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PhD students receive ISMRM awards for motion correction research

Congratulation to PhD students Adam van Niekerk and Gizeaddis Simegn who were both awarded Magna Cum Laude Merit Awards for their research presented at the recent ISMRM meeting in Paris.

Adam also received first prize for the best trainee abstract in the motion correction study group. Read an interview with Adam here.


The Cape Universities Body Imaging Centre (CUBIC) within the Faculty of Health Sciences seeks to employ a Senior MR Radiographer to conduct Magnetic Resonance Imaging (MRI) of research subjects, public and private patients on the 3T Siemens Skyra MRI located at Groote Schuur Hospital and to perform MR-related administration. The radiographer will function under the supervision of the Principal Technical Officer. If you meet the requirements we invite you to apply for this 3-years, full-time, contract position for soonest appointment.

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CUBIC recently acquired slim OPTOACTIVE II™ headphones with active noise cancellation and a FOMRI III™ adaptive noise cancelling microphone from OptoAcoustics. These use both passive and active noise cancellation to reduce 95% of the MR EPI gradient noise, allowing clear two way communication between the patient and the control room. This opens up possibilities for research in speech and hearing, delivering auditory stimuli during fMRI scans, and increasing comfort for children and other noise-sensitive participants.

PhD student Adam van Niekerk has been elected as a trainee representative for the 'Detection & Correction of Motion in MRI & MRS Study Group' of the International Society for Magnetic Resonance in Medicine (ISMRM). He will hold the position for one year starting from June 2018 when the joint annual meeting of the ISMRM-ESMRMB is held in Paris.


CUBIC radiographers were awarded not one but two first prize oral presentations in the SMRT abstract submissions this year - in both the clinical and research categories!

Petty Samuels received the First Place Clinical Focus Award for her abstract titled  'Improving MR Spectroscopy in the liver with a small number of averages by accurate voxel placement'. She and her co-authors showed that placing a spectroscopy voxel at least 10mm from the periphery in segment 7 of the liver rather than in segment 8 achieves narrower linewidths and improves discrimination between middle chain methylene, methyl groups and glycogen peaks.

Ingrid Op't Hof was awarded the First Place Research Focus Award for her abstract "Examining the effects of SMS and GRAPPA acceleration on resting state fMRI signal quality" where she showed that acceleration of fMRI acquisition using parallel imaging (GRAPPA) and simultaneous multi-slice imaging (SMS) reduces temporal SNR (tSNR), with a larger effect for GRAPPA. She and her co-authors suggest that a GRAPPA factor of 2 with an SMS factor of 2 provides a good compromise between fast acquisition and acceptable tSNR.

They will both present their work at the 27th annual meeting of the Society for MR radiographers and technologists (SMRT) in Paris in June. Congratulations on this excellent recognition!

The UCT Legacy Society invites you to our annual Summer School Guest Lecture

Topic: The intersection of cardiovascular disease and ageing: A global health perspective

Professor Ntusi, a UCT alumnus, is the Head of the Department of Medicine at UCT and the Clinical Lead for cardiovascular magnetic resonance (CMR) and cardiovascular computed tomography (CCT) at Groote Schuur Hospital. He holds the Chair of Medicine in the Faculty of Health Sciences in the Department of Medicine. His primary research interests comprise inflammatory heart disease (including HIV-associated cardiovascular disease), non-ischaemic cardiomyopathy and non-invasive imaging, in particular with CMR. He has in-depth training and expertise in CMR and CCT. He currently supervises postgraduate students and is conducting several single-centre mechanistic clinical studies, which are mostly CMR-based.

Join us for what promises to be an engaging talk by Prof Ntusi, with plenty of time for Q&A
Date: 20 January 2018
Venue: Kramer Lecture Theatre 1
Time: 17h00 Cocktail reception followed by talk at 18h00

Kindly RSVP online by 13 January 2018

For more information, please email Lwando Nteya at lu.nteya@uct.ac.za.

Even Treated, HIV-Positive Children Have Ongoing White Matter Brain Damage

Posted on November 8, 2017

MedicalResearch.com Interview with:
Marcin Jankiewicz  University of Cape Town Cape Town, South Africa
Marcin Jankiewicz 
University of Cape Town
Cape Town, South Africa 

MedicalResearch.com: What is the background for this study?

