2024

Abstracts accepted at FLUX and FITNG 2024!

The MoCo project has two abstracts accepted at FLUX and FITNG 2024 in Baltimore in September. Research nurse Thurid Waagstein Madsen will travel to Baltimore and present our work.

Invited speaker at the ISMRM Workshop on Motion Correction in MR, September 2024

Additionally, I was invited as speaker to the ISMRM Workshop on Motion Correction in MR taking place in September in Quebec City. My contribution will center on "Image Quality Assessments for MRI".

Invited speaker at Gordon Research Conference (GRC) In Vivo Magnetic Resonance, July 2024

I was invited to speak at the GRC In Vivo Magnetic Resonance to participate in the session on "Big Questions in Imaging and AI" by discussion leader Prof. Julia Schnabel (Helmholtz Munich, Germany). I am excited to talk about "AI in MRI: What About Generalizability, Bias and Fairness?" and to discuss with Prof. Daniel Rueckert (TU Munich / Imperial College London, Germany) his views on "Trustworthy and Reliable AI for MRI" and with Prof. Daniel Alexander (University College London, United Kingdom) how to work on "Enabling and Enhancing Low-Cost MRI through Machine Learning".

New ISMRM and OHBM abstracts accepted!

1) With the MoCo project, we were involved in three ISMRM abstract submissions! We will present work on "Assessing Image Quality Metric Alignment with Radiological Evaluation in Datasets with and without Motion Artifacts", "Hybrid Motion Correction: Prospective Thresholding and Retrospective Residual Correction" and "Hybrid Motion Correction: Latency Compensation In The Presence Of Respiratory Motion". 

The tentative schedule will be posted on the ISMRM website at www.ismrm.org/24m/. 

2) In the OpenNeuroPET project we have also been productive and will be presenting several abstracts on work done within OpenNeuroPET! 

Specifically the abstract titled "Quantifying the impact of preprocessing strategies on statistical analyses" by Brice Ozenne, Martin Nørgaard, Cyril Pernet, Melanie Ganz will be a thrill to present in South Korea.

2023

BIDS news and call for participation

Following the awesome BIDS derivative meeting in June in Copenhagen, we have been active in restructuring the BIDS specification, specifically regarding the definitions of what an atlas is. If you are interested in contributing, please check out the atlas BEP: https://bids.neuroimaging.io/bep038 It a new BEP that is collecting community comments and feedback and all collaborators are welcome. So please chime in!

FLUX News! 

There is some news regarding the FLUX conference in September (https://fluxsociety.org/2023-santa-rosa/).

1) I will co-organize a symposium at FLUX titled "Emerging Methods for MRI in Infants and Young Children" together with Rhodri Cusack, Cameron Ellis, Brittany Howell and Aine Dineen.

2) Our abstract (ID #1555) with the title "Reducing the Need for General Anesthesia in Children Undergoing Neuroimaging by Preparation and Motion Correction" has been selected as a poster presentation at the 2023 Annual Meeting in Santa Rosa, California, USA.

Hope to see you in California to discuss children's imaging!

New abstracts accepted!

1) With the MoCo project, we were involved in an ISMRM abstract submission together with TracInnovations and Lars Hanson from DRCMR titled "Selective MRI reacquisition to extend the working range of retrospective motion correction" that will be presented as an oral presentation during the ISMRM:

Session: Motion Detection & Correction Techniques

Day/Date: Wednesday, 07 June 2023

Session Time: 15:45

The tentative schedule will be posted on the ISMRM website at www.ismrm.org/23m/. 

2) In the OpenNeuroPET project we have also been productive and Douglas N. Greve from the Martinos center has together with collaborators from NIMH and us submitted and abstract titled "A PET Molecular Imaging Brain Atlas of Cyclooxygenase-1" that also got accepted! 

I finally had time to finalize the first MoC project data release! The data is distributed on Openneuro: https://openneuro.org/datasets/ds004332/versions/1.0.0 and while there's a descirption there, there is also a preprint on PsyArxiV with lots of details: https://psyarxiv.com/vzh4g

The scripts to reproduce the results are on our MoCo GitHub: https://github.com/melanieganz/MoCoProject

There are still minor details missing, but check it out and reach out to me if you have any questions!

