.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.5.
.TH TIMESCCAN "1" "October 2017" "TimeSCCAN 2.2.0" "User Commands"
.SH NAME
TimeSCCAN \- part of ANTS registration suite
.SH DESCRIPTION
.SS "COMMAND:"
.IP
TimeSCCAN
.IP
A tool for sparse statistical analysis on connectivity within a subject :
.SS "OPTIONS:"
.HP
\fB\-h\fR
.IP
Print the help menu (short version).
.HP
\fB\-\-help\fR
.IP
Print the help menu (long version).
<VALUES>: 1
.HP
\fB\-o\fR, \fB\-\-output\fR outputImage
.IP
Output is a 2D correlation matrix.
.HP
\fB\-l\fR, \fB\-\-number\-consecutive\-labels\fR 0
.IP
Number of consecutive labels in data
.HP
\fB\-R\fR, \fB\-\-minimum\-region\-size\fR 1
.IP
Minimum size of a region: regions below this size are given a 0.0 connectivity
value
.HP
\fB\-i\fR, \fB\-\-iterations\fR 20
.IP
Number of iterations
.HP
\fB\-s\fR, \fB\-\-sparsity\fR 0.10
.IP
Sparsity \- a float from (0,1] indicating what fraction of the data to use
.HP
\fB\-n\fR, \fB\-\-n_eigenvectors\fR 2
.IP
Number of permutations to use in scca.
.HP
\fB\-r\fR, \fB\-\-robustify\fR 0
.IP
rank\-based scca
.HP
\fB\-l\fR, \fB\-\-l1\fR 0
.IP
use l1 ( > 0 ) or l0 ( < 0 ) penalty, also sets gradient step size e.g. \fB\-l\fR 0.5 (
L1 ) , \fB\-l\fR \fB\-0\fR.5 (L0) will set 0.5 grad descent step for either penalty
.HP
\fB\-\-ClusterThresh\fR 1
.IP
cluster threshold on view P
.HP
\fB\-e\fR, \fB\-\-ridge_cca\fR 0
.IP
Number of permutations to use in scca.
.HP
\fB\-\-partial\-scca\-option\fR PminusRQ
.IP
Choices for pscca: PQ, PminusRQ, PQminusR, PminusRQminusR
.HP
\fB\-\-timeseriesimage\-to\-matrix\fR [four_d_image.nii.gz,three_d_mask.nii.gz]
.IP
takes a timeseries (4D) image and converts it to a 2D matrix csv format as
output.If the mask has multiple labels ( more the one ) then the average time
series in each label will be computed and put in the csv.
.HP
\fB\-\-labelsimage\-to\-matrix\fR [three_d_mask.nii.gz]
.IP
takes a labeled (3D) image and converts it to a 2D matrix csv format as output.
.HP
\fB\-\-network\fR scca[time\-matrix.mhd,label\-matrix.mhd]
.IP
region\-averaging[time\-matrix.mhd,label\-matrix.mhd]
.IP
Build the network connectivity matrix