cobidas_mri

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	W	X	Z
1	0	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	22	23	25
2	row_formating	row_formating	activity_order	include	neurovault_or_carp	mandatory	activity	activity_pref_label	activity_description	activity_preamble						item	question	details	choices

3	FALSE	FALSE	1	1	0	1	experimental_design	Experimental Design	Experimental Design		Design specifications	Design type	rest or task			rest_or_task	Was it task based MRI or resting state MRI?
4	TRUE	TRUE	1	1	0	1	experimental_design	Experimental Design	Experimental Design		Design specifications	Length of the experiment	total scanning time			total_scanning_time	What was the total scanning time?	Important to assess subject fatigue. If differing by subject, specify summary statistics (ean, range and/or standard deviation)
5	TRUE	TRUE	1	1	1	1	experimental_design	Experimental Design	Experimental Design		Design specifications	Design optimization used				design_optimization_used	Was the design efficiency optimized?
6	TRUE	TRUE	1	1	1	0	experimental_design	Experimental Design	Experimental Design		Design specifications	Design optimization method				design_optimization_method	What method was used for optimization?
7	TRUE	FALSE	1	1	0	1	experimental_design	Experimental Design	Experimental Design		Task specification	Scanner synchronisation				scanner_synchronisation	How was the equipment was synched to the scanner?		scanner TTL \| manual synch
8	TRUE	FALSE	1			0	experimental_design	Experimental Design	Experimental Design		Power analysis	Power analysis used				power_analysis_used
9	TRUE	TRUE	1	0	0	1	experimental_design	Experimental Design	Experimental Design		Power analysis	Power analysis parameters	Effect size			effect_size	Effect size used for the power calculation (magnitude and standard deviation)
10	TRUE	TRUE	1	0	0	1	experimental_design	Experimental Design	Experimental Design		Power analysis	Power analysis parameters	Outcome			outcome	The type of outcome used as the basis of power computations		signal in a prespecified ROI \| signal in a whole image voxelwise \| signal in a whole image clusterwise \| signal in a whole image peakwise
11	TRUE	TRUE	1	0	0	1	experimental_design	Experimental Design	Experimental Design		Power analysis	Power analysis parameters	Source of predicted effect size			source_of_predicted_effect_size	Source of predicted effect size	previous literature with citation; pilot data with description
12	TRUE	TRUE	1	0	0	1	experimental_design	Experimental Design	Experimental Design		Power analysis	Power analysis parameters	Significance level			significance_level	Significance level	uncorrected alpha 0.05 for an ROI \| FWEcorrected alpha 0.05	uncorrected alpha 0.05 for an ROI \| FWEcorrected alpha 0.05
13	TRUE	TRUE	1	0	0	1	experimental_design	Experimental Design	Experimental Design		Power analysis	Power analysis parameters	Target power			target_power	Target power
14	TRUE	TRUE	1	0	0	1	experimental_design	Experimental Design	Experimental Design		Power analysis	Power analysis parameters	Other power analysis parameters			other_power_analysis_parameters	Any other parameters set (e.g. for spatial methods a brain volume and smoothness may be needed to be specified)
15	FALSE	FALSE	2	0	0	0	acquisition	Acquisition	Acquisition		Subject preparation	Mock scanning	Mock scanning used			mock_scanning_used	Was an MRI simulator used to acclimate subjects to scanner environment?
16	TRUE	TRUE	2			0	acquisition	Acquisition	Acquisition		Subject preparation	Mock scanning	Mock scanning description			mock_scanning_description	Report type of mock scanner and protocol (i.e. duration, types of simulated scans, experiments)
17	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		Subject preparation	Special accommodations				special_accommodations		For example, for pediatric scanning, presence of parent/guardian in the room
18	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		Subject preparation	Experimenter personnel				experimenter_personnel	How many experimenters interacted with the participants?