Response: The Children with HIV Early Antiretroviral (CHER) trial, conducted in Cape Town and Soweto, was designed when there was uncertainty whether to start antiretroviral therapy (ART) as soon as HIV was diagnosed (below 12 weeks of age) or to wait until there was evidence of immuno-compromise and disease progression. Also, there were concerns about maintaining adherence, long-term toxicity and also resistance in the setting of few antiretroviral options. Early outcomes showed a decreased risk in childhood mortality in the early treatment arms compared to deferred treatment, becoming standard of care globally.

The CHER cohort is one of the largest and best documented of children receiving ART within the first year of life. Also, age- and community-matched HIV exposed uninfected (HEU) and HIV unexposed (HU) uninfected infants were enrolled in parallel for a linked vaccine study.

We therefore had an amazing opportunity to link with a neurodevelopmental sub-study in participants from Cape Town and apply sophisticated neuroimaging modalities that could link with clinical, virological and immunological characteristics.


MedicalResearch.com: What are the main findings?

Response: At age 7, despite early (before age 2 years) ART and viral load suppression, we continue to observe differences in white matter integrity compared to uninfected children. White matter damage observed at age 5 years persists, with new damage evident. The continued observation of regions with lower fractional anisotropy (FA) and higher mean diffusivity (MD) in HIV infected (HIV+) children point to disruptions in ongoing white matter development regardless of early ART. Lastly, in HEU children we find higher FA and lower MD in clusters in the cortical-spinal tract, compared to HU children, suggesting that HIV/ART exposure in utero and/or ART in infancy has a long-term impact on WM development.

MedicalResearch.com: What should clinicians and patients take away from your report?

Response: We find that white matter regions of the brain are still vulnerable to the effects of HIV and/or ART, regardless of early treatment. This is in line with other studies finding that HIV+ children continue to experience developmental delays and cognitive deficits. Insults to white matter may be responsible for some of the delays and/or deficits observed in HIV+ children on ART.

Although HIV+ children on ART, particularly early ART, are healthier than previous generations of children not on treatment, more research is needed to better understand how HIV in conjunction with ART continues to influence the path of healthy brain development.

In addition, we find that uninfected children born to HIV+ mothers reveal differences in white matter properties, which suggests more study is need on how HIV/ART exposure may impact brain development in HEU infants.

Should we identify parts of the brain particularly vulnerable to HIV and/or ART, or how timing of ART affects brain development, this could inform treatment policy, improved drug combinations, and early intervention strategies.

MedicalResearch.com: What recommendations do you have for future research as a result of this study?

Response: More work is needed linking alterations in HIV+ children to neuropsychological, behavioral and developmental data. While we observe signs of damage to white matter, without directly linking it to a measurable outcome(s) we can only conjecture about the possible ways in which damage manifests in the developing brain. Our research team will soon be analyzing this data.

MedicalResearch.com: Is there anything else you would like to add?

Response: A limitation of this study is that we were not able to measure inflammation from other infections in these children and this may also have had a role in the findings. 

MedicalResearch.com: Thank you for your contribution to the MedicalResearch.comcommunity.


Marcin Jankiewicz, Martha J. Holmes, Paul A. Taylor, Mark F. Cotton, Barbara Laughton, André J. W. van der Kouwe, Ernesta M. Meintjes. White Matter Abnormalities in Children with HIV Infection and Exposure. Frontiers in Neuroanatomy, 2017; 11 DOI: 3389/fnana.2017.00088

Paper "White Matter Abnormalities in Children with HIV Infection and Exposure" by Marcin Jankiewicz and colleagues attracts instantaneous media attention in ScienceDaily.

Dr Martha Holmes, with collaborators Dr Mamadou Kaba from UCT's division of Medical Microbiology and Dr André van der Kouwe from Massachusetts General Hospital, was recently awarded a 5 year R01 grant from the US National Institutes of Health to investigate neuroimaging and gut microbiome markers of development in HIV-exposed uninfected infants.

Dr Marcin Jankiewicz, in collaboration with Dr Peter Torre from San Diego State University and Dr Barbara Laughton from Stellenbosch University, was recently awarded a new 5-year NIH R01 grant to examine effects of HIV on the central auditory network. Dr Jankiewicz is the local PI and will assume primary responsibility for the imaging components of this project.



