Please refer to this site/make edits here for the most updated information:

This page describes Andre's collaboration with investigators in South Africa studying the effects of HIV on neural development in children.

Data Location


Note: /cluster/gerenuk/user/andre_hiv/HIV_UCT is all of Andre's development work on the project before 2014. For the most part, you will always be working in the HIV_UCT_longitudinal directory.

UNIX group- "ucthiv"



new Skyra scan data since Andre's March 2016 visit which Leah copied from UCT server


mprage scans processed with FS 5.3


Bruce modified mri_ca_label to stop overlabeling the putamen


mprage scans re-processed w/ FS 6.0 when released in Jan. 2017


all scan data for all time points from South Africa


tables and spreadsheets with info on subjects


new scan data Andre brought back from S. Africa in Mar. '16 on his yearly visit


modified versions of v5.3 mri_ca_label and mri_ca_register binaries used for fixed putamen


Allison M. testing how demographics files would be merged w/ command line tools. can probably be deleted.




text files listing paths to input data used for analyses


ones written by Boston and S. Africa people


used for processing and analyzing data




total = 152 - according to our spreadsheet


Subject ID's:

Subject ID # (<subjid>) = one - three digit code; 1 to 252

Short number (1-252) is unique identifier to use that matches for all time points. use that one.

Longer, six digit number (seen in data_orig directory names - yyyymmdd_time_longID_shortID) is probably the master study ID, which corresponds to one of the shorter IDs. We don't use the long form ID #'s.FreeSurfer subject directories:

<subjid>_<5/7/9> = cross-sectionally processed time point

<subjid> = subject base

<subjid>_<5/7/9>.long.<subjid>= longitudinally processed time point

Data Processing

Andre's primary role in the project is technical development for image acquisition. As such, we don't have any pre-defined role in data processing. We see it as really Ernesta's data and want to be respectful of that. We help analyze the data in whatever way they ask us to, while they also do their own analyses. So far, they have asked for our help with the two most FreeSurfer-related analyses:

Longitudinal Stream

Children participating in the study were scanned (ideally) at 5, 7 and 9 years old. Some children only have data from one or two timepoints. The FreeSurfer Longitudinal stream was used to generate the most accurate morphometric measures possible.

To do:

  1. Edit (QA/QC) v6.0 recons
  2. Re-run longitudinal stream w. edited recons
  3. Statistical analyses w. accurate morphometric measures

Parameter Maps

Two multi-echo FLASH scans were collected during 5 year old scans to estimate T1 relaxation time and proton density (PD). This was done using the FreeSurfer tool mri_ms_fitparms. Allison and Andre compared these parameter values for T1, PD, T2* between healthy controls and children infected with HIV, using v5.3 recon-all output. These comparisons should be rerun once the 6.0 recons have been QA'ed.

To do:

  1. Register newer, edited v6.0 aparc+aseg.mgz to parameter maps.
  2. Redo statistical analysis comparing values across groups

People Involved

From Cape Town

Ernesta Meintjes (joint-PI on the project)

physicist in the Department of Biomedical Engineering at the University of Cape Town (UCT)

Barbara Laughton (also joint-PI)

[ ] pediatrician at Stellenbosch University (sometimes abbreviated SUN) and Tygerberg Hospital (east of the city), where the children come for study.

Ken Mbugua

Completed a PhD in biomedical engineering through UCT. He visited the Martinos Center for a couple of weeks two or three years ago and specialized analyzing the spectroscopy data and the 5 year old morphometry data.

Leah Morgan

Past Msc bioengineering student from UCT, did a few months of coordinating between Martinos and UCT lab

Frances Robertson

Project coordinator on the UCT side, postdoctorate researcher in Ernesta's lab

Keri Woods

PhD student in Ernesta's lab

Martha Holmes

Post-doc researcher in Ernesta's lab, did lots of analyses for spectroscopy

Emmanuel Nwosu

PhD student using HIV data for thesis/dissertation.

Mark Cotton

[ ] professor at Stellenbosch University. on some of the abstracts.

From MGH

Andre van der Kouwe

developed technical acquistion methods for un-sedated children, oversees MGH work for grant

Leah Morgan

Now an RA working in Bruce's lab, taken over from Allison M


Our study is part of a larger study that was an international drug trial (CIPRA- Comprehensive International Program of Research on AIDS). South African piece and then Cape Town subset of that. CHER (Children w/ HIV early antiretroviral therapy)- local study name. piggybacked on for imaging. now can get demographics.


Dates of funding: ?

The project was originally an R21 titled "Neuroimaging Technology for Pediatric Development Disorders in South Africa". Ernesta and Andre developed a set of techniques for imaging young children without sedation:

This grant funded the study of the 5-year-old children for the HIV Project.


Dates of funding: 7/1/2011 - 6/40/2017

This grant continued the work of the HIV project by providing funding to continue scanning the same (and new) children at 7 and 9 years old, using the techniques developed during the R21.


Since the advent of highly active Anti-retroviral Therapy (HAART), HIV has transitioned from a fatal disease to a chronic condition in which there may be ongoing damage to the central nervous system (CNS) especially in the developing brain of the young child. Because CNS penetration by ART is limited, the brain becomes a reservoir for the virus, and few drugs are available that impact these reservoirs. NeuroAIDS affects children differently and more dramatically than adults. Few studies of school-age HIV positive children exist and even fewer include neuroimaging. These studies are practically non- existent in the developing world. In this project we have the unique opportunity to study the effects of HIV and ART on the developing brain over a period of 4 years in a well-characterized cohort of young children using neuropsychological and behavioural assessments combined with advanced neuroimaging techniques in the region with the highest prevalence of HIV in the world, and the population most representative of the world pandemic.



The four aims of the proposed study are:

1. Clinical and comprehensive cognitive assessment of children at 7 and 9 years of age at KID CRU:

2. Image children at 7 and 9 years at CUBIC in a 1 hour session:

3. Technical development of pediatric imaging techniques and longitudinal data analysis:

4. Capacity building through exchange of technology, students and technical training:

We will acquire three types of imaging data:

Structural imaging: We will collect multiecho MPRAGE (MEMPR) for cortical thickness estimation, cortical parcellation, and estimation of subcortical structure volumes using Freesurfer software. If time permits, we will collect two multiecho FLASH (MEF) scans for estimating T1 relaxation time and proton density (PD).

Spectroscopy: We will collect spectra in left peritrigonal white matter, midfrontal gray matter and basal ganglia, using a PRESS sequence with 2 mL voxels and 64 excitations analyzed with LCModel to estimate metabolite ratios and absolute concentrations (since Cr concentrations increase with HIV-associated gliosis).

.Diffusion imaging: We will collect a high-resolution (2 mm isotropic), 30 direction, whole brain diffusion tensor volume and analyze with TrackVis, DTIStudio, and the TBSS tool in FSL.*

HIVProject (last edited 2021-09-22 09:43:24 by DevaniCordero)