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Dutch Connectome Lab
Installation
Download
Installation executable
Installation MATLAB Toolbox
Installation additional software
Getting started
How to use CATO
Docker
Running a subject again
Parameters
Examples
Structural processing example
Functional processing example
BIDS formatted data
fMRI preprocessing with Melodic + Fix
Cortical reconstruction with FreeSurfer
Structural pipeline
Structural preprocessing
Anatomical steps
Reconstruction diffusion
Reconstruction fibers
Reconstruction fiber properties
Network reconstruction
Functional pipeline
Preprocessing
Anatomical steps
Compute motion metrics
Network reconstruction
Structural configuration
general step
structural_preprocessing step
parcellation step
collect_region_properties step
reconstruction_diffusion step
reconstruction_fibers step
reconstruction_fiber_properties step
reconstruction_network step
Functional configuration
general step
functional_preprocessing step
parcellation step
collect_region_properties step
compute_motion_metrics step
reconstruction_functional_network step
Configuration Assistant
References
Citing CATO
Bibliography
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
A
acqpFactor
acqpFile
B
bandpass_filter.filter
bandpass_filter.frequencies
bValueScalingTol
bValueZeroThreshold
C
computedConfigFile
,
[1]
connectivityMatrixFile
,
[1]
CSD.CCRegions
CSD.FAThreshold
CSD.lambda
CSD.maxPeaks
CSD.minPeakRatio
CSD.outputPeaks
CSD.shOrder
CSD.tau
D
diffusionMeasuresFile
diffusionPeaksFile
DTI.thresCondNum
DTI.thresVarProjScores
dwiB0ReversedFile
dwiFile
dwiProcessedFile
dwiReferenceFile
dwiReversedFile
E
eddyVersion
exportNifti.diffusionMeasuresFileNifti
exportNifti.exportNifti
exportNifti.measures
F
fiberFile
fiberPropertiesFile
fmriFile
fmriInfo
fmriProcessedFile
fmriReferenceFile
forbiddenRegions
forceFreesurferOverwrite
,
[1]
freesurferDir
,
[1]
freesurferRootDir
,
[1]
fslRootDir
,
[1]
G
general.FAMeasure
GQI.maxPeaks
GQI.meanDiffusionDistanceRatio
GQI.minPeakRatio
GQI.outputPeaks
gradientNonlinearities.correctNonlinearities
gradientNonlinearities.nonlinearitiesFile
I
includeGMVoxelsFlag
indexFile
L
logFile
,
[1]
lutFile
,
[1]
M
matchROIs
,
[1]
maxAngleDeg
,
[1]
maxFiberRadius
maxMemoryGB
maxNumberCompThreads
,
[1]
MCRDIR
methodDescription
minFA
,
[1]
minLengthMM
minRepetitionTime
motionMetricsFile
motionParametersFile
N
NumberOfSeedsPerVoxel
O
outputDir
,
[1]
P
PARAM1 VAL1 name-value pair arguments
parameterPropertiesFile
parcellationFile
,
[1]
preprocessingScript
,
[1]
processedBvalsFile
processedBvecsFile
R
rawBvalsFile
rawBvecsFile
reconstructionMethod
reconstructionMethods
reconstructionSteps
,
[1]
regionPropertiesFile
,
[1]
registrationMatrixFile
,
[1]
regression.globalMeanRegression
regression.regressionMask
revPhaseEncDim
ROIsFile
,
[1]
S
saveTimeSeries
scrubbing.backwardNeighbors
scrubbing.forwardNeighbors
scrubbing.maxDVARS
scrubbing.maxFD
scrubbing.minViolations
scrubbing.scrubbing
segmentationFile
,
[1]
sliceTimerOptions
sliceTimingCorrection
startRegions
statsLhFile
,
[1]
statsRhFile
,
[1]
statsSubFile
,
[1]
statusFile
,
[1]
STEP
stopRegions
SUBJECTDIR
T
templates
,
[1]
templateScript
,
[1]
templatesDir
,
[1]
timeSeriesFile