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Welcome to the PanLab HCP Pipelines wiki! Forked from WashU ~Nov 16

Settings

Pre FreeSurfer: AvgrdcSTRING="NONE" TE="2.46" T1wSampleSpacing="0.000011999" # For General Electric scanners, 1/((0018,0095)(0028,0010)) T2wSampleSpacing="0.000008000" # For General Electric scanners, 1/((0018,0095)(0028,0010)) Tempaltes: Use .8mm MNI templates Brain Size = 150 FreeSurfer

No changeable settings

Post FreeSurfer

GrayordinatesResolutions="2" #Usually 2mm, but will we need to change this since our functionals are 2.46
HighResMesh="164" #Usually 164k vertices
LowResMeshes="32" #Usually 32k vertices, if multiple delimit with @, must already exist in templates dir
SubcorticalGrayLabels="${HCPPIPEDIR_Config}/FreeSurferSubcorticalLabelTableLut.txt"
FreeSurferLabels="${HCPPIPEDIR_Config}/FreeSurferAllLut.txt"
ReferenceMyelinMaps="${HCPPIPEDIR_Templates}/standard_mesh_atlases/Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii"
RegName="MSMSulc" #MSMSulc is recommended

Generic Volume:

DwellTime= ".001600"  #Echo Spacing or Dwelltime of fMRI image, set to NONE if not 
used. Dwelltime = 1/(BandwidthPerPixelPhaseEncode * # of phase encoding samples): DICOM field (0019,1028) = 
BandwidthPerPixelPhaseEncode, DICOM field (0051,100b) AcquisitionMatrixText first value (# of phase encoding 
samples).  

DistortionCorrection="TOPUP" # TOPUP is recommended, though there are GE specific options

FinalFMRIResolution="2" #Marked by an if statement for 1 or 2-- stick with 2 but investigate the resolution of 
mni space.  #Target final resolution of fMRI data. 2mm is recommended for 3T 
HCP data, 1.6mm for 7T HCP data (i.e. should match acquired resolution).  Use 2.0 or 1.0 to avoid standard FSL 
templates

GradientDistortionCoeffs="NONE", not as big an issue with GE scanners, or so was told by Adam and Hua. 

BiasCorrection="NONE" #Outdated and not used in Lifespan. Cut the scans necessary for this in early iterations

Generic Surface Volume:

LowResMesh="32" #Needs to match what is in PostFreeSurfer, 32 is on average 2mm spacing between the vertices 
on the midthickness

FinalfMRIResolution="2" #Needs to match what is in fMRIVolume, i.e. 2mm for 3T HCP data and 1.6mm for 7T HCP 
data

SmoothingFWHM="2" #Recommended to be roughly the grayordinates spacing, i.e 2mm on HCP data

GrayordinatesResolution="2" #Needs to match what is in PostFreeSurfer. 2mm gives the HCP standard 
grayordinates space with 91282 grayordinates.  Can be different from the FinalfMRIResolution 

RegName="MSMSulc" #MSMSulc is recommended

Task fMRI

critical_z: based on design matrix, estimated
dwell time: for pre-stat analysis, defaults to .7, not relevant for PanLab use
highpass temporal filtering: 200 default in connectome, will continue to use 200