I am looking forward to an action-packed spring with many site visits for the NIBS-CP project as well as some events targeting BIDS derivatives! I'll try and keep posting what we are up to here. You cna also follow me on Mastodon: 

https://mastodon.online/@melanieganzben1

or Twitter (if it survives 2022):

https://twitter.com/melanieganzben1

Until then happy holidays and a good start in the new year to everyone!

2022

 The results of the BIDS steering group election are in! Check them out here. It turns out that Russ Poldrack and I will be replaced by my colleague Cyril Pernet, who works with me on OpenneuroPET, as well as Yaroslav Halchenko from Darthmouth College. Congratulations to the new steering group members!

 As part of the Bias and Fairness in medicine project, I was part of the organizing team of a small workshop on "Responsible Machine Learning in Healthcare" on October 27th and 28th. The aim with this invited workshop was to bring together a diverse and interdisciplinary group of internationally renowned scientists along with junior participants. We tried to discuss and exchange views about the progress towards medical machine learning systems that are trustworthy, equitable, and beneficial for society at large. Recordings of all talks are provided on a YouTube channel as well.

 On October 5th, I co-organized a workshop on Fairness of AI in Medical Imaging (FAIMI 2022). You cna chekc out the workshop webpage here: https://faimi-workshop.github.io/2022/#organizers Recordings of all talks are provided on a YouTube channel here.

I am delighted to announce that Eike Petersen will present our work titled "Feature robustness and sex differences in medical imaging: a case study in MRI-based Alzheimer's disease detection" (see https://arxiv.org/abs/2204.01737) at Miccai 2022 in Singapore. You can catch Eike and Aasa on site!

Finally, I will wrap up my summer travels with a visit to Paris, where I will participate in the first FITNG (Fetal, Infant, Toddler Neuroimaging Group) conference (https://fitng.org/2022-conference/) as panel speaker in the the session an data sharing. Check out the program here: https://fitng.org/wp-content/uploads/2022/08/FITNG-PAAG-Aug-13-DESKTOP-5SSSCTN.pdf 

Our work on characterizing children's head motion will be presented at the ISMRM Workshop on Motion Detection & Correction happening from 30 August - 02 September 2022 at Merton College, Oxford, England, United Kingdom (https://www.ismrm.org/workshops/2022/Motion/). It will be a joy to finally be able to meet the motion correction community face2face. 

Keep checking out the program for the Open Science Room at OHBM 2022: https://ohbm.github.io/osr2022/ We will plan for some OpenNeuroPET related activities!

Join us for the BIDS PET hackathon at BRAINPET 2022 on Sunday, May 29, 2022! You can see more details on https://brain2022.scot/scientific-programme/ 

2021

I am part of three different abstracts to be presented at NRM2021 (https://www.nrm2021.org/). We are looking forward to present our work on: "The Positron Emission Tomography Brain imaging Data structure (PET-BIDS) extension: A new standard for sharing PET data", "Estimating PET partial volume full-width-half-maximum directly from human data" and "A high-resolution in vivo atlas of the human brain's benzodiazepine binding site of GABAA receptors". 

Join us for our Brainhack Global in Copenhagen! https://openneuropet.github.io/brainhack/ 

We were again visited by Rigshospitalet's media team, which resulted in an article that gives an update about our project and shows the mock scanner. You can read it here. 

We are finally starting our prospective study for the clinical application of motion correction together with preparation in a clinical MRI scans in a pediatric population. 

On September 1st 2021, I officially transitioned from the Machine Learning to the Image section at the Department of Computer Science and started my position as Associate professor.

I am excited to participate as an invited speak er at the EANM 2021 (https://eanm21.eanm.org/) Pre-Congress Symposium "PET/MR – The Cross Path of Morphology and Functionality " to present our work on motion correction for MRI (see program, here). 

We will present a sneak peek into our results regarding prospective motion correction in a healthy adult population in our OHBM abstract titled "Prospective motion correction and reacquisition in a complete clinical protocol for brain MR imaging". Please reach out to us during OHBM!

