• design request
• other

Current behavior

We can see on some figures where we need to click but it's unintuitive.
eg, https://brainhack.org/brainhack_cloud/admins/admins/#create-a-new-admin

Bug report information

No response

Expected behavior

Additional instruction mentioning the link and the steps.

If the current behavior is a bug, please tell us about your environment

• all
• Chrome XX
• Firefox XX
• Internet explorer XX
• Safari XX
• Mobile Chrome XX
• Android X.X Web Browser
• iOS XX Safari
• iOS XX UIWebView
• iOS XX WKWebView

Other information

No response

Title

Big Linear Mixed Models

Is this a new project?

This is the first time we have posted it here. But it is a few years old.

People involved

Thomas Maullin-Sapey @TomMaullin [email protected]
Thomas Nichols @nicholst [email protected]
Vicente Ferrer @vinferrer [email protected]

Project Description

Large-scale, shared datasets are becoming increasingly commonplace in fMRI, challenging existing tools both in terms of overall scale and complexity of the study designs. As sample sizes grow, new opportunities arise to detect and account for grouping factors and covariance structures present in large experimental designs. To facilitate large sample analysis, we have created two Python toolboxes for use on HPC clusters:

• “Big” Linear Models (BLM); a toolbox for large-scale distributed fMRI Linear Model analyses.
• “Big” Linear Mixed Models (BLMM); a toolbox for large-scale distributed fMRI Linear Mixed Model analyses.

At present, both tools are functioning and can be used for the analysis of tens of thousands of fMRI images. However, there is plenty that could be improved. Some current goals include:

1. Developing a rigorous testing suite, potentially with continuous integration via Travis CI.
2. Using Dask to streamline the current code base (at present there are a lot of bash scripts for 'qsub'bing).
3. Package releases. Neither of the toolboxes are currently on the Python Package Index.
4. Adding customized covariance support. In previous work, we showed how the underlying methods BLMM uses could model custom covariance structures (e.g. AR, Diagonal, Toeplitz etc). However, at present BLMM does not support analyses with these features.

Link to project repository/sources

https://github.com/TomMaullin/BLMM

What resources do you require?

HPC

Anything else?

I believe we shouldn't need a virtual machine but as I am still learning how to use github actions (which we plan to use for continuous integration testing), this may change in future.

I think it would be good to add the bookmarking link https://cloud.oracle.com/?region=eu-frankfurt-1&tenant=brainhack to the cloud the website so that people can re-sign in more easily via the cloud website.

Hi,

I'm actually wondering at this point if I am allowed to use the brainhack cloud or not for the data I plan to use.

The participant consent for the data I want to use goes as follows:

"Individual identifying information will be kept confidential and only authorized personnel will have access to it. However, the Research Ethics Board or Quality Assurance Officers duly authorized by it may access study data. Data will be coded (identifying information replaced by a code) and the code key will be kept in a separate secure location. The data from the study will be maintained in a secure database, and used for purposes of analysis and comparison with other data, and for scientific dissemination and publication in the Principal Investigator’s lab and collaborating labs."

What are your thoughts would there be any confidentiality breach in using the brainhack cloud?

Project plan:

For my dataset, I'm want to use data I collected at the MNI during my Master's (~5 GB in size). I have received the raw data on my computer already and there are about 50 children with autism who followed a music intervention with pre-post scans for 10 minutes of rsFMRI and a T1. There has already been a publication on it for auditory-motor networks: https://www.nature.com/articles/s41398-018-0287-3
So I would like to see if I can associate changes in resting-state functional connectivity with networks related to joint attention using the brain imaging data set. My plan would be to convert it to NIFTY and BIDS and then get it preprocessed by Beluga. I don't know exactly how many resources are necessary but I'm guessing 1 node is enough.

Thanks for any help!

Title

Hi, I'm co-hosting BrainHackHFX 2023 in Halifax, Nova Scotia and hoping to try out the BrainHack Cloud Computing resources. https://neural-data-science-hackathon.github.io/BrainHackHFX_global2023/

Is this a new project?

yes

People involved and contact details (including email address!)

Carl Helmick, affilliation="Dalhousie University, Psychiatry Dept", GitHubID="hfxcarl", email="[email protected]".

Project Description

I am co-hosting a smallish (30-50 people) brain hackathon in Halifax, NS. I'm looking for some cloud computing resources that will allow running simultaneous hacker code on relatively small datasets for the 3-day event.

Link to project repository/sources

https://neural-data-science-hackathon.github.io/BrainHackHFX_global2023/

What resources do you require?

Virtual Machines, Object Storage, GPU resources, HPC

Anything else?

Assuming there would be options for running Jupyter notebooks in either the HPC or VM?

Hi @stebo85 ,

I tried testing out the neurodesk to use the freesurfer tool via the link you supplied and there seems to be a license issue. Do I need to add another license file as indicated ? Here is the shown error message below
ERROR: FreeSurfer license file /usr/local/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. A path to an alternative license file can also be specified with the FS_LICENSE environmental variable.

Title

The project requires usage of a docker container to extract time stamps of subtitles of a show to be aligned with the fMRI data.

Is this a new project?

yes

People involved and contact details (including email address!)

Isil Bilgin

Project Description

• What are you doing, for whom, and why

Link to project repository/sources

https://github.com/user_name/my_awesome_project

What resources do you require?

Virtual Machines

Anything else?

No response

Title

Twin normative modelling

Is this a new project?

yes

People involved and contact details (including email address!)

@likeajumprope

Project Description

I'd need a notebook resource for the brainhack school 22 to do normative modelling on a twin data set

Link to project repository/sources

https://github.com/likeajumprope/normative_twins_project

What resources do you require?

Virtual Machines, HPC

Anything else?

No response

feels more appropriate for documentation, no?

• change licence in the root of the repo
• add licence mention in the footer rather than copy pasting it manually in all pages

Title

Identifying Neuropsychiatric Diagnoses using fMRI Connectivity Data.

Is this a new project?

yes

People involved and contact details (including email address!)

Peter Brotherwood ([email protected])

Project Description

• What are you doing, for whom, and why?
  Requesting access to HPC services for utilisation during my brainhack school project.

Link to project repository/sources

https://github.com/brainhack-school2022/brotherwood_project

What resources do you require?

HPC

Anything else?

No response