Connectivity within the brainstem is impaired in chronic fatigue syndrome

Connectivity within the brainstem is impaired in chronic fatigue syndrome

Presented During: Poster Session
Thursday, June 13, 2019: 12:45 PM - 02:45 PM


Leighton Barnden1, Zack SHAN1, Donald Staines1, Sonya Marshall-Gradisnik1, Kevin Finegan2, Timothy Ireland2, Sandeep Bhuta2


1Griffith University, Gold Coast, QLD, Australia, 2Gold Coast University Hospital, Gold Coast, QLD, Australia


Chronic fatigue syndrome or myalgic encephalomyelitis (CFS) is a common, debilitating, multisystem disorder of uncertain pathogenesis, for which there exists evidence of dysregulation of the central nervous system (Carruthers. 2011). Quantitative T1wSE and T2wSE MRI studies of CFS have reported abnormal correlations with severity and autonomic measures which implied brainstem conduction deficits (Barnden. 2015, Barnden. 2016). The aim of this study was to directly measure connectivity within the brainstem (midbrain, pons and medulla) to confirm these implied deficits.


Resting-state and Stroop-task functional MRI (rsfMRI and tfMRI) studies with companion hemodynamic and respiratory parameters were acquired for 27 healthy control (HC) and 45 chronic fatigue syndrome (CFS) subjects who met Fukuda criteria.

Each fMRI consisted of 1100 sagittal images and was acquired for 15 minutes on a 3T Siemens Skyra with a simultaneous multi-slice echo-planar imaging (EPI) pulse sequence(Auerbach. 2013) with 72 slices, multiband factor = 8, TR = 798 ms, TE = 30 ms, flip angle = 40°, acquisition matrix = 106 x 106, and voxel size 2 x 2 x 2 mm. Given that this study was focused on connectivity within the brain stem whereas routine spatial normalization of fMRI is focused on the cerebral cortex, we optimized spatial normalization for alignment of the brain stem.

A two-stage normalization strategy was performed on the single band reference (SBRef) images which were acquired before the 1100 fMRI volumes. Stage I was a 9DF deformation to the MNI T2 template constrained to 20° rotation for all 3 axes using FSL's 'flirt'. The 9DF accounted for individual magnification differences and angular constraints prevented some grossly inaccurate deformations.

For stage II, a mask was manually created using FSL's 'fslview' to isolate the brainstem and thalamus (Fig 1A). This mask excluded the ventral half of the pons and medulla where variable signal dropout/distortion was seen (Fig 1C). The deformed images from stage I were then further deformed with 6DF (rigid) to the T2 template within this thalamus-brainstem mask, again with 20° angular constraints.

The two deformations were then merged and applied to the 1100 EPI images. ROIs (Fig 1B) were constructed for the brainstem left and right medulla (Mdul_L, Mdul_R) and midbrain cuneiform nucleus (CnF_L, CnF_R) based on locations where abnormal CFS autonomic regressions were detected earlier (Barnden. 2016); and for the left and right hippocampus subiculum (subic_L and subic_R) which have medulla connections (Edlow. 2016). BOLD fMRI time series were computed for these ROIs and de-noised using 15 RETROICOR covariates derived from the physiological measures with the PhysIO toolbox (Kasper. 2017) and QA and principle components of white matter and CSF BOLD variations from the CONN toolbox (Whitfield-Gabrieli. 2012). Second-level testing for group difference in connectivities were then performed with CONN.

Fig 1A: Brainstem+thalamus mask to exclude ventral medulla & pons dropout (see C). B: Mdul_L&R, CnF_L&R and subic_L&R ROIs. C: Stem normalised tfMRI images of 6 subjects with Mdul_R, CnF_R ROIs.


For the task fMRI, group connectivity differences were found between Mdul_R and CnF_L (FDR-corrected P = 0.003) – see Fig 2; Mdul_L and CnF_L (0.004); and Mdul_R and subic_L (0.007). No connectivitiy differences were found in the resting state fMRI.

Fig 2 Connectivity between 3 pairs of nodes was significantly different for CFS and HC groups. Mdul_R right medulla; CnF_L left cuneiform nucleus; subic_L subiculum of left hippocampus.