I have participated in Forskningen Døgn, a Danish initiative to furthe routreach of the scientific community to the pulic. I gave a talk to IDA, the engineering union, and you cna watch it her (in Danish): https://videos.ida.dk/media/Hjerneskanninger+af+b%C3%B8rn+uden+bed%C3%B8velse+kan+blive+en+realitet+/1_cbh7nulc/209069043 

The PET Brain Imaging Data Structure (BIDS) has finally been released with BIDS v. 1.6.0. You can read it here!

Our article showing a high-resolution in vivo atlas of the human brain's benzodiazepine binding site of GABAA receptors is out in NeuroImage: https://www.sciencedirect.com/science/article/pii/S1053811921001555 

Our  OpenNeuroPET project has started! We have kicked of the year with the PET BIDS community review. Hence, we are seeking final community feedback for the PET BIDS standard. We are looking for feedback on GitHub and specifically to the BIDS-PET extension proposal. We have also developed an extension for the validator and added PET examples into BIDS examples. 

This BIDS extension seeks to establish how PET data and additional metadata are organized within the BIDS structure. This encompasses the recent guidelines for brain PET data in publications and in archives provided in the consensus paper (Knudsen et al. 2020), including blood and metabolite data. 

2020

The Novo Nordisk foundation has decided to support our application for the research infrastructure OepnNeuroPET!!! You can read the announcement here.

The Bias and Fairness project team published an article describing the project in Videnskab.dk's Forskerzone.

Congratulations to Marc Fuglsang Christensen and  Anders Lykkebo-Valløe who finished their master thesis projects titled "Gamificering af tålmodighed til MRI scanninger med VR teknologi" and "Novel brain-states during psilocybin intervention" in the summer and fall of 2020!

You can review the highlight of the PET BIDS workshop we organized right before OHBM on YouTube: https://www.youtube.com/playlist?list=PLJt5N2qosssehpeT_Uv5VYlzTq4AeB7Gv 

During the upcoming ISMRM conference (https://www.ismrm.org/20m/), Giske Opheim will present a poster at ISMRM with the title "Optimizing a preprocessing pipeline for structural 7T MR analyses in FreeSurfer" showcasing our work on 7T preprocessing improvements for segmentation: 

Automated cortical segmentations benefit from higher SNR and spatial resolutions on 7T MR images, but are also challenged by B1 inhomogeneities, causing faulty surface inflations primarily in the temporal lobes. We investigated how FreeSurfer outputs were affected by applying eight different preprocessing schemes prior to reconstructions of submillimeter 7T MPRAGE images.  The highest segmentation robustness across subjects was obtained by setting bias-field correction FWHM to 60mm and adding light regularization, and additionally performing intensity normalization. 

I have finished the spring semester by being involved in several bachelor and master thesis, congratulations to Ella, Emil, Marcus and Andreea for finishing their thesis work!

• Ella Hedebø, "Evaluating subcortical volumetric differences in major depressive disorder", Bachelor thesis project.

• Emil Rasmussen, "Working on the cutting edge of neuroimaging - extending the BIDS validator to positron emission tomography (PET)", Bachelor thesis project.

• Marcus Astrup Hansen,"Text Mining and Processing on Patients Experiences on Psilocybin", Bachelor thesis project.

• Andreea-Veronica Vascan, "How do children move in the MR scanner with and without anaesthesia?", Master thesis project.

You can re-watch the BIDS town hall and the BIDS PET extension talks that were given at the OHBM Open Science Room here: BIDS town hall and PET BIDS extension discussion

Martin Nørgaard and Douglas N. Greve will both present work I am involved in at OHBM 2020.  You can see their virtual presentations here: Gaba-a atlas and PET partial volume estimation

We will present the BIDS PET extension at the OHBM Open Science Room on July 2nd. Please see the schedule here.

Matching to the startup of our "Bias and Fairness in Medicine" project, we have published an opinion piece in the Danish paper Politiken here. 

We have started our "Bias and Fairness in Medicine" project 1. April! Have a look at our website: http://fairmed.compute.dtu.dk/  

Our motion correction abilities were just featured on the national evening news in Denmark!!! DR (Danish Radio) came by the hospital for the opening ceremony of the North Wing, which the queen attended. They filmed Gitte and myself in our scanner room where Gitte shows images acquired with and without prospective motion correction. You can see the short clip here around 8:15 min.