19	TRUE	FALSE	2	1	1	1	acquisition	Acquisition	Acquisition		MRI system description	Scanner	make			make	Manufacturer of MRI scanner		Siemens \| Philips \| General Electric
20	TRUE	TRUE	2	1	1	1	acquisition	Acquisition	Acquisition		MRI system description	Scanner	model			model	Model of MRI scanner
21	TRUE	TRUE	2	1	1	1	acquisition	Acquisition	Acquisition		MRI system description	Scanner	field strength			field_strength	Field strength of MRI scanner (in Tesla)
22	TRUE	TRUE	2	1	0	1	acquisition	Acquisition	Acquisition		MRI system description	Coil	receive coil			receive_coil	What type of receive coil was used?		standard: receive coil \| non-standard openfield
23	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		MRI system description	Coil	transmit coil			transmit_coil
24	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		MRI system description	Coil	gradient			gradient
25	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		MRI system description	Coil	other			other
26	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		MRI system description	Significant hardware modifications				significant_hardware_modifications		For example, special gradient inserts/sets
27	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		MRI system description	Software version				software_version		Highly recommended when sharing vendor-specific protocols or exam cards, as version may be needed to correctly interpret that information
28	TRUE	FALSE	2	1	1	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Functional MRI	number of volumes		number_of_volumes	Specify the number of volumes
29	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Functional MRI	Sparse sampling delay		sparse_sampling_delay		(delay in TR) if used
30	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	B0 field maps	Echo time difference		echo_time_difference		(dTE)
31	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Diffusion MRI	Number of directions		number_of_directions
32	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Diffusion MRI	Direction optimization, if used and type		direction_optimization,_if_used_and_type	Was direction optimization used?
33	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Diffusion MRI	B-values		b-values
34	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Diffusion MRI	Number of b=0 images		number_of_b=0_images
35	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Diffusion MRI	Number of averages (if any)		number_of_averages_(if_any)
36	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Diffusion MRI	Single shell, multishell (specify equal or unequal spacing)		single_shell,_multishell_(specify_equal_or_unequal_spacing)			Single shell \| multishell (specify equal or unequal spacing)
37	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Diffusion MRI	Single or dual-spin-echo, gradient mode (serial or parallel)		single_or_dual-spin-echo,_gradient_mode_(serial_or_parallel)			Single or dual-spin-echo \| gradient mode (serial or parallel)
38	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Essential sequence and imaging parameters	Diffusion MRI	Cardiac gating		cardiac_gating	Was cardiac gating used?
39	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Scanner-side preprocessing				scanner-side_preprocessing		Reconstruction matrix size differing from acquisition matrix size
40	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Scanner-side preprocessing	prospective moco used			prospective_moco_used	Was prospective motion correction used?
41	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Scanner-side preprocessing	prospective moco param			prospective_moco_param	Describe the prospective motion correction (details of any optical tracking, how motion parameters are used, ...
42	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Scanner-side preprocessing	signal inhomogeneity correction used			signal_inhomogeneity_correction_used	Was there signal inhomogeneity correction?
43	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Scanner-side preprocessing	signal inhomogeneity correction param			signal_inhomogeneity_correction_param	Describe the signal inhomogeneity correction
44	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Scanner-side preprocessing	distortion correction used			distortion_correction_used	Was distortion-correction applied?