Significant differences were found between CFS and HC for connectivity within the brainstem between the rostral medulla and midbrain cuneiform nucleus and between the rostral medulla and subiculum of the left hippocampus. Impaired brainstem connectivity can explain reported autonomic and compensatory structural changes in CFS (Barnden. 2015, 2016), and may also explain the impaired cognitive performance, sleep quality and pain of CFS. The fast 0.798s multiband fMRI used here yielded suboptimal brainstem image quality although it will have provided superior physiological artefact correction. Studies with improved image quality may yield deeper insights into the nature and location of brainstem conduction deficits in CFS.
Disorders of the Nervous System:

Disorders of the Nervous System Other 1
Imaging Methods:

Modeling and Analysis Methods:

fMRI Connectivity and Network Modeling 2



Data Registration

Degenerative Disease




1|2Indicates the priority used for review
My abstract is being submitted as a Software Demonstration.
No Please indicate below if your study was a "resting state" or "task-activation” study.
Resting state Task-activation Healthy subjects only or patients (note that patient studies may also involve healthy subjects):
Patients Was any human subjects research approved by the relevant Institutional Review Board or ethics panel? NOTE: Any human subjects studies without IRB approval will be automatically rejected.
Yes Was any animal research approved by the relevant IACUC or other animal research panel? NOTE: Any animal studies without IACUC approval will be automatically rejected.
Not applicable Please indicate which methods were used in your research:
Functional MRI For human MRI, what field strength scanner do you use?
3.0T Provide references using author date format
Auerbach, E. J., J. Xu, E. Yacoub, S. Moeller and K. Ugurbil (2013). ‘Multiband accelerated spin-echo echo planar imaging with reduced peak RF power using time-shifted RF pulses.’ Magnetic Resonance in Medicine vol 69, no. 5, pp. 1261-1267.
Barnden, L. (2015). ‘Evidence in Chronic Fatigue Syndrome for severity-dependent upregulation of prefrontal myelination that is independent of anxiety and depression.’ NMR in Biomedicine, 28, no.3, pp. 404-413.
Barnden, L. (2016). ‘Autonomic correlations with MRI are abnormal in the brainstem vasomotor centre in Chronic Fatigue Syndrome.’ NeuroImage: Clinical, vol 11, pp. 530-537.
Carruthers, B. (2011). ‘Myalgic encephalomyelitis: International Consensus Criteria.’ Journal of Internal Medicine, vol 270, pp 327-338.
Edlow, B. L. (2016). ‘The Structural Connectome of the Human Central Homeostatic Network.’ Brain Connectivity, vol 6, no. 3, pp. 187-200.
Kasper, L. (2017). ‘The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data.’ Journal of Neuroscience Methods, vol 276, pp. 56-72.
Whitfield-Gabrieli, S. (2012). ‘Conn: a functional connectivity toolbox for correlated and anticorrelated brain networks.’ Brain Connectivity vol 2, no. 3, pp. 125-141.


Senior Member
What i do not understand is whether there appears to be also a structural abnormality although an fMRI suggests that they are looking at blood flow.

These are very encouraging results i believe. Please see my tweets on the subject below. machine Learning identified the Brainstem along with acetylcholine and cholinergic signalling :

JenB Tweet.png


Senior Member
Encouraging they see something. But is this a dead end for treatment?
Not at all. Temporary remissions show that ME is reversible in a very short time frame (hours if not minutes). During one of these remissions, those parts of the brain probably switch to normal healthy function. I see this new finding as more data to help point to whatever is malfunctioning. If they get enough data of this type, they can hopefully figure out which chemical is out of balance, and then how to restore that.


Senior Member
United States, New Hampshire
Encouraging they see something. But is this a dead end for treatment? Have they ever suggested a possible remedy of any kind?
This looks to me like they are saying, basically, the brain isn't working right in the areas they mention. It doesn't look like they are saying this a structural issue but maybe a blood flow issue. It might be inflammation causing it, as Jarred Younger has found.

Jarred Thinks that the brain inflammation and issues are caused by immune activation from the body. He is doing a study this year to see if B and T cells from the body are getting into the brain and causing this inflammation.

He says they shouldn't be able to get through the blood brain barrier, unless it's compromised and more "leaky" than it should be. If he finds these B or T cells from the body are causing the brain issues.

He's going to try to trace the B and T cells back to where they originate in the body, which could be the actual cause of CFS. That would allow very focused research into treatment of the actual cause of CFS.


Senior Member
Jarred Thinks that the brain inflammation and issues are caused by immune activation from the body. He is doing a study this year to see if B and T cells from the body are getting into the brain and causing this inflammation.
This made me think: It would be interesting to know if mast cells play a role here (mast cells on the brain side also regulate the BBB). Would this make sense at all, i.e. could (dysregulated) mast cells explain this connectivity problem and the inflammation Jarred Younger found?


Senior Member
Did they say what type of connectivity they measured in this study? According to this Wikipedia article,
Connectivity can be considered at different levels of the brain's organisation: from neurons, to neural assemblies and brain structures.
So connectivity can mean anything from neuron to neuron connections, to long-distance pathways between different areas of the brain.