BIOGRAPHY - Dr. Barbara Mason

BIOGRAPHY - Dr. George Koob 


ISMRM Workshop on Motion Correction in MRI & MRS to take place from 8th - 11th September 2017 at the Vineyard Hotel, Cape Town South Africa.


The Society for Magnetic Resonance Angiography's 29th Annual International Conference will take place in October 2017. MRA: New perspectives will take place from 4th - 6th October in Stellenbosch, South Africa.

The pre-conference educational workshop MRI/A advanced con

cepts to take place on the  3rd of October 2017.


PhD student Adam van Niekerk and co-authors including Ernesta Meintjes were awarded an ISMRM Magna Cum Laude Merit Award and one of 200 power pitch presentations selected from 6700 abstracts at the recent ISMRM 25th Annual Meeting and Exhibition in Honolulu, Hawaii. Adam presented the implementation of a 2.4 GHz wireless sensing platform for transmission of motion data from within a head coil at 3T.

 Please also see http://www.bme.uct.ac.za/bme/news-niekerk-ismrm2017award.


MRI research group abstracts to be presented at OHBM annual meeting

 Abstracts by Martha Holmes, Emmanuel Nwosu, Jia Fan and Werner Stoltsz were accepted for presentation at the 2017 annual meeting of the Organization for Human Brain Mapping to be held in Vancouver from June 25-29. Congratulations to Werner, who was awarded an OHBM merit travel stipend to attend the meeting.

At the recent meeting of the Society for MR Radiographers & Technologists (SMRT) in Honolulu, Petty Samuels presented a poster titled Reproducibility of Brain Morphometry from MRI Scans Performed at Different Times of Day. Ingrid Op’t Hof presented pedriatric neuroimaging acquisition and analysis success rates at ages 5 and 7 years. They both received SMRT travel scholarships to attend the conference. 

Poster 1

Poster 2

CUBIC UCT held its second Cardiovascular Magnetic Resonance workshop on Friday 31st March - Sunday 2nd April 2017 at Groote Schuur Hospital.

This three day hands-on Cardiovascular Magnetic Resonance Workshop is specifically designed to benefit Radiographers, Radiologists and Cardiologists working on, or interested in MRI, both in a clinical and research environment.

The workshop consisted of a series of lectures, followed by practical sessions based on the theory. During the hands-on sessions, participants had the opportunity to experiment with MRI where they gained a deeper understanding on how to plan, execute and analyse Cardiac MRI scans.

Mrs Petronella Samuels and colleagues from the division of cardiology recently presented the case study of a young woman with rheumatic heart disease at the annual meeting of the Society for Cardiovascular Magnetic Resonance. Investigating the cause of a conduction abnormality using multiparametric cardiovascular magnetic resonance imaging including cine, cine tagging, T2-weighted (STIR), pre contrast T1 and T2 mapping and late gadolinium enhancement (LGE) imaging, they were able to find evidence of myocarditis and valvulitis.

See Abstract here


Image: Mrs Petty Samuels and Dr Ntobeko Ntusi

Jia Fan and Ali Alhamud, as well as students Adam van Niekerk and Leah Morgan had abstracts accepted for presentation at the 25th Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM), to be held in Honolulu, Hawaii in April. 

Adam's abstract "Implementation of a 2.4 GHz wireless sensing platform for transmission of motion data from within a head coil at 3T" was among only 220 abstracts selected for a Power Pitch presentation, designed to give maximum exposure to the most interesting abstracts at the meeting.

CUBIC UCT held yet another successful Basics of MRI workshop on Friday 14th & Saturday 15th October 2016 at Groote Schuur Hospital. 

The two day hands-on workshop consisted of a series of lectures followed by practical session which were based on the theory. The course content focused specifically on components of the scanner, signal creation, pulse sequences, MR contrast, imaging gradients, creation and parameters. 

Participants had the opportunity to experiment with MRI parameters on the various MRI pulse sequences.


Image: Mrs Mazwi Maishi, Mrs Ingrid Op' Hof, Mrs Petty Samuels, Mr Marcin Jankiewicz and Mr Stephen Jermy 


The course will be repeated in 2017. Dates to be confirmed. If you ar interested in attending this course please email cubic@uct.ac.za for further information.