2019

I attended Informationens medieskole this fall and they made these super nice videos of us telling in layman terms about the projects we work on: https://www.phdcup.dk/kurser/  You can also see my video on our Children's Moco project page above.

Currently, we have visitors from the A. A. Martinos Center for Biomedical Imaging. Andre van der Kouwe and Stephen Robert Frost are in town to help us set up prospective motion correction sequences on the new NRU research scanner for our project "Imaging children without anesthesia".

We just had our paper titled "The structure of the serotonin system: A PET imaging study "published in Neuroimage. Thanks for finishing this, Vincent! Is has been a long road. https://www.sciencedirect.com/science/article/abs/pii/S1053811919308316  

Since fall 2017 I have been part of the BIDS community and tried to promote data sharing in PET. And now I have just been elected as member of the BIDS Steering Group. 

Together with Aasa Feragen and Sune Holm I received funding for the project "Bias and Fairness in medicine" from the Danish Research council. You can read a case description of the grant in Danish here: https://dff.dk/cases/kunstig-intelligens-skal-stoppe-diskrimination-i-sundhedsvaesenet  or have a closer look at the project page as soon as it is up.

See us at the 22nd International Conference on Medical Image Computing and Computer Assisted Intervention which will be held from October 13th to 17th, 2019 in Shenzhen, China. We will present our work on "Preprocessing, Prediction and Significance: Framework and Application to Brain Imaging" on Monday, October 14. from 1 to 2 pm. Come and see our poster!

We just had our work on "Different Preprocessing Strategies Lead to Different Conclusions: A [11C]DASB-PET Reproducibility Study, " accepted at the Journal for Cerebral Blood Flow and Metabolism (JCBFM).

During the 32nd ECNP Congress of Applied and Translational Neuroscience in Copenhagen in September (7.-10. September) you will be able to visit our poster "The impact of different preprocessing strategies in positron emission tomography: a [11C]DASB Study".

We will also present our work on "THE STRUCTURE OF THE SEROTONIN SYSTEM: A PET IMAGING STUDY " at the BrainPET meeting (http://brain2019.jp/ ) taking place from July 4th – 7th, 2019 in Yokohama.

We just had our work on "Optimization of Preprocessing Strategies in Positron Emission Tomography (PET) Neuroimaging: A [11C]DASB PET Study " accepted in NeuroImage.

Congratulations to Martin Nørgaard who has defended his PhD thesis on May 3rd!

We will present our work on "The Impact of Different Preprocessing Strategies in PET Neuroimaging: A [11C]DASB-PET Study" at the BrainPET meeting (http://brain2019.jp/ ) taking place from July 4th – 7th, 2019 in Yokohama.

From 1. of July on I will be involved in the BrainDrugs initiative. Professor Gitte Moos Knudsen, head of NRU, has received this major grant worth 40 million Danish kroner from the Lundbeck Foundation. The aim of the new thematic alliance is to establish which key features predict drug response in patients with epilepsy or depression. The BrainDrugs consortium is composed of a multidisciplinary team of experienced investigators from The Capital Region, Aarhus and the specialized epilepsy hospital Filadelfia, assisted by two international experts within the field. The project will start July 1st, 2019 and run for five years.

A 2-min video pitch of the project can be found here.

Listen to an interview with Gitte on DR P1 Morgen here. 

More details cane be found on the NRU homepage here.

2018

Our collaborative work titled "Comparing fully automated state-of-the-art cerebellum parcellation from magnetic resonance images"  on cerebellum segmentation resulting from the Miccai Enigma challenge has been published in NeuroImage: https://www.sciencedirect.com/science/article/pii/S1053811918306906 

Our work on relibaility of EEG and ERP with NRU PhD student Cheng Teng Ip has been published: https://www.sciencedirect.com/science/article/pii/S0167876018300606  

I have been involved in some really cool work together with Rasmus R. Paulsen about "Multi-view consensus CNN for 3D facial landmark placement " which was presented at the Asian Conference for Computer Vision (http://accv2018.net/ ) in December 2018.

On a more personal note, we have welcomed a new addition to our family and hence I have been on maternity leave from June 2018 until March 2019. 

In the start of April I have received nearly 3.9 mio DKK from Elsass Foundation for my new 3-year project "How can you avoid to put children with cerebral palsy in general anesthesia while they are in a brain scanner?" which will be hosted at the Neurobiology Research Unit at Rigshsopital starting in April 2019.

