Review Paper: Reporting Practices for Task fMRI Studies

Abstract

What are the standards for the reporting methods and results of fMRI studies, and how have they evolved over the years? To answer this question we reviewed 160 papers published between 2004 and 2019. Reporting styles for methods and results of fMRI studies can differ greatly between published studies. However, adequate reporting is essential for the comprehension, replication and reuse of the study (for instance in a meta-analysis). To aid authors in reporting the methods and results of their task-based fMRI study the COBIDAS report was published in 2016, which provides researchers with clear guidelines on how to report the design, acquisition, preprocessing, statistical analysis and results (including data sharing) of fMRI studies (Nichols et al. in Best Practices in Data Analysis and Sharing in Neuroimaging using fMRI, 2016). In the past reviews have been published that evaluate how fMRI methods are reported based on the 2008 guidelines, but they did not focus on how task based fMRI results are reported. This review updates reporting practices of fMRI methods, and adds an extra focus on how fMRI results are reported. We discuss reporting practices about the design stage, specific participant characteristics, scanner characteristics, data processing methods, data analysis methods and reported results.

Appendices

Appendix A. Table with overview of all variables that were registered

Identification	PubMedID	ID of the publication on PubMed
	pub_year	Year of publication
	Title	Title of the pulication
	include?	Do we include this paper, and if not, relevant exclusion criterium
Design	Design	Is the design paradigm described?
	Type of design	Block/event related
	Optimalisation	Was the design optimized? For instance, were the stimuli jittered? (0 = no, 1 = yes)
	Multiple experiments?	Was more than one experiment included in the paper? (0 = no, 1 = yes)
	Was this the main experiment?	Was the fMRI experiment and univariate approach the main focus of the paper? (0 = no, 1 = yes)
Study characteristics	N	Number of participants
	Gender v	Number of female participants
	Gender m	Number of male participants
	Ratio gender	If equal or close to 1 = balance, > 1 more women, < 1 more men
	Exclusion crit	Are the exclusion criteria for participants clearly described in the paper? (0 = no, 1 = yes)
Scanning	T	Field strength of the scanner in Tesla (list: 1.5, 3, 4, 7)
	Whole brain meas	Was the whole brain scanned? (0 = no, 1 = yes)
	Vox res	Voxel resolution (number x number x number in mm)
	Image dim	Dimensions of the scanned image (number x number x number in voxels)
Processing the data	Software	Software + version number
	Motion correction	Mentioned? 0 = no, 1 = mentioned, 2 = clearly described and can be reproduced
	Registration	Mentioned? 0 = no, 1 = mentioned, 2 = clearly described and can be reproduced
	Spatial Filtering	Mentioned? 0 = no, 1 = mentioned, 2 = clearly described and can be reproduced
	Temporal Filtering	Mentioned? 0 = no, 1 = mentioned, 2 = clearly described and can be reproduced
	Preprocessing	Score for how well the preprocessing has been described, sum of previous three
	Coordinate space	Which coordinate space was used?
	Smoothing (FWHM)	FWHM of the smoothing kernel (number)
Data analysis	HRF model	Is the HRF model mentioned? (0 = no, 1 = yes)
	HRF model	If yes, which model was used for the HRF (text)
	Contrast	Was the contrast clearly described? (0 = no, 1 = yes)
	Contrast scale	Was the scaling of the contrast reported? (0 = no, 1 = yes)
	Predictor scaling	Was the scaling of the predictors reported? (0 = no, 1 = yes)
	Contrast group level	Is the interpretation of contrast estimates at group level clear? (0 = no, 1 = yes)
	Participant analysis	What is the statistical model and estimation method used for the first level?
	Group analysis	What is the statistical model and estimation method used for the group analysis?
	Inference method	Cluster, peak, … NA if not mentioned
	Inf spec	Specific details about the inference method
	Cluster forming threshold	In case of topological inference, was cluster forming threshold specified? (give values)
	Thresholding method	Which method was used, what was the threshold? (NA if not mentioned)
Reporting	Whole brain	Were results analyzed and reported on whole brain level? (0 = no, 1 = yes)
	Standardized effect size	Are maps with standardized effect sizes available? (0 = no, 1 = yes)
	Stat maps	Are statistical maps available? (0 = no, 1 = yes)
	Share maps	How were the maps shared? (after e-mail, in which database, …)
	test statistic	Is a z/t/F-map shared? (0 = no, 1 = yes)
	contrast/parameter estimates	(0 = no, 1 = yes)
	standard errors	(0 = no, 1 = yes)
	Peak stat	Were local maxima with statistical value shared? (0 = no, 1 = yes)
	peak	Were only the local maxima shared? (0 = no, 1 = yes)
	Data after e-mail	Was the data available after an e-mail was sent to the authors? (0 = no, 1 = for collaboration, 2 = could be made publicly available, -1 cant reach author)

Appendix B. Frequency of use of analysis software

Software	2004	2005	2006	2007	2008	2009	2010	2011	2012	2013	2014	2015	2016	2017	2018	2019
AFNI	3	0	0	1	1	1	1	1	2	0	2	1	0	0	1	2
BrainVoyager	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
BrainVoyager 2000	1	2	1	1	0	1	1	0	0	0	0	0	0	0	0	0
BrainVoyager 4.8	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
BrainVoyager QX	0	0	1	1	2	1	0	0	1	1	0	1	0	0	0	1
Own software	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
FSL	0	0	0	1	3	3	0	2	1	3	1	2	2	1	4	1
IDL	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
MATLAB	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	2
MEDx3.2	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
NA	0	2	0	0	0	0	0	0	0	0	0	0	1	0	0	0
SPM	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
SPM12	0	0	0	1	0	0	0	0	0	0	0	0	0	2	2	4
SPM2	0	0	2	0	3	4	4	1	0	1	2	0	0	1	0	0
SPM5	0	0	0	0	0	0	1	4	2	0	2	2	3	1	0	0
SPM8	0	0	0	0	0	0	1	1	3	4	3	4	5	5	3	3
SPM99	6	4	6	3	1	0	1	0	1	0	0	0	0	0	0	0
XBAM	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0