Adam van Niekerk: The student inventor

Image: PHD student Adam van Niekerk

Adam van Niekerk a PhD student in the MRI research group, was recently featured in UCT news. He has invented a s,all, cost-effective device that uses vector observations of the scanner's magnetic field and gravity to perform high temporal resolution motion detection and correction during MRI scans.

Local researchers feature in NIH Global Health Matters newsletter

The May/June 2016 issue of the NIH Global Health Matters newsletter features research performed in Cape Town that uses neuroimaging to understand how alcohol consumed during pregnancy affects children’s brains. This represents a long-standing collaboration between Drs. Sandra and Joseph Jacobson from Wayne State University in Detroit, and Dr. Christopher Molteno and Prof. Ernesta Meintjes from the University of Cape Town.

Read the article

Prof Ernesta Meintjes' Research Chair in Brain Imaging was just renewed for a further 5-year term! The chair is funded through the South African Research Chairs Initiative (SARChI). Through this renewal, the South African National Research Foundation and the Department of Science and Technology confirm the excellence of Ernesta's contributions to science over the last ten years. Congratulations to Ernesta!


CUBIC UCT held its first Cardiovascular Magnetic Resonance workshop on Friday 5th - Sunday 7th August at Groote Schuur Hospital.

This three day hands-on Cardiovascular Magnetic Resonance Workshop is specifically designed to benefit Radiographers, Radiologists and Cardiologists working on, or interested in MRI, both in a clinical and research environment.

The workshop consisted of a series of lectures, followed by practical sessions based on the theory. During the hands-on sessions, participants had the opportunity to experiment with MRI where they gained a deeper understanding on how to plan, execute and analyse Cardiac MRI scans.


A dedicated infant coil was purchased from a University Research Committee equipment grant awarded to Prof Kirsty Donald (PI, Department of Paediatrics) and Prof Ernesta Meintjes.

The coil can be used for high resolution scanning of the head and neck in infants from newborn to 18 months, enabling investigation of early brain development. During the first few months of life many new network connections are being formed, and there is not yet a large influence of confounding environmental factors on brain development.


HIV Paediatrics Workshop

Martha Holmes and Frances Robertson attended the 8th International Workshop on HIV Pediatrics in Durban on 15/16 July, where they presented some findings from the neuroimaging substudy of the CHER (Children with HIV Early Antiretroviral) trial. Results from MR spectroscopy show that at age 7 and 9 the children with HIV have higher choline and lower glutamate levels in the frontal gray matter compared to uninfected control children of the same age, in spite of having been on antiretroviral treatment since early infancy.

See Poster 1

See Poster 2

See Poster 3

AIDS Conference

Martha Holmes presented findings from the neuroimaging substudy of the CHER (Children with HIV Early Antiretroviral) trial at the 21st International AIDS conference (AIDS 2016) from 18-22 July. A synopsis of differences found on multimodal neuroimaging between HIV negative children who were born to HIV positive mothers (HIV-exposed, uninfected) and HIV negative children who were born to HIV negative mothers (HIV-unexposed, uninfected), shows that in utero exposure to HIV/ART may affect multiple aspects of brain development.

Sixteen abstracts authored by members of the division of Biomedical Engineering and the department of Psychiatry and Psychology were presented at the 22nd Annual Meeting of the Organization for Human Brain Mapping in Geneva in June. 

These included studies on emotion regulation and functional connectivity in methamphetamine-induced psychosis and fMRI of social cognition subsequent to early childhood trauma; as well investigations into the effects of teratogens and infectious disease on brain structure and function.

Dr Frances Robertson & Dr Martha Holmes to talk at Pint of Science Festival

Dr Frances Robertson & Dr Martha Holmes will talk about their research at the Pint of Science Festival to be held in Cape Town during 23-25 May 2016. Come to Sgt Peppers in Long St, Cape Town, on Wednesday 25 May 2016, at 7.30pm for an evening with the theme 'Beautiful Mind' and hear 'What's in your head? Looking at the brain with neuroimaging'.

Ingrid Op'tHof, M.J. Holmes, T.Hamana, T.Van de Water M.F. Cotton, A.J.W. Van Der Kouwe, E.M. Meintjes, B. Laughton's poster on PEDRIATRIC NEUROIMAGING ACQUISITION AND ANALYSIS SUCCESS RATES AT AGES 5 AND 7 YEARS.



were invited to present their posters at ISMRM 24th Annual Meeting & Exhibition which took place in Singapore from 7 - 13 May 2016. 