Project abstract:

It is standard procedure in most Danish hospitals to employ general anesthesia when small children are in need of medical imaging procedures that demand anesthesia. Anesthesia is used to prevent the child from leaving the scanner, to reduce motion artefacts and for dealing with children that are too anxious to enter the scanning environment. Movement during the image acquisition can cause serious distortions of the imaging data, which can invalidate its quality and potentially lead to an erroneous conclusion. Even though complications directly related to general anesthesia are rare, there is an increasing concern about the potential neurotoxic effects of general anesthesia. Additionally, there are logistic and financial challenges associated with the use of general anesthesia.

The aim of our project is to utilize recent developments in medical imaging hardware technology in order to show that most young children can undergo medical imaging procedures without anesthesia and that it is still possible to obtain a high-quality diagnostic scan. We want to test the clinical efficacy of a marker-less motion tracking device that can register the child’s movements while scanning which allows for motion correction of the acquired images.

Our goal is to demonstrate the clinical utility of a novel approach of imaging including training, preparation and the use of the tracking device in children with cerebral palsy that undergo MRI scans for diagnostic purposes. Results from this project can be used when the new dedicated childhood brain damage MRI system funded by the Elsass Foundation is installed at BørneRiget, the new childrens’s hospital to open in Copenhagen in 2024. 

We will also present our work on "The Impact of Preprocessing Pipeline Choice in Univariate and Multivariate Analyses of PET Data" at the 8th International Workshop on Pattern Recognition in Neuroimaging (http://sites.google.com/site/prnisg2018/) taking place from June 12th-14th, 2018 in Singapore. You cna read the article published afterwards here: https://ieeexplore.ieee.org/abstract/document/8423962 

We will present our work on "False Positive Rates in PET" at the Neuro Recpetor Mapping meeting (http://www.nrm2018.org/nrm-conference/) taking place from July 9th – 12th, 2018 in London.

We just published a review titled "Cerebral serotonin transporter measurements with [11C] DASB: A review on acquisition and preprocessing across 21 PET centres" in the journal for cerebral blood flow and metabolism. Full text is available here: http://journals.sagepub.com/doi/full/10.1177/0271678X18770107

Congratulations to Vincent Beliveau who has successfully defended his PhD thesis titled "Functional and Molecular Imaging of the Serotonin System in the Human Brain"!

2017

We published a journal paper regarding the study on seasonal affective disorder presented at OHBM with the tile "Brain Networks Implicated in Seasonal Affective Disorder: A Neuroimaging PET Study of the Serotonin Transporter" in Frontiers in Neuroscience. Full text is available here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5682039/

We presented our work titled "Brain Networks involved in Seasonal Affective Disorder: A Neuroimaging PET Study of 5-HTT Expression" at OHBM June 25-29 2017 in Vancouver, Canada. Please find the abstract and poster below.

We presented our paper titled "Permutation tests for classification:Revisited" at the 2017 International Workshop on Pattern Recognition in Neuroimaging (PRNI). You cand find a preprint of the paper and the presentation from PRNI below.

Starting from May 2017, I will spend my time split between the Department for Computer Science of the University of Copenhagen (DIKU) where I recently got an appointment as assistant professor and the Neurobiology Research Unit (NRU) at Rigshsopital. My time at DIKU will be evenly divided between teaching (mainly in the fall) and establishing new research collaborations between the hospital and the university.

My fascination with the cerbellum is ongoing and we have published a study titled "Cerebellar heterogeneity and its impact on PET data quantification of 5-HT receptor radioligands" in the journal for cerebral blood flow and metabolism. Full text is available here: http://journals.sagepub.com/doi/full/10.1177/0271678X16686092

We will present a sneak peek into our results regarding prospective motion correction in a healthy adult population in our OHBM abstract titled "Prospective motion correction and reacquisition in a complete clinical protocol for brain MR imaging". Please reach out to us during OHBM!

I am excited to announce that I will be not only participating, but act as an invited speaker at the 2022 ISMRM Workshop on Motion Detection & Correction (https://www.ismrm.org/workshops/2022/Motion/)  in Oxford in the end of August 2022.