Usage¶
To diplay options, simply run the following line in terminal:
$ branesta -h
Usage:
branesta [-h] [--subnetpath SUBNETPATH] [--tot_len TOT_LEN]
[--tot_roi_num TOT_ROI_NUM]
srcdir outdir win_len
positional arguments:
srcdir path to source directory with time-series
outdir path to out directory for results and logs
win_len number of time-frames in each snapshot
optional arguments:
-h, --help show this help message and exit
--subnetpath, -s
path to csv file with subnetwork labels and ixs,
optional
--tot_len, -l
expected total number of time frames, optional
--tot_roi_num, -r
expected total number of ROIs, optional
Options are explained below in more details:
srcdir: path to times-series to analyze. There are certain requirements for the input time-series:
Must be parcelled into ROIs, should not be more than a few hundred ROIs.
Shape must be 2D: time x space
File format must be .csv with no header row or index column
Filenames must follow BIDS convention (https://bids.neuroimaging.io/) (see example time-series for reference)
outdir: path to output directory. Computed metrics and log files will be placed here.
win_len: number of time-frames within each time window. With a TR of ~1s, at least 30 is recommended. The more regions we use, the more time-frames we need to properly estimate the covariance matrix
–subnetpath: optional, path to subnetwork indexes file. If provided, network stability is computed separately for edges corresponding to subnetworks. If not provided, the program defaults to a default subnetwork (labeled as whole_brain) consisting of all ROIs. Must be a .csv with two columns and a header row (roi, network). (see example subnetworks_willard.csv for reference)
–tot_len: optional, expected length of input time-series. If provided together with tot_roi_num, the program checks for proper shape of every input file.
–tot_roi_num: optional, expected number of spatial ROIs. If provided together with tot_len, the program checks for proper shape of every input file.
Example:
$ branesta data/derivatives/parcelled data/derivatives/network_stability 30 -s utils/subnetworks.csv -l 720 -r 498
To use branesta in a python shell:
import branesta.branesta as bns
bns.analyze?
We plan to add more details here. Contact Botond Antal if you need help.