Data acquired to investigate new approaches to cerebrovascular reactivity mapping using 
MRI

The data in this archive was acquired to investigate several new approaches to 
cerebrovascular reactivity mapping using MRI and will form the basis of forthcoming
publications. Please reference this dataset if you use it in your work.

Blockley NP, Harkin JW, Stone AJ, Bulte DP. Data acquired to investigate new approaches to
cerebrovascular reactivity mapping using MRI. Oxford University Research Archive 2017. 
doi: <Please see ORA entry for DOI>

Data sets consist of (in order of acquisition):
	1. Single post-labelling delay PCASL during a hypercapnia block paradigm
	2. Multiple post-labelling delay PCASL at steady state normocapnia 
	3. Multiple post-labelling delay PCASL at steady state hypercapnia
	4. Single TE BOLD-weighted imaging with Toronto hypercapnia block protocol
	5. Single TE BOLD-weighted imaging with Sinusoidal hypercapnia protocol
	6. Multiple Tau value R2'-weighted imaging with GASE acquisition
	7. High resolution T1-weighted anatomical imaging
	8. Respiratory data including end-tidal O2 and CO2
	9. Pre-scan resting physiological data
	
Images are encoded as compressed NIFTI files and contain basic information about voxel
size, repetition time and orientation. Further information is contained in a JSON file, 
which is both human and machine readable. These files are inherited by image files at 
lower levels of the directory structure unless they are overridden by a file at the lower 
level. In this way the data structure follows the Brain Imaging Data Structure (BIDS) 
version 1.0.0-rc2. 

Single post-labelling delay PCASL

Pseudo-Continuous Arterial Spin Labelling (PCASL) with a single post-labelling delay was 
used to investigate a dynamic hypercapnia stimulus. In addition ASL weighted images were 
interleaved with BOLD weighted images to provide a complementary CVR measure. Images are 
stored at tag-control ASL images, BOLD images and an ASL calibration. The stimulus
consisted of alternating 2 minute blocks of baseline normocapnia and hypercapnia, defined 
as baseline end-tidal CO2 (PetCO2) +10mmHg. End-tidal O2 (PetO2) was targetted to be 
maintained constant at the subjects individual baseline level.

Multiple post-labelling delay PCASL

Multiple post-labelling delay PCASL was used to measure perfusion at two steady state 
levels: normocapnia and hypercapnia. The former based on the individuals baseline PetCO2
and the latter based on the baseline +10mmHg. Again PetO2 was targetted to be maintained
constant throughout.

Single TE BOLD

A standard BOLD fMRI protocol was used to investigate BOLD CVR using two different 
protocols: Toronto and Sinusoid. The Toronto protocol is a commonly used protocol by the 
research group in Toronto, Canada (1), whilst the Sinusoid protocol was based on our own
previous work (2).

R2'-weighted GASE data

R2'-weighted GESEPI Asymmetric Spin Echo data were acquired to act as an estimate of the
calibrated BOLD scaling parameter M via a measurement of R2' (3). The GESEPI acquisition
was implemented to prospectively correct for macroscopic magnetic field gradients which
would otherwise result in overestimates of R2' and thus M (4).

High resolution anatomical

T1-weighted MPRAGE images were acquired for tissue segmentation and registration to 
standard space.

Respiratory data

End-tidal gas concentrations were measured by gas analysers within the RespirAct Gen 3
used in this study (Thornhill Research Inc., Toronto, Canada). Within each subject folder
this information is provided in the following format. Firstly, a list of events 
(*_events.tsv) is provided with start and finish times in minutes. Secondly, breath by 
breath estimates (*_bbb.tsv) of end-tidal CO2 and O2 are provided alongside time in
minutes. Finally, the full raw data (*_raw.tsv) are provided alongside time in minutes
and the pressure change from a sampling tube at the mouth (Pmouth).

Pre-scan physiological data

Prior to the scan basic physiological information was acquired (participants.tsv). This 
included pulse rate (PR), arterial oxygen saturation (spO2) and total haemoglobin 
concentration (spHb) all measured non-invasively using a Pronto-7 pulse oximeter 
(Masimo, California). The atmospheric pressure (Patm) at the time of the scan session was 
recorded for reference. Finally, the subjects self-reported weight (kg) and height (m) 
were recorded.

Full pulse sequence protcol

A PDF copy of the entire pulse sequence protocol is included for reference and includes 
parameters not included in BIDS metadata.

References

1. Spano VR, Mandell DM, Poublanc J, Sam K, Battisti-Charbonney A, Pucci O, Han JS, 
   Crawley AP, Fisher JA, Mikulis DJ. CO2 Blood Oxygen Level-dependent MR Mapping of 
   Cerebrovascular Reserve in a Clinical Population: Safety, Tolerability, and Technical 
   Feasibility. Radiology 2012;266:592–598. doi: 10.1148/radiol.12112795. 
2. Blockley NP, Driver ID, Francis ST, Fisher JA, Gowland PA. An improved method for 
   acquiring cerebrovascular reactivity maps. Magn. Reson. Med. 2010;65:1278–1286. 
   doi: 10.1002/mrm.22719.
3. Blockley NP, Griffeth VEM, Simon AB, Dubowitz DJ, Buxton RB. Calibrating the BOLD 
   response without administering gases: Comparison of hypercapnia calibration with 
   calibration using an asymmetric spin echo. Neuroimage 2015;104:423–429. 
   doi: 10.1016/j.neuroimage.2014.09.061.
4. Blockley NP, Stone AJ. Improving the specificity of R2' to the deoxyhaemoglobin content
   of brain tissue: Prospective correction of macroscopic magnetic field gradients. 
   Neuroimage 2016;135:253–260. doi: 10.1016/j.neuroimage.2016.04.013.