45	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		MRI acquisition	Scan duration				scan_duration		In seconds
46	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		MRI acquisition	Other nonstandard procedures				other_nonstandard_procedures		Turning off the cold head(s) (e.g. during EEG/fMRI or spectroscopy measurements)
47	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		MRI acquisition	Other nonstandard procedures				other_nonstandard_procedures		Reduce sound pressure by limiting the gradient slew rate
48	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		MRI acquisition	Diffusion MRI gradient table				diffusion_mri_gradient_table		Also referred to as the bmatrix (but not to be confused with the 3×3 matrix that describes diffusion weighting for a single diffusion weighted measurement)
49	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	All acquisitions	Labelling method	labelling_method			continuous ASL (CASL) \| pseudo-continuous ASL (PCASL) \| Pulsed ALS (PASL) \| velocity selective ASL (VSASL)
50	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	All acquisitions	Use of background suppression pulses and their timing	use_of_background_suppression_pulses_and_their_timing
51	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PCASL or CASL	Label Duration	label_duration
52	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PCASL or CASL	Post-labeling delay (PLD)	post-labeling_delay_(pld)
53	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PCASL or CASL	Location of the labelling plane	location_of_the_labelling_plane
54	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PCASL	Average labelling gradient	average_labelling_gradient
55	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PCASL	Slices elective labeling gradient	slices_elective_labeling_gradient
56	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PCASL	Flip angle of B1 pulses	flip_angle_of_b1_pulses
57	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PCASL	Assessment of inversion efficiency; QC used to ensure off-resonance artifacts not problematic, signal obtained over whole brain	assessment_of_inversion_efficiency;_qc_used_to_ensure_off-resonance_artifacts_not_problematic,_signal_obtained_over_whole_brain
58	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	CASL	Use of a separate labelling coil	use_of_a_separate_labelling_coil
59	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	CASL	Control scan/pulse used	control_scan/pulse_used
60	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	CASL	B1 amplitude	b1_amplitude
61	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PASL	PASL-TI	pasl-ti
62	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PASL	Labelling slab thickness	labelling_slab_thickness
63	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	PASL	Use of QUIPSS pulses and their timing	use_of_quipss_pulses_and_their_timing
64	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	VSASL	VSASL-TI	vsasl-ti
65	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Arterial Spin Labelling MRI	VSASL	Choice of velocity selection cutoff (“VENC”)	choice_of_velocity_selection_cutoff_(“venc”)
66	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Dynamic Susceptibility Contrast MRI	Number of baseline volumes		number_of_baseline_volumes		Number of baseline volumes
67	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Dynamic Susceptibility Contrast MRI	Type, name and manufacturer of intravenous bolus		type,_name_and_manufacturer_of_intravenous_bolus		e.g. gadobutrol, Gadavist, Bayer	Type \| name and manufacturer of intravenous bolus (e.g. gadobutrol \| Gadavist \| Bayer)
68	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Dynamic Susceptibility Contrast MRI	Bolus amount and concentration		bolus_amount_and_concentration		e.g. 0.1 ml/kg and 0.1 mmol/kg	Bolus amount \| bolus concentration
69	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Dynamic Susceptibility Contrast MRI	Injection rate		injection_rate		e.g. 5 ml/s
70	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Dynamic Susceptibility Contrast MRI	Post-injection of saline		post-injection_of_saline		e.g. 20 ml
71	TRUE	TRUE	2	0	0	1	acquisition	Acquisition	Acquisition		MRI acquisition	Perfusion	Dynamic Susceptibility Contrast MRI	Injection method		injection_method		e.g. power injector
72	TRUE	FALSE	2	0	1	1	acquisition	Acquisition	Acquisition		Preliminary quality control	Motion monitoring				motion_monitoring		For functional or diffusion acquisitions, any visual or quantitative checks for severe motion; likewise, for structural images, checks on motion or general image quality
73	TRUE	TRUE	2	0	0	0	acquisition	Acquisition	Acquisition		Preliminary quality control	Incidental findings				incidental_findings		Protocol for review of any incidental findings, and how they are handled in particular with respect to possible exclusion of a subject’s data
74	FALSE	FALSE	3	0	0	1	preprocessing	Preprocessing	Preprocessing		single preprocessing software					single_preprocessing_software	Was a single software package was used for preprocessing?
75	TRUE	FALSE	3	1	1	1	preprocessing	Preprocessing	Preprocessing		preprocessing software					preprocessing_software	If a single software package was used for all analyses, specify that here
76	TRUE	FALSE	3	1	1	0	preprocessing	Preprocessing	Preprocessing		preprocessing software version					preprocessing_software_version	Version of software package used
77	TRUE	FALSE	3	0	0	0	preprocessing	Preprocessing	Preprocessing		Software citation					software_citation		Include URL and Research Resource Identifier for each software used	Indicate software - URL \| Research Resource Identifier for each software used
78	TRUE	FALSE	3	0	0	0	preprocessing	Preprocessing	Preprocessing		Steps					steps	What preprocessing steps were performed?		realign \| slice time correction \| brain extraction \| normalization \| smoothing
79	TRUE	FALSE	3	1	1	0	preprocessing	Preprocessing	Preprocessing		Operation performed					operation_performed	Specify which preprocessing steps were performed		brain extraction \| anatomical image segmentation \| realignment \| slice timing correction \| functional-anatomical coregistration \| normalization (intersubject coregistration) \| smoothing
80	TRUE	FALSE	3	1	1	0	preprocessing	Preprocessing	Preprocessing		Order of operation					order_of_operation	Specify order of preprocessing operations
81	TRUE	FALSE	3	1	1	1	preprocessing	Preprocessing	Preprocessing		T1 stabilization					t1_stabilization	number of “dummy” scans discarded if any
82	TRUE	FALSE	3	1	0	1	preprocessing	Preprocessing	Preprocessing		Brain extraction	BET software				bet_software	Software used for the brain extraction	also skull-stripping
83	TRUE	TRUE	3	1	0	1	preprocessing	Preprocessing	Preprocessing		Brain extraction	BET version				bet_version	Software version used for the brain extraction
84	TRUE	TRUE	3	1	0	0	preprocessing	Preprocessing	Preprocessing		Brain extraction	BET method				bet_method	Method used for the brain extraction	e.g., BET, recon-all in FreeSurfer...
85	TRUE	TRUE	3	1	0	1	preprocessing	Preprocessing	Preprocessing		Brain extraction	BET parameters				bet_parameters	Parameters used for the brain extraction	e.g. BET’s fractional intensity threshold
86	TRUE	TRUE	3	1	0	1	preprocessing	Preprocessing	Preprocessing		Brain extraction	BET manual edit				bet_manual_edit	Describe any eventual manual editing done to the brainmask.
87	TRUE	FALSE	3	1	0	1	preprocessing	Preprocessing	Preprocessing		Segmentation	segmentation software				segmentation_software	Software used for segmentation
88	TRUE	TRUE	3	1	0	1	preprocessing	Preprocessing	Preprocessing		Segmentation	segmentation version				segmentation_version	Software version used for the segmentation
89	TRUE	TRUE	3	1	0	1	preprocessing	Preprocessing	Preprocessing		Segmentation	segmentation method				segmentation_method	Method used for segmentation	For structural images, method used to extract gray, white, CSF and other tissue classes
90	TRUE	TRUE	3	1	0	1	preprocessing	Preprocessing	Preprocessing		Segmentation	segmentation parameters				segmentation_parameters	What parameters were used for the segmentation?
91	TRUE	FALSE	3	1	1	1	preprocessing	Preprocessing	Preprocessing		Slice time correction	STC software				stc_software	Software used for slice timing	Slice timING correction
92	TRUE	TRUE	3	1	0	0	preprocessing	Preprocessing	Preprocessing		Slice time correction	STC version				stc_version	Software version used for slice timing	Slice timING correction
93	TRUE	TRUE	3	1	0	0	preprocessing	Preprocessing	Preprocessing		Slice time correction	STC method				stc_method	Method used for the slice timing	Slice timING correction
94	TRUE	TRUE	3	1	1	1	preprocessing	Preprocessing	Preprocessing		Slice time correction	STC reference				stc_reference	What slice was used as reference for the slice timing?	Slice timING correction
95	TRUE	TRUE	3	1	1	1	preprocessing	Preprocessing	Preprocessing		Slice time correction	STC interpolation				stc_interpolation	Interpolation method used for the slice timing	Slice timING correction
96	TRUE	FALSE	3	1	1	1	preprocessing	Preprocessing	Preprocessing		Motion correction	moco software				moco_software	Software used for the motion correction
97	TRUE	TRUE	3	1	0	0	preprocessing	Preprocessing	Preprocessing		Motion correction	moco version				moco_version	Software version used for the motion correction
98	TRUE	TRUE	3	1	0	1	preprocessing	Preprocessing	Preprocessing		Motion correction	non-rigid registration				non-rigid_registration	Was non-rigid registration applied?
99	TRUE	TRUE	3	1	1	0	preprocessing	Preprocessing	Preprocessing		Motion correction	moco dof				moco_dof	Number of degrees of freedom for the motion correction		6 (rigid body transformation)
100	TRUE	TRUE	3	1	1	1	preprocessing	Preprocessing	Preprocessing		Motion correction	motion-susceptibility correction used				motion-susceptibility_correction_used	Was motion-susceptibility correction used?