#####################################################################################################################################
# Data description for the manuscript "A test-retest reliability analysis of diffusion measures of white matter tracts relevant for #
#	cognitive control" by Boekel, Keuken and Forstmann. 									    #
#																    #
# For any questions regarding the data please contact w.e.boekel@uva.nl or mckeuken@gmail.com			   		    #
#																    #
#####################################################################################################################################

##################
# Folder structure:
##################
	"subject number"
		 "subject number" _ "scan type" _ "scan session"

##################
# The MRI scans that are made available are:
##################
	- b0 	(magnitude (de-faced) and phase)
	- t1 	(de-faced)
	- dwi 	(4 runs per scan session)	
			each run contains 34 volumes:
				volume 1: B0
				Volume 2-33: the 32 directions
				Volume 34: the isotropic weighted average of the diffusion directions (phillips specific)
##################
# The MRI scan parameters are:
# (The scan parameters are taken from https://www.spinozacentre.nl/wiki/index.php/NeuroWiki:Sequences)
##################
# b0:
	Scan technique		3D-FFE, multishot FFE
	Duration			108 seconds
	profile 			Linear
	turbo direction		Z
	TE					3 ms
	TR					11 ms
	delta-TE			5
	FA					8
	Sense P (RL)		2.5
	Sense S (FH)		2
	slices				128
	FOV					256x208x256
	Voxel size			2^3 mm
	matrix				128
	Foldover			RL
	Fat shift			P
	Water fat shift 	1.13 Pixels
	Bandwidth			383 Hz
	TFE Factor			90
	TFE shots			44
##################
# t1:
	Scan technique		3DFFE, multishot TFE
	Duration			3.06 minutes
	profile 			linear
	turbo direction		Z
	TR					8.2
	TE					3.8
	FA					8
	Sense P (RL)		2.5
	Sense S (FH)		2
	slices				220
	FOV					240*188
	Voxel size			1^3 mm
	matrix				240
	Foldover			RL
	Fat shift			P
	Water fat shift 	2,269 pixel
	Bandwidth			191.4 Hz
	TFE Factor			154
	TFE shots			78
	Shot interval		2375
	slice orientation	TRA
	NR of averages		2
##################
# dwi:
	Scan technique		MS-SE, single shot DWI
	Duration			5.3 minutes
	TR					7542
	TE					86
	FA					90
	SENSE (AP)			2
	slices				60
	FOV					224*224
	Voxel size			2^3 mm
	Slice gap			0
	matrix				112
	Foldover			AP
	Fat shift			A
	Dyn Stab			Yes
	Prepation			Full
	Water fat shift		13.5
	Bandwidth			32.1
	EPI Factor			59
	Fat supression		SPIR
	frequency offset	250
	gradient duration	maximum
	NR of directions	32
	b value				1000
	gradient mode		default
##################

##################
# NOTES
##################
	Due to technical issues, for subject "pp06", we were unable to succesfulyl acquire the B0 image in the 2W session.

	Subject "pp20" - "pp34"  were part of a new batch of subjects, in which the extra T1 measurements were dropped to 
		optimize total scan duration since a single t1 image was sufficient for registration purposes.
	
	The t1 and b0 magnitude volumes per subject were "de-faced" using the "MRI_deface" tool as described in Bischoff-Grethe 
		et al. (2007). A technique for the deidentification of structural brain MR images. Human Brain Mapping, 28(9): 
		892-903.