NEURO

Section: User Commands (1)
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NAME

neuro - data capture and analysis for neurosciences  

SYNOPSIS

neuro [X-options]  

DESCRIPTION

Neuro provides a front-end menu to the Spinal Cord Research Centre's data capture and analysis software for neurosciences. Before beginning, it will check to see if the NEURODIR environment variable has been set. If not, it will run all the commands in the environment variable setup file, /usr/neuro/lib/setup.sh, so that all variables are set as required for proper operation of this software package.

You can start up any of the major applications in this package by pressing the key corresponding to it. On an X terminal, you can also select an application by using the pointing device to move the cursor to the menu entry you want, then press button A or B to select it. Below is a description of all of these menu entries, and the keys used to select them.  

D Directory

This selection allows you to select the directory in which applications will be started. When prompted, type in the name of the directory you want, and neuro will position itself there, provided it is a valid directory to which you have access. This directory name will be remembered from one invocation of neuro to the next, as it will be stored in the file .neuro.ini in your home directory when you quit.  

S Set Calibration

This selection invokes the calibrate(1) application, so you can set up the calibration information prior to capturing data.  

C Capture

This selection invokes the cap(1) application, to capture raw data for analysis.  

B Capture & Average

This selection invokes the cavg(1) application, to capture data and average it on the fly.  

F Frame Selection

This selection invokes the frmsel(1) application, to select frames for analysis. By default, it begins with the most recently modified run in the directory, but you can easily pick another run using its File selection.  

V View List of Runs

This selection invokes lsrun(1), to list run files available for analysis in the current directory.  

A Analysis

This selection invokes the analysis(1) application, to analyse run files in the current directory. By default, it begins with the most recently modified run in the directory, but you can easily pick another run using its Load operation.  

M Quick Measure

This selection invokes the qm(1) application, to obtain cursor measurements from run files in the current directory. By default, it begins with the most recently modified run in the directory, but you can easily pick another run using its Set/File, Set/Next-File or Set/Prev-File operation.  

E Exponential Peeling

This selection invokes the peel(1) application, to perform and exponential peel analysis on a trace from a run file in the current directory. By default, it begins with the most recently modified run in the directory, but you can easily pick another run using its File-select operation.  

R Raster Graphs

This selection invokes the raster(1) application, to produce a pseudo-3D raster graph, or waterfall plot, of traces from a run file in the current directory. By default, it begins with the most recently modified run in the directory, but you can easily pick another run using its File selection.  

W Weighted Sums

This selection invokes the wtsum(1) application, to produce weighted sums of traces from a run file in the current directory, or a number of run files. By default, it begins with the most recently modified run in the directory, but you can easily pick other runs, in this or other directories, using its File-select operation.  

L Layout

This selection invokes the layout(1) application, to prepare final graphs from your HPGL plot files. You can select an existing layout file using its Layout selection, or you can begin a new layout from scratch.  

T List of Files

This selection invokes the ls(1) program, to list all files in the current directory. The options given to ls are specified via the O selection described below.  

O Options for List

This selection allows you to specify which options will be used by ls(1) when you select the T operation above. When prompted, type in any valid option arguments you want, complete with the leading hyphen (-). These options will be remembered from one invocation of neuro to the next, as they will be stored in the file .neuro.ini in your home directory when you quit.  

U Unix Shell

This selection invokes the Unix shell, to allow you to type in Unix commands, or run any of the utility programs that come with this package but aren't in the menu. Normally, it will run the same shell as you have set for your login shell, which is typically sh(1) or csh(1). When running on an X Window terminal, this selection invokes xterm(1) instead, which in turn starts up your shell. Many options are passed on to xterm, but additional or overriding options can be specified via the X selection described below.  

P Print Window Dump

This selection, available only when running on an X Window terminal, allows you to print out an image of any window currently displayed on your X terminal. It does this by invoking sdump(1), with no window ID specified in the WINDOWID environment variable. The target window is selected by clicking the mouse in the desired window, when the cursor changes to a crosshair. There is a pause of about 2 seconds before this happens, to give you time to bring the window you want up to the front, so it is not partly obscured.  

X Options for Xterm

This selection, available only when running on an X Window terminal, allows you to specify which options will be used by xterm(1) when you select the U operation above. When prompted, type in any valid option arguments you want, complete with the leading hyphen (-) if needed. These options will be remembered from one invocation of neuro to the next, as they will be stored in the file .neuro.ini in your home directory when you quit.

The options "-132 -cu -rw -sb -sl 480 -ls" are always passed on to xterm, but the options you specify are given after these, so you can override any you wish to. The -n and -title options are also passed on to xterm, but these are given after any you specify here.  

! Shell Escape

This selection allows you to run a single Unix shell command. After it runs, you are returned to the menu. This is of use primarily on non-X terminals. On an X terminal, you are better off running commands from an xterm window, so the standard input, output and error streams are dealt with properly.  

Q Quit

This selection allows you to quit the neuro program. You are prompted for confirmation before it actually quits. Press Y to quit, or N to resume.  

X WINDOW SUPPORT

When neuro is run from an xterm (or kterm) window on an X Window terminal, a new window will be shown for the menu. Like the other X Window programs in this package, neuro will recognise the usual X command line options, such as -display, -geometry, -font, etc. The environment variables for setting these options will also work. (This is provided that the DISPLAY environment variable is set, and TERM is set to xterm or kterm, or that the -display option is used.) See analysis(1) for details on X options and environment variables.

When running this way on an X terminal, neuro will start applications in the background, so that you can return to the menu at any time to start up another application. Applications that must be run from an xterm window, such as calibrate, cap, lsrun, ls and the Unix Shell, will each have their own xterm application started up in the background. Error messages from the standard error output of any of these applications will be sent to the file .neuro.err in your home directory.  

FILES

$HOME/.neuro.ini                      user's initialisation file

$HOME/.neuro.err                       user's error log file for X

/usr/neuro/lib/setup.sh                environment setup file

/usr/neuro/lib/parmgrps/neuromnu.ini   configuration file (non-X)

/usr/neuro/lib/parmgrps/xneurmnu.ini   configuration file for X
 

SEE ALSO

calibrate(1), cap(1), cavg(1), frmsel(1), lsrun(1), analysis(1), qm(1), peel(1), raster(1), wtsum(1), layout(1), ls(1), sh(1), csh(1)
 

Index

NAME
SYNOPSIS
DESCRIPTION
D Directory
S Set Calibration
C Capture
B Capture & Average
F Frame Selection
V View List of Runs
A Analysis
M Quick Measure
E Exponential Peeling
R Raster Graphs
W Weighted Sums
L Layout
T List of Files
O Options for List
U Unix Shell
P Print Window Dump
X Options for Xterm
! Shell Escape
Q Quit
X WINDOW SUPPORT
FILES
SEE ALSO

This document was created by man2html, using the manual pages.
Time: 20:21:28 GMT, November 21, 2017
Copyright © G. R. Detillieux, Spinal Cord Research Centre, The University of Manitoba.