CUBIC UCT held its second workshop on Basics of MRI on Friday 26 & Saturday 27 February 2016. Radiographers from all over the Western Cape attended this two day MRI hands-on workshop which was specifically designed to benefit radiographers working on, or interested in MRI in both a clinical and research environment. 

Due to the good feedback received, CUBIC will repeating the course towards the end of the year (dates to be announced at a later stage) if you are interesting in attending the course please email cubic@uct.ac.za for further details. 

An NRF Thuthuka Grant has been awarded to Dr Ali Alhamud for a project entitled "CEST MRI for detecting Glycogen changes (depletion and repletion) pre and post exercise".

The goal of this project is to measure muscle glycogen levels during exercise, and following carbohydrate ingestion after exercise.

To achieve this, we will develop and implement a novel magnetic resonance imaging (MRI) technique called Chemical Exchange Saturation Transfer (CEST) for imaging glycogen levels of tissue.

This technology will be implemented on the full body research-dedicated 3 T Siemens Skyra scanner at the Cape Universities Body Imaging Centre at the University of Cape Town (CUBIC-UCT). 

CUBIC UCT held its first workshop on the Basics of MRI on Friday 27th & Saturday 28th November 2015 at Groote Schuur Hospital.

This two day MRI hands-on workshop was specifically designed to benefit radiographers working on, or interested in, MRI in both a clinical and research environment.

The workshop consisted of a series of lectures, followed by practical sessions based on the theory. During the hands-on sessions, participants had the opportunity to experiment with MRI parameters on the various MRI pulse sequences.

The course content specifically focused on MR safety, components of the scanner, signal creation, image creation, image formation and MR contrast.

The course will be repeated on 26th & 27th February 2016. 

A paper by Dr Ali Alhamud and colleagues on real-time measurement and correction of both B0 changes and subject motion in diffusion tensor imaging using a double volumetric navigated (DvNav) sequence is to appear in NeuroImage with an ISI impact factor of 6.357. In this paper, a novel technique is introduced to simultaneously measure, report and correct in real time subject motion and changes in B0 field homogeneity, both in and through the imaging plane.

Read article

Azim Celik, one of GE's top imaging physicists will be talking on advanced MRI neuroimaging Thursday 27 August 2015 from 4.30 pm, C7 MRI Seminar Room​.​

More on Azim Celik


CUBIC Launch 31 July 2015

Shown here are a few of the collaborators cutting the ribbon at the launch of CUBIC which was celebrated on 31 July 2015,

(From left to right) Dr Max Price, Dr Daniel Adams, Dr Sibongile Gumbi, Mr Barlow Manilal, Prof Nico Gey van Pittius and Dr Bhavna Patel.

Congratulations to Mr Jia Fan, Prof Ernesta Meintjes, Dr Ali Alhamud, Dr Bruce Spottiswoode and collaborators for selection of their recently published paper detailed below as one of the top articles by the SAMRC.

Please see the March issue of the MRC Celebrates Sciences E-Newsletters available here



Valentine’s Day 2015 marked a historical event as the first research full-body high-field Magnetic Resonance Imaging (MRI) scanner in Africa was delivered to CUBIC-UCT (Cape Universities Body Imaging Centre).

The Siemens Skyra, valued at R24 million, presents the culmination of four years of fundraising by a multi-disciplinary team headed up by Profs Mayosi and Meintjes. Funds were secured from the Technology Innovation Agency, the National Research Foundation, and the Cancer Research Trust. CUBIC, a national imaging facility, is a collaboration between UCT, Stellenbosch University, the MRC and Siemens.

The new site, adjacent to the Psychiatry block at Groote Schuur Hospital, is an extension of the original facility located at Tygerberg Hospital where a brain-only research MRI scanner has been operational since January 2007. This new state-of-the-art machine ushers in a new era of imaging research, including cardiac, abdominal and muscoskeletal.

Shown here to celebrate the arrival of the scanner are (back, left to right) Dr Alhamud, Mrs Samuels, Dr Ntobeko, Prof Douglas, Dr Jankiewicz, Mr Lipsitz, Prof Stein, (front, left to right) Mr Saleh, Mr Denzler, Prof Meintjes.

 Shown here is the scanner being lowered into